301 results on '"Crop Development Centre"'
Search Results
2. Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.)
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Petr Smýkal, Judith Burstin, Alison Sackville, T. H. Noel Ellis, Endale G. Tafesse, Claire Domoney, Thomas D. Warkentin, V. B. Reddy Lachagari, Bunyamin Tar’an, Alexander Mikić, Kevin McPhee, Krishna K. Gali, Rebecca J. McGee, Mick Hybl, Crop Development Centre, University of Saskatchewan, AgriGenome Labs Pvt Ltd, Partenaires INRAE, Dep Plant Sci, North Dakota State University (NDSU), Centre of the Region Haná for Biotechnological and Agricultural Research - Department of Genetic Resources for Vegetables - Medicinal and Special Plants, Crop Research Institute, Forage Crops Department, Institute of Field and Vegetable Crops [Novi Sad], Department of Botany, Faculty of Sciences, Palacky University Olomouc, Grain Legume Genetics Physiology Research, USDA-ARS : Agricultural Research Service, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Metabolic Biology, John Innes Centre [Norwich], School of Biological Sciences [Auckland], University of Auckland [Auckland], and Saskatchewan Ministry of Agriculture and Saskatchewan Pulse Growers
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0106 biological sciences ,0301 basic medicine ,[SDV]Life Sciences [q-bio] ,Single-nucleotide polymorphism ,Genome-wide association study ,Plant Science ,lcsh:Plant culture ,Biology ,01 natural sciences ,Pisum ,03 medical and health sciences ,Field pea ,single nucleotide polymorphisms ,Sativum ,genotyping-by-sequencing ,lcsh:SB1-1110 ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Cultivar ,Original Research ,2. Zero hunger ,Genetic diversity ,genome-wide association study ,food and beverages ,genetic diversity ,biology.organism_classification ,Minor allele frequency ,030104 developmental biology ,Agronomy ,field pea ,010606 plant biology & botany - Abstract
Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.
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- 2019
3. Development of a sequence-based reference physical map of pea (Pisum sativum L.)
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Abdelhafid Bendahmane, Reddy V. B. Lachagari, Jan van Oeveren, Mohammed-Amin Madoui, Bunyamin Tar’an, Edwin A. G. van der Vossen, Thomas D. Warkentin, Karine Labadie, Krishna K. Gali, Judith Burstin, Hélène Bergès, Crop Development Centre, University of Saskatchewan, Genomics Institute, Clemson University, Keygene N.V., Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), AgriGenome Labs Pvt Ltd, Partenaires INRAE, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Saskatchewan Pulse Growers (SPG), University of Saskatchewan [Saskatoon] (U of S), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), and Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)
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0106 biological sciences ,0301 basic medicine ,Positional cloning ,Plant Science ,Computational biology ,lcsh:Plant culture ,01 natural sciences ,Genome ,DNA sequencing ,Restriction fragment ,analyse de génome ,03 medical and health sciences ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,lcsh:SB1-1110 ,sequence-based physical map ,Pisum sativum ,Original Research ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,Bacterial artificial chromosome ,Vegetal Biology ,biology ,Contig ,food and beverages ,bacterial artificial chromosome ,fingerprinted contigs ,whole genome profiling ,030104 developmental biology ,biology.protein ,cartographie ,Restriction digest ,Biologie végétale ,010606 plant biology & botany - Abstract
Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (~4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.
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- 2019
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4. The use of an agricultural waste material from Ziziphus jujuba as a novel adsorbent for humic acid removal from aqueous solutions
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André Donnot, André Merlin, Michael D. Holtz, Oumessaâd Benturki, Noureddine Bouras, Hadj Daoud Bouras, Mouloud Attou, Fatima Addoun, Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB), École normale supérieure - Kouba-Alger (ENS Kouba-Alger), Centre de Recherche Nucléaire de Draria (CRND), Laboratoire d'Etude et de Recherche sur le Matériau Bois (LERMAB), Université de Lorraine (UL), and Field Crop Development Centre (FCDC)
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Langmuir ,Activated carbon ,[SDV]Life Sciences [q-bio] ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Ziziphus jujuba ,symbols.namesake ,Adsorption kinetics ,Adsorption ,Oxidation ,Materials Chemistry ,medicine ,Organic chemistry ,Humic acid ,Freundlich equation ,Physical and Theoretical Chemistry ,Spectroscopy ,chemistry.chemical_classification ,Chemistry ,Langmuir adsorption model ,Sorption ,Microporous material ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,symbols ,0210 nano-technology ,medicine.drug ,Nuclear chemistry - Abstract
The purpose of our work is the development of a local agricultural waste biomass material, Ziziphus jujuba known as Nebka (NB), into activated carbons to remove humic acid (HA) from aqueous solutions. This was further treated with nitric acid solutions. The surface characteristics of the adsorbent were calculated using the standard Brunauer-Emmet-Teller method (BET). The microstructures of the samples were observed with scanning electron micrographs. Chemical characterization of the samples was carried out by selective titrations and Fourier Transform Infrared Spectroscopy (FT-IR). On the basis of the BET results, we have obtained the best microporous activated carbon oxidized (surface area of 970 m(2)/g, microporous volume of 0.170 cm(3)/g and total pore volume of 0326 cm(3)/g). Adsorption studies were conducted using a batch process, to study the effects of contact time, pH and temperature. The pH dependent sorption of HA was found maximum at pH range 4-6 for an initial concentration of 50 mg/L. The equilibrium adsorption data was analyzed using Langmuir and Freundlich isotherm models, and the kinetic data was analyzed using pseudo-first order and pseudo-second order kinetic models. The equilibrium data were well fitted to the Freundlich isotherm. The adsorption reached equilibrium after 300 mm and the maximum adsorption capacity was about 76.92 mg/g at 20 degrees C according to the Langmuir model. The adsorption kinetic was found to follow the pseudo-second-order kinetic model. Thermodynamic study showed that the adsorption of HA onto oxidized activated carbons was feasible, spontaneous and endothermic at 20-40 degrees C.
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- 2015
5. Structural features of two major nucleolar organizer regions (NORs), Nor-B1 and Nor-B2, and chromosome-specific rRNA gene expression in wheat
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Handa, Hirokazu, Kanamori, Hiroyuki, Tanaka, Tsuyoshi, Murata, Kazuki, Kobayashi, Fuminori, Robinson, Stephen J., Koh, Chu S., Pozniak, Curtis J., Sharpe, Andrew G., Paux, Etienne, International Wheat Genome Sequencing Consortium, ., Wu, Jianzhong, Nasuda, Shuhei, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Graduate School of Agriculture, Laboratory of Plant Genetics, Kyoto University, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Global Institute for Food Security, University of Saskatchewan, Crop Development Centre, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), International Wheat Genome Sequencing Consortium (IWGSC), Ministry of Agriculture, Forestry and Fisheries of Japan [NGB-1003], Institute of Crop Sciences of CAAS [Beijing] (ICS CAAS), Agriculture and Agri-Food [Ottawa] (AAFC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Handa, Hirokazu, Agriculture and Agri-Food (AAFC), and University of Saskatchewan [Saskatoon] (U of S)
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0106 biological sciences ,0301 basic medicine ,Triticum aestivum L ,rDNA unit subtypes ,DNA Copy Number Variations ,gene expression ,nucleolar dominance ,nucleolar organizer region ,sequence structure ,Plant Science ,Biology ,Genes, Plant ,Polymerase Chain Reaction ,01 natural sciences ,Genome ,Chromosomes, Plant ,ribosomal dna ,03 medical and health sciences ,blé ,Gene Expression Regulation, Plant ,Gene density ,wheat ,Gene expression ,Genetics ,RefSeq ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,In Situ Hybridization, Fluorescence ,Triticum ,2. Zero hunger ,Vegetal Biology ,Chromosome ,Cell Biology ,Ribosomal RNA ,adn ribosomique ,External transcribed spacer ,structure génétique ,030104 developmental biology ,Genetic Loci ,RNA, Plant ,RNA, Ribosomal ,nucleolus organizer region ,Nucleolus organizer region ,Genome, Plant ,Biologie végétale ,010606 plant biology & botany ,expression des gènes ,organisateur nucléolaire - Abstract
The reference genome sequence of wheat 'Chinese Spring' (CS) is now available (IWGSC RefSeq v1.0), but the core sequences defining the nucleolar organizer regions (NORs) have not been characterized. We estimated that the total copy number of the rDNA units in the wheat genome is 11 160, of which 30.5%, 60.9% and 8.6% are located on Nor-B1 (1B), Nor-B2 (6B) and other NORs, respectively. The total length of the NORs is estimated to be 100 Mb, corresponding to approximately 10% of the unassembled portion of the genome not represented in RefSeq v1.0. Four subtypes (S1-S4) of the rDNA units were identified based on differences within the 3' external transcribed spacer regions in Nor-B1 and Nor-B2, and quantitative PCR indicated locus-specific variation in rDNA subtype contents. Expression analyses of rDNA subtypes revealed that S1 was predominantly expressed and S2 weakly expressed, in contrast to the relative abundance of rDNA subtypes in the wheat genome. These results suggest a regulation mechanism of differential rDNA expression based on sequence differences. S3 expression increased in the ditelosomic lines Dt1BL and Dt6BL, suggesting that S3 is subjected to chromosome-mediated silencing. Structural differences were detected in the regions surrounding the NOR among homoeologous chromosomes of groups 1 and 6. The adjacent regions distal to the major NORs were expanded compared with their homoeologous counterparts, and the gene density of these expanded regions was relatively low. We provide evidence that these regions are likely to be important for autoregulation of the associated major NORs as well as silencing of minor NORs.
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- 2018
6. Rhizobial diversity associated with the spontaneous legume Genista saharae in the northeastern Algerian Sahara
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Philippe de Lajudie, Khaled Chaich, Souhir Soussou, Noureddine Bouras, Lucette Maure, Abdelkader Bekki, Michael D. Holtz, Brigitte Brunel, Jean Claude Cleyet-Marel, Laboratoire Génie de l’eau et de l’Environnement en Milieu Saharien, Université de Ouargla, Laboratoire de Microbiologie, Faculté des Sciences, University of Oran Es-Sénia [Oran], École normale supérieure - Kouba-Alger (ENS Kouba-Alger), Département de Biologie, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaïa, Alberta Agriculture and Rural Development, Field Crop Development Centre (FCDC), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Fertil'Innov Environnement, University of Oran Es-Senia [Oran] | Université d'Oran Es-Senia [Oran], and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
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0301 basic medicine ,phylogénétique ,sol ,ved/biology.organism_classification_rank.species ,algérie ,Shrub ,stabilisation du sol ,Spontaneous legume ,caractérisation génétique ,N-2-fixation ,genista saharae ,biology ,soil stabilization ,Mesorhizobium ,legume ,genêtic variation ,spontaneous legume ,fixation de l'azote ,Sinorhizobium ,diversité génétique ,General Agricultural and Biological Sciences ,Algerian Sahara ,food.ingredient ,030106 microbiology ,Drought tolerance ,housekeeping genes ,Genista saharae ,légumineuse ,soil ,dune ,03 medical and health sciences ,food ,Botany ,Genetic variation ,Genetic diversity ,Housekeeping genes ,desertization ,sahara ,préservation de l'environnement ,ved/biology ,rhizobial diversity ,15. Life on land ,biology.organism_classification ,16S ribosomal RNA ,030104 developmental biology ,Neorhizobium ,Rhizobial diversity ,désertification ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology - Abstract
Genista saharae is an indigenous shrub legume that spontaneously grows in the northeastern Algerian Sahara. It is known for efficient dune fixation and soil preservation against desertification, due to its drought tolerance and its contribution to sustainable nitrogen resources implemented by biological N-2-fixation. In this study, the root nodule bacteria of G. saharae were investigated using phenotypic and phylogenetic characterization. A total of 57 rhizobial strains were isolated from nodules from several sites in the hyper-arid region of Metlili and Taibet (east Septentrional Sahara). They all nodulate G. saharae species but they differed in their symbiotic efficiency and effectiveness. The genetic diversity was assessed by sequencing three housekeeping genes (atpD, recA and 16S rRNA). The majority of isolates (81 %) belonged to the genus Ensifer (previously Sinorhizobium), represented mainly by the species Ensifer meliloti. The next most abundant genera were Neorhizobium (17 %) with 3 different species: N. alkalisoli, N. galegae and N. huautlense and Mesorhizobium (1.75 %) represented by the species M. camelthorni. Most of the isolated strains tolerated up to 4%(w/v) NaCl and grew at 45 degrees C. This study is the first report on the characterization of G. saharae microsymbionts in the Algerian Sahara.
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- 2017
7. Comparison of the epidemiology of ascochyta blights on grain legumes
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Sabine Banniza, Bernard Tivoli, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Crop Development Centre, University of Saskatchewan, Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and University of Saskatchewan [Saskatoon] (U of S)
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2. Zero hunger ,0106 biological sciences ,0303 health sciences ,biology ,fungi ,food and beverages ,Plant Science ,Fungi imperfecti ,Horticulture ,biology.organism_classification ,Ascochyta ,01 natural sciences ,Vicia faba ,Conidium ,03 medical and health sciences ,Agronomy ,Genus ,Ascospore ,POIS CHICHE ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Blight ,Agronomy and Crop Science ,Legume ,030304 developmental biology ,010606 plant biology & botany - Abstract
International audience; Asochyta blights of grain legumes are caused by fungal pathogens in the genus Ascochyta. Different species infect the different legume species, and in pea three species including Phoma medicaginis var. pinodella have been implicated in ascochyta blight. The impact of the diseases varies between crops, countries, seasons and cropping systems, and yield loss data collected under well-defined conditions is scarce. However, ascochyta blights are considered major diseases in many areas where legumes are grown. Symptoms appear on all aerial parts of the plant, and lesions are similar for most of the species, except for M. pinodes and P. medicaginis var. pinodella. Infected seed, stubble and/or air-borne ascospores are major sources of primary inoculum. Their importance varies between species and also between regions. All Ascochyta spp. produce rain-splashed conidia during the cropping season which are responsible for the spread of the disease within the crop canopy. Only in pea are ascospores involved in secondary disease spread. Limited data suggests that Ascochyta spp. may be hemibiotrophs; however, toxins characteristic for necrotrophs have been isolated from some of the species. Modelling of ascochyta blights is still in the developmental stage and implementation of such models for disease forecasting is the exception
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- 2007
8. Breeding Annual Grain Legumes for Sustainable Agriculture: New Methods to Approach Complex Traits and Target New Cultivar Ideotypes
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S. Bao, M. C. Vaz Patto, A. Tullu, X. Zong, C. L. L. Gowda, Aleksandar Mikić, Gérard Duc, Jens Berger, Karam B. Singh, Thomas D. Warkentin, Hesham A. Agrama, V. Bourion, A. M. De Ron, Albert Vandenberg, D. Millot, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, International Institute of Tropical Agriculture, Yunnan Academy of Agricultural Sciences (YAAS), University of Western Australia, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institute of Field and Vegetable Crops [Novi Sad], Crop Development Centre, University of Saskatchewan, Instituto de Technologia Quimica e Biologica, Institute of Crop Sciences of CAAS [Beijing] (ICS CAAS), Chinese Academy of Agricultural Sciences (CAAS), Grains Research and Development Corporation-Australia UWA00147, ECONET- PAVLE SAVIC projects, Ministry of Foreign Affairs-France, PARI-1 Agrale 6-2010-2013, Burgundy Council-France, Fundacao para a Ciencia e a Tecnologia-Portugal PEst-OE/EQB/LA0004/2013 PTDC/AGR-TEC/3555/2012, Ciencia program, Ministry of Education, Science and Technological Development- Republic of Serbia TR-31024, Government of Spain PET2008-0167-01 AGL2011-25562, Government of Galicia-Spain INCITE07PXI403088ES, European Project: 613551,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,LEGATO(2014), The University of Western Australia (UWA), and University of Saskatchewan [Saskatoon] (U of S)
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0106 biological sciences ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Grain legumes ,Ecosystem service ,soybean/pigeonpea intercropping system ,grain legumes ,Cicer-arietinum L ,lentil Lens-culinaris ,Plant Science ,Breeding ,01 natural sciences ,Rhizobia ,Ecosystem services ,Green manure ,mediterranean-type environment ,Sustainable agriculture ,Lathyrus-sativus ,Cultivar ,Vicia-faba L ,Legume ,2. Zero hunger ,biology ,Forage ,Agroforestry ,food ,bean Phaseolus-vulgaris ,forage ,Ideotype ,04 agricultural and veterinary sciences ,15. Life on land ,biology.organism_classification ,ideotype ,ecosystem service ,Agronomy ,13. Climate action ,Food ,breeding ,host-bacteria interaction ,040103 agronomy & agriculture ,pea Pisum-sativum ,0401 agriculture, forestry, and fisheries ,Cropping ,northern great-plain ,010606 plant biology & botany - Abstract
Although yield and total biomass produced by annual legumes remain major objectives for breeders, other issues such as environment-friendly, resource use efficiency including symbiotic performance, resilient production in the context of climate change, adaptation to sustainable cropping systems (reducing leaching, greenhouse gas emissions and pesticide residues), adaptation to diverse uses (seeds for feed, food, non-food, forage or green manure) and finally new ecological services such as pollinator protection, imply the need for definition of new ideotypes and development of innovative genotypes to enhance their commercialization. Taken as a whole, this means more complex and integrated objectives for breeders. Several illustrations will be given of breeding such complex traits for different annual legume species. Genetic diversity for root development and for the ability to establish efficient symbioses with rhizobia and mycorrhiza can contribute to better resource management (N, P, water). Shoot architectures and phenologies can contribute to yield and biotic constraint protection (parasitic weeds, diseases or insects) reducing pesticide use. Variable maturity periods and tolerance to biotic and abiotic stresses are key features for the introduction of annual legumes to low input cropping systems and for enlarging cultivated area. Adaptation to intercropping requires adapted genotypes. Improved health and nutritional value for humans are key objectives for developing new markets. Modifying product composition often requires the development of specific cultivars and sometimes the need to break negative genetic correlations with yield. A holistic approach in legume breeding is important for defining objectives with farmers, processors and consumers. The cultivar structures are likely to be more complex, combining genotypes, plant species and associated symbionts. New tools to build and evaluate them are important if legumes are to deliver their exciting potential in terms of agricultural productivity and sustainability as well as for feed and food.
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- 2015
9. Abiotic stress enhances androgenesis from isolated microspores of some legume species (Fabaceae)
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C. Conreux, C. Pech, Louis Jacas, Sergio Ochatt, Monika M. Lulsdorf, Ravinder Kaur Grewal, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Crop Development Centre, and University of Saskatchewan
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0106 biological sciences ,electroporation ,Genotype ,Physiology ,Cell Survival ,pea ,Stamen ,Plant Science ,Biology ,Buffers ,01 natural sciences ,Gametogenesis ,03 medical and health sciences ,Field pea ,Microspore ,Osmotic Pressure ,Stress, Physiological ,Botany ,Microspora ,030304 developmental biology ,Cell Proliferation ,0303 health sciences ,Medicago ,Abiotic stress ,Osmolar Concentration ,Temperature ,food and beverages ,Fabaceae ,medicago truncatula ,microspores ,biology.organism_classification ,Medicago truncatula ,Electric Stimulation ,Culture Media ,[SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy ,Seeds ,Pollen ,Agronomy and Crop Science ,Cell Division ,grasspea ,010606 plant biology & botany - Abstract
International audience; To induce androgenesis in field pea, grass pea and the model legume species Medicago truncatula, isolated microspores of various genotypes of these three species were submitted to a range of abiotic stresses prior to and during their initial culture, in order to stimulate them to divide and form embryos. Some stress agents had a positive effect on androgenesis from the treated microspores. Submission of flower buds to a cold period prior to anther excision or microspore isolation, modifying the osmotic pressure of the medium during initial culture and electroporation of isolated microspores were the three major individual stress agents to have an impact on the efficiency of androgenetic proliferation and subsequent differentiation from the microspores of pea, grass pea and M. truncatula genotypes. A combination of osmotic and electric shocks significantly improved responses from isolated microspores and yielded microcalluses and then calluses, but only few underwent morphogenesis. Further work is under way to improve responses and extend them to other genotypes. The results reported here are, to the best of our knowledge, the first successful results from isolated microspores of these species.
- Published
- 2009
10. Doubled-haploid production in chickpea (Cicer arietinum L.): role of stress treatments
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Sergio Ochatt, Janine Croser, Ravinder Kaur Grewal, Thomas D. Warkentin, Albert Vandenberg, Monika M. Lulsdorf, Crop Development Centre, University of Saskatchewan, University of Western Australia, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), and Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
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0106 biological sciences ,Stamen ,Cell Culture Techniques ,Plant Science ,Flowers ,Biology ,Haploidy ,CHICKPEA ,01 natural sciences ,Chromosomes, Plant ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,03 medical and health sciences ,Tissue culture ,Osmotic Pressure ,Stress, Physiological ,Botany ,Regeneration ,Cultivar ,Cells, Cultured ,030304 developmental biology ,0303 health sciences ,HIGH OSMOTIC PRESSURE LIQUID MEDIUM ,fungi ,Embryo ,General Medicine ,Cicer ,ANTHER CULTURE ,Culture Media ,CENTRIFUGATION ,Cold Temperature ,Plant morphology ,Callus ,Doubled haploidy ,ELECTROPORATION ,Ploidy ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
International audience; This is the first report on the production of double-haploid chickpea embryos and regenerated plants through anther culture using Canadian cultivar CDC Xena (kabuli) and Australian cultivar Sonali (desi). Maximum anther induction rates were 69% for Sonali and 63% for CDC Xena. Under optimal conditions, embryo formation occurred within 15–20 days of culture initiation with 2.3 embryos produced per anther for CDC Xena and 2.0 embryos per anther for Sonali. For anther induction, the following stress treatments were used: (1) flower clusters were treated at 4°C for 4 days, (2) anthers were subjected to electric shock treatment of three exponentially decaying pulses of 50–400 V with 25 μF capacitance and 25 Ω resistance, (3) anthers were centrifuged at 168–1,509g for 2–15 min, and finally (4) anthers were cultured for 4 days in high-osmotic pressure (563 mmol) liquid medium. Anthers were then transferred to a solid embryo development medium and, 15–20 days later, embryo development was observed concomitant with a small amount of callus growth of 0.1–3 mm. Anther-derived embryos were regenerated on plant regeneration medium. Electroporation treatment of anthers enhanced root formation, which is often a major hurdle in legume regeneration protocols. Cytological studies using DAPI staining showed a wide range of ploidy levels from haploid to tetraploid in 10–30-day-old calli. Flow cytometric analysis of calli, embryos and regenerated plants showed haploid profiles and/or spontaneous doubling of the chromosomes during early regeneration stages.
- Published
- 2009
11. Weeds of corn, soybean, and winter wheat fields under conventional, conservation, and no-till management systems in Southwestern Ontario 1988 and 1989
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Frick, B., Thomas,A. G., Wise, R. F., Crop Development Centre, University of Saskatchewan, and Agriculture Canada, Research Station
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farm management practices ,weed species ,weeds ,agricultural ecosystems ,conservation tillage - Abstract
The primary goal of the weed survey project, which is reported in this publication, is the identification of weed species likely to be the greatest problems under various tillage systems in southwestern Ontario. Information on the response of the weed community to changes in tillage practices is vital for a sensible farm management program. As well as the field survey for weeds, data on farm management practices were gathered through a questionnaire. This report is a summary of the results from 1988 and 1989. Agriculture Canada
- Published
- 1990
12. Taxonogenomic analysis of the Xanthomonas translucens complex leads to the descriptions of Xanthomonas cerealis sp. nov. and Xanthomonas graminis sp. nov.
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Tambong JT, Xu R, Fleitas MC, and Kutcher R
- Subjects
- Nucleic Acid Hybridization, Whole Genome Sequencing, RNA, Ribosomal, 16S genetics, Host Specificity, Fatty Acids, Xanthomonas genetics, Xanthomonas classification, Xanthomonas isolation & purification, Phylogeny, Genome, Bacterial, DNA, Bacterial genetics, Bacterial Typing Techniques, Sequence Analysis, DNA, Plant Diseases microbiology
- Abstract
The pathovar-based taxonomy of the Xanthomonas translucens group is very confusing due to an overlap of plant host ranges and level of host specificity. Here, whole-genome sequence-based parameters (digital DNA-DNA hybridization and blast-based average nucleotide identity), phylogenomic, biochemical and phenotypical data were used to taxonomically analyse the 11 known pathovars of the X. translucens complex. This polyphasic approach taxonomically assigned the 11 pathovars of X. translucens complex into three distinct species, two of which are new: X. translucens , X. cerealis sp. nov. and X. graminis sp. nov. X. translucens consists of three pathovars: pv. translucens (=pv. hordei ), pv. pistaciae strain A ICMP 16316
PT and pv. undulosa (=pv. secalis ). X. cerealis sp. nov. encompasses the pv. cerealis strain LMG 679PT and pv. pistaciae strain B ICMP 16317PT with genome similarity of 92.7% (dDDH) and 99.0% (ANIb) suggesting taxonomically similar genotypes. The other new species, X. graminis sp. nov., consists of the remaining five designated pathovars (pv. graminis , pv. arrhenatheri, pv. poae , pv. phleipratensis and pv. phlei ) with highly variable dDDH and ANIb values ranging from 74.5 to 93.0% and from 96.7 to 99.2%, respectively, an indication of a very divergent taxonomic group. Only strains of pvs. phlei and phleipratensis showed the highest genomic similarities of 93.0% (dDDH) and 99.2% (ANIb), suggesting synonymic pathovars as both infect the same plant hosts. The dDDH and ANI data were corroborated by phylogenomics clustering. The fatty acid contents were similar but the type strain of X. graminis sp. nov. exhibited 20% less C15 : 0 iso and 40% more C17 : 0 iso fatty acids than the other species. Based on phenotypic, biochemical and whole-genome sequence data, we propose two new species, Xanthomonas cerealis sp. nov. and Xanthomonas graminis sp. nov. with type strains LMG 679T (=NCPPB 1944T ) and LMG 726T (=NCPPB 2700T ), respectively.- Published
- 2024
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13. Origin and evolution of the bread wheat D genome.
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Cavalet-Giorsa E, González-Muñoz A, Athiyannan N, Holden S, Salhi A, Gardener C, Quiroz-Chávez J, Rustamova SM, Elkot AF, Patpour M, Rasheed A, Mao L, Lagudah ES, Periyannan SK, Sharon A, Himmelbach A, Reif JC, Knauft M, Mascher M, Stein N, Chayut N, Ghosh S, Perovic D, Putra A, Perera AB, Hu CY, Yu G, Ahmed HI, Laquai KD, Rivera LF, Chen R, Wang Y, Gao X, Liu S, Raupp WJ, Olson EL, Lee JY, Chhuneja P, Kaur S, Zhang P, Park RF, Ding Y, Liu DC, Li W, Nasyrova FY, Dvorak J, Abbasi M, Li M, Kumar N, Meyer WB, Boshoff WHP, Steffenson BJ, Matny O, Sharma PK, Tiwari VK, Grewal S, Pozniak CJ, Chawla HS, Ens J, Dunning LT, Kolmer JA, Lazo GR, Xu SS, Gu YQ, Xu X, Uauy C, Abrouk M, Bougouffa S, Brar GS, Wulff BBH, and Krattinger SG
- Subjects
- Disease Resistance genetics, Phylogeny, Genetic Variation genetics, Domestication, Genes, Plant genetics, Polyploidy, Crops, Agricultural genetics, Triticum genetics, Genome, Plant genetics, Bread, Haplotypes genetics, Evolution, Molecular, Aegilops genetics, Alleles
- Abstract
Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks
1,2 . Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch's goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement., (© 2024. The Author(s).)- Published
- 2024
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14. Dietary Quality and Nutrient Intakes of Elite Paracyclists.
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Shaw KA, Chilibeck PD, Warkentin TD, and Zello GA
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- Humans, Female, Male, Adult, Young Adult, Para-Athletes, Dietary Fiber administration & dosage, Nutritional Requirements, Nutritional Status, Nutrients administration & dosage, Nutrients analysis, Diet statistics & numerical data, Recommended Dietary Allowances
- Abstract
Nutrient requirements for para-athletes will be influenced by a variety of factors secondary to their impairment and, therefore, recommendations for para-athletes cannot be drawn directly from that of able-bodied athletes. Information on the dietary intakes of para-athletes is lacking and therefore needs to be examined. This study assessed the nutrient intakes and diet quality of 31 paracyclists via food frequency questionnaires. Based on the dietary reference intakes, most paracyclists consumed intakes above the recommended dietary allowance (RDA) or adequate intake (AI). Recommendations were not met for iodine (males = 87% RDA; females = 62% RDA) or fibre in males (84% AI). A 26% risk of inadequacy was noted for vitamins D and E in females. A total of 42% of females and 75% of males did not meet fibre recommendations (14 g/1000 kcal), and only three athletes (all females) consumed fatty acids in the recommended omega-6 to omega-3 ratio of 4:1 or less. Athletes consumed grains, fruits, and vegetables frequently, though whole grains, pulses, and oily fish were generally consumed less often. Paracyclists appear to be consuming intakes at or above recommendations for most nutrients, though several nutrients were consumed below the recommended amounts; therefore, increasing the variety of foods consumed is suggested.
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- 2024
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15. Nitrogen deficiency tolerance conferred by introgression of a QTL derived from wild emmer into bread wheat.
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Govta N, Fatiukha A, Govta L, Pozniak C, Distelfeld A, Fahima T, Beckles DM, and Krugman T
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- Phenotype, Genetic Introgression, Chromosome Mapping, Stress, Physiological genetics, Droughts, Chromosomes, Plant genetics, Triticum genetics, Triticum growth & development, Quantitative Trait Loci, Nitrogen metabolism
- Abstract
Key Message: Genetic dissection of a QTL from wild emmer wheat, QGpc.huj.uh-5B.2, introgressed into bread wheat, identified candidate genes associated with tolerance to nitrogen deficiency, and potentially useful for improving nitrogen-use efficiency. Nitrogen (N) is an important macronutrient critical to wheat growth and development; its deficiency is one of the main factors causing reductions in grain yield and quality. N availability is significantly affected by drought or flooding, that are dependent on additional factors including soil type or duration and severity of stress. In a previous study, we identified a high grain protein content QTL (QGpc.huj.uh-5B.2) derived from the 5B chromosome of wild emmer wheat, that showed a higher proportion of explained variation under water-stress conditions. We hypothesized that this QTL is associated with tolerance to N deficiency as a possible mechanism underlying the higher effect under stress. To validate this hypothesis, we introgressed the QTL into the elite bread wheat var. Ruta, and showed that under N-deficient field conditions the introgression IL99 had a 33% increase in GPC (p < 0.05) compared to the recipient parent. Furthermore, evaluation of IL99 response to severe N deficiency (10% N) for 14 days, applied using a semi-hydroponic system under controlled conditions, confirmed its tolerance to N deficiency. Fine-mapping of the QTL resulted in 26 homozygous near-isogenic lines (BC
4 F5 ) segregating to N-deficiency tolerance. The QTL was delimited from - 28.28 to - 1.29 Mb and included 13 candidate genes, most associated with N-stress response, N transport, and abiotic stress responses. These genes may improve N-use efficiency under severely N-deficient environments. Our study demonstrates the importance of WEW as a source of novel candidate genes for sustainable improvement in tolerance to N deficiency in wheat., (© 2024. The Author(s).)- Published
- 2024
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16. Effects of Pea ( Pisum sativum ) Prebiotics on Intestinal Iron-Related Proteins and Microbial Populations In Vivo ( Gallus gallus ).
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Armah A, Jackson C, Kolba N, Gracey PR, Shukla V, Padilla-Zakour OI, Warkentin T, and Tako E
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- Animals, Plant Extracts pharmacology, Intestines microbiology, Seeds, Bifidobacterium metabolism, Cotyledon, Lactobacillus metabolism, Cation Transport Proteins, Pisum sativum, Chickens, Prebiotics, Gastrointestinal Microbiome drug effects, Iron metabolism
- Abstract
Iron deficiency remains a public health challenge globally. Prebiotics have the potential to improve iron bioavailability by modulating intestinal bacterial population, increasing SCFA production, and stimulating expression of brush border membrane (BBM) iron transport proteins among iron-deficient populations. This study intended to investigate the potential effects of soluble extracts from the cotyledon and seed coat of three pea ( Pisum sativum ) varieties (CDC Striker, CDC Dakota, and CDC Meadow) on the expression of BBM iron-related proteins (DCYTB and DMT1) and populations of beneficial intestinal bacteria in vivo using the Gallus gallus model by oral gavage (one day old chicks) with 1 mL of 50 mg/mL pea soluble extract solutions. The seed coat treatment groups increased the relative abundance of Bifidobacterium compared to the cotyledon treatment groups, with CDC Dakota seed coat (dark brown pigmented) recording the highest relative abundance of Bifidobacterium . In contrast, CDC Striker Cotyledon (dark-green-pigmented) significantly increased the relative abundance of Lactobacillus ( p < 0.05). Subsequently, the two dark-pigmented treatment groups (CDC Striker Cotyledon and CDC Dakota seed coats) recorded the highest expression of DCYTB. Our study suggests that soluble extracts from the pea seed coat and dark-pigmented pea cotyledon may improve iron bioavailability by affecting intestinal bacterial populations.
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- 2024
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17. Effects of Genotype and Growing Year on the Nutritional Composition and Pasting Properties of Glabrous Canary Seed ( Phalaris canariensis L.) Groat Flours.
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Malunga LN, Thandapilly SJ, Hucl PJ, and Ames N
- Abstract
Canary seed flour is a new food ingredient that the United States Food and Drug Administration (FDA) and Health Canada recently granted Generally Regarded as Safe (GRAS) status. Stability in nutritional composition and functional properties is an essential characteristic of food ingredients for consistency in nutritional quality and performance in processing. This work assessed the effect of genotypic and environmental variation on the nutritional (protein, starch, amylose, oil, dietary fiber, minerals and fat-soluble vitamins) and pasting (as measured in viscosity (peak, trough, breakdown, final, and setback), peak time, and pasting temperatures) properties of Canary seed. The samples included four Canary seed varieties grown in randomized complete block design experiments at one location for two growing seasons. In general, the nutritional composition of Canary seed flour was not affected by genotype, growing year, and their interaction except for starch content, which was significantly affected by the growing year ( p < 0.0001), and iron content, which was affected by genotypic variation ( p < 0.0001). The pasting properties of Canary seed flour were significantly ( p < 0.001) affected by both genotypic and growing year variation but not their interaction. Our results suggest that the food industry should measure starch and iron content prior to processing to ensure consistency in nutritional labeling. Also, for those applications where starch pasting properties are essential, the manufacturer should consider measuring the RVA pasting viscosities for every batch of raw material. The results have provided the baseline knowledge of which nutritional or functional properties of Canary seed flour can be improved through breeding and agronomy programs to ensure the reliability of Canary seed as an ingredient.
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- 2024
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18. Editorial: Advances in pea breeding and genomics.
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Warkentin TD, Smýkal P, Xu P, and McPhee K
- Abstract
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.
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- 2024
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19. TaqMan Real-Time PCR Assay for Specific Detection and Differentiation of Xanthomonas translucens pv. undulosa from Other Pathovars Targeting a Recombination Mediator Gene, rec F.
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Tambong JT, Xu R, Fleitas MC, Wang L, Akuma M, Chi SI, and Kutcher HR
- Subjects
- Bacterial Proteins genetics, DNA, Bacterial genetics, Phylogeny, Sensitivity and Specificity, Xanthomonas genetics, Xanthomonas isolation & purification, Xanthomonas classification, Plant Diseases microbiology, Real-Time Polymerase Chain Reaction methods, Triticum microbiology
- Abstract
Bacterial leaf streak and black chaff diseases of wheat caused by Xanthomonas translucens pv. undulosa is becoming a major constraint to growers and trade since it is seedborne. Molecular tools for specific detection/differentiation of pv. undulosa are lacking. We report the development of a TaqMan real-time PCR for specific detection/identification of pv. undulosa targeting the recombination mediator gene ( rec F). Analysis of the complete rec F (1,117 bp) sequences identified the gene as a reliable phylogenetic marker for identification of pv. undulosa , differentiating it from the other pathovars; rec F-based sequence homology values among the 11 pathovars correlated well with genome-based DNA-DNA hybridization values. The discriminatory power of rec F to differentiate pv. undulosa from the other pathovars is due to nucleotide polymorphic positions. We used these nucleotide polymorphisms to develop a TaqMan PCR for specific detection of pv. undulosa . The specificity of the assay was validated using 67 bacterial and fungal/oomycete strains. The selected primers and the double-quenched FAM-labeled TaqMan probe were specific for the detection of 11 pv. undulosa / secalis strains. The 56 strains of other X. translucens pathovars ( n = 39) and non- Xanthomonas spp. ( n = 17) did not exhibit any detectable fluorescence. Also, greenhouse-inoculated and naturally infected wheat leaf samples showed positive reactions for the presence of pv. undulosa DNA but not healthy control plants. The TaqMan assay reliably detected as low as 1-pg DNA amount and 10 colony forming units of the target pathogen per reaction. This TaqMan assay could be useful to regulatory agencies with economic benefits to wheat growers., Competing Interests: The author(s) declare no conflict of interest.
- Published
- 2024
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20. Future of durum wheat research and breeding: Insights from early career researchers.
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Peters Haugrud AR, Achilli AL, Martínez-Peña R, and Klymiuk V
- Abstract
Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding., (© 2024 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)
- Published
- 2024
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21. Insights into Wheat Genotype‒ Sphaerodes mycoparasitica Interaction to Improve Crop Yield and Defence against Fusarium graminearum : An Integration of FHB Biocontrol in Canadian Wheat Breeding Programmes.
- Author
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Powell A, Kim SH, Hucl P, and Vujanovic V
- Abstract
Fusarium head blight (FHB) is a major threat to wheat crop production and food security worldwide. The creation of resistant wheat cultivars is an essential component of an integrated strategy against Fusarium graminearum , the primary aetiological agent that causes FHB. The results of this study show that the deployment of proto-cooperative interactions between wheat genotypes and mycoparasitic biocontrol agents (BCAs) can improve crop yield and plant resistance in controlling the devastating effects of FHB on wheat agronomic traits. A Fusarium-specific mycoparasite, Sphaerodes mycoparasitica , was found to be compatible with common and durum wheat hosts, thus allowing the efficient control of F. graminearum infection in plants. Four genotypes of wheat, two common wheat, and two durum wheat cultivars with varying FHB resistance levels were used in this greenhouse study. The BCA treatments decreased FHB symptoms in all four cultivars and improved the agronomic traits such as spike number, spike weight, seed weight, plant biomass, and plant height which are vital to grain yield. Conversely, the F. graminearum 3ADON chemotype treatment decreased the agronomic trait values by up to 44% across cultivars. Spike number, spike weight, and seed weight were the most improved traits by the BCA. A more measurable improvement in agronomic traits was observed in durum wheat cultivars compared to common wheat.
- Published
- 2024
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22. Editorial: Legume root diseases.
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Pilet-Nayel ML, Coyne CJ, Le May C, and Banniza S
- Abstract
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
- Published
- 2024
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23. Genetic mapping of deoxynivalenol and fusarium damaged kernel resistance in an adapted durum wheat population.
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Berraies S, Ruan Y, Knox R, DePauw R, Bokore F, Cuthbert R, Blackwell B, Henriquez MA, Konkin D, Yu B, Pozniak C, and Meyer B
- Subjects
- Plant Breeding, Canada, Plant Diseases genetics, Disease Resistance genetics, Triticum genetics, Fusarium, Trichothecenes
- Abstract
Background: Fusarium head blight (FHB) infection results in Fusarium damaged kernels (FDK) and deoxynivalenol (DON) contamination that are downgrading factors at the Canadian elevators. Durum wheat (Triticum turgidum L. var. durum Desf.) is particularly susceptible to FHB and most of the adapted Canadian durum wheat cultivars are susceptible to moderately susceptible to this disease. However, the durum line DT696 is less susceptible to FHB than commercially grown cultivars. Little is known about genetic variation for durum wheat ability to resist FDK infection and DON accumulation. This study was undertaken to map genetic loci conferring resistance to DON and FDK resistance using a SNP high-density genetic map of a DT707/DT696 DH population and to identify SNP markers useful in marker-assisted breeding. One hundred twenty lines were grown in corn spawn inoculated nurseries near Morden, MB in 2015, 2016 and 2017 and the harvested seeds were evaluated for DON. The genetic map of the population was used in quantitative trait locus analysis performed with MapQTL.6® software., Results: Four DON accumulation resistance QTL detected in two of the three years were identified on chromosomes 1 A, 5 A (2 loci) and 7 A and two FDK resistance QTL were identified on chromosomes 5 and 7 A in single environments. Although not declared significant due to marginal LOD values, the QTL for FDK on the 5 and 7 A were showing in other years suggesting their effects were real. DT696 contributed the favourable alleles for low DON and FDK on all the chromosomes. Although no resistance loci contributed by DT707, transgressive segregant lines were identified resulting in greater resistance than DT696. Breeder-friendly KASP markers were developed for two of the DON and FDK QTL detected on chromosomes 5 and 7 A. Markers flanking each QTL were physically mapped against the durum wheat reference sequence and candidate genes which might be involved in FDK and DON resistance were identified within the QTL intervals., Conclusions: The DH lines harboring the desired resistance QTL will serve as useful resources in breeding for FDK and DON resistance in durum wheat. Furthermore, breeder-friendly KASP markers developed during this study will be useful for the selection of durum wheat varieties with low FDK and DON levels in durum wheat breeding programs., (© 2024. Crown.)
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- 2024
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24. Identification of QTLs associated with seed protein concentration in two diverse recombinant inbred line populations of pea.
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Gali KK, Jha A, Tar'an B, Burstin J, Aubert G, Bing D, Arganosa G, and Warkentin TD
- Abstract
Improving the seed protein concentration (SPC) of pea ( Pisum sativum L.) has turned into an important breeding objective because of the consumer demand for plant-based protein and demand from protein fractionation industries. To support the marker-assisted selection (MAS) of SPC towards accelerated breeding of improved cultivars, we have explored two diverse recombinant inbred line (RIL) populations to identify the quantitative trait loci (QTLs) associated with SPC. The two RIL populations, MP 1918 × P0540-91 (PR-30) and Ballet × Cameor (PR-31), were derived from crosses between moderate SPC × high SPC accessions. A total of 166 and 159 RILs of PR-30 and PR-31, respectively, were genotyped using an Axiom® 90K SNP array and 13.2K SNP arrays, respectively. The RILs were phenotyped in replicated trials in two and three locations of Saskatchewan, Canada in 2020 and 2021, respectively, for agronomic assessment and SPC. Using composite interval mapping, we identified three QTLs associated with SPC in PR-30 and five QTLs in PR-31, with the LOD value ranging from 3.0 to 11.0. A majority of these QTLs were unique to these populations compared to the previously known QTLs for SPC. The QTL SPC-Ps-5.1 overlapped with the earlier reported SPC associated QTL PC-QTL-3. Three QTLs, SPC-Ps-4.2 , SPC-Ps-5.1 , and SPC-Ps-7.2 with LOD scores of 7.2, 7.9, and 11.3, and which explained 14.5%, 11.6%, and 11.3% of the phenotypic variance, respectively, can be used for marker-assisted breeding to increase SPC in peas. Eight QTLs associated with the grain yield were identified with LOD scores ranging from 3.1 to 8.2. Two sets of QTLs, SPC-Ps-2.1 and GY-Ps-2.1 , and SPC-Ps-5.1 and GY-Ps-5.3 , shared the QTL/peak regions. Each set of QTLs contributed to either SPC or grain yield depending on which parent the QTL region is derived from, thus confirming that breeding for SPC should take into consideration the effects on grain yield., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Gali, Jha, Tar’an, Burstin, Aubert, Bing, Arganosa and Warkentin.)
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- 2024
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25. Genetic Analysis of Partially Resistant and Susceptible Chickpea Cultivars in Response to Ascochyta rabiei Infection.
- Author
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Deokar AA, Sagi M, and Tar'an B
- Subjects
- Plant Diseases genetics, Plant Diseases microbiology, Cicer genetics, Ascomycota physiology
- Abstract
The molecular mechanism involved in chickpea ( Cicer arietinum L.) resistance to the necrotrophic fungal pathogen Ascochyta rabiei is not well documented. A. rabiei infection can cause severe damage in chickpea, resulting in significant economic losses. Understanding the resistance mechanism against ascochyta blight can help to define strategies to develop resistant cultivars. In this study, differentially expressed genes from two partially resistant cultivars (CDC Corinne and CDC Luna) and a susceptible cultivar (ICCV 96029) to ascochyta blight were identified in the early stages (24, 48 and 72 h) of A. rabiei infection using RNA-seq. Altogether, 3073 genes were differentially expressed in response to A. rabiei infection across different time points and cultivars. A larger number of differentially expressed genes (DEGs) were found in CDC Corinne and CDC Luna than in ICCV 96029. Various transcription factors including ERF, WRKY, bHLH and MYB were differentially expressed in response to A. rabiei infection. Genes involved in pathogen detection and immune signalings such as receptor-like kinases (RLKs), Leucine-Rich Repeat (LRR)-RLKs, and genes associated with the post-infection defence response were differentially expressed among the cultivars. GO functional enrichment and pathway analysis of the DEGs suggested that the biological processes such as metabolic process, response to stimulus and catalytic activity were overrepresented in both resistant and susceptible chickpea cultivars. The expression patterns of eight randomly selected genes revealed by RNA-seq were confirmed by quantitative PCR (qPCR) analysis. The results provide insights into the complex molecular mechanism of the chickpea defence in response to the A. rabiei infection.
- Published
- 2024
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26. Fine-mapping of a major locus for Fusarium wilt resistance in flax (Linum usitatissimum L.).
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Cloutier S, Edwards T, Zheng C, Booker HM, Islam T, Nabetani K, Kutcher HR, Molina O, and You FM
- Subjects
- Humans, Plant Breeding, Alleles, Lectins, Flax genetics, Fusarium, Arabidopsis
- Abstract
Key Message: Fine-mapping of a locus on chromosome 1 of flax identified an S-lectin receptor-like kinase (SRLK) as the most likely candidate for a major Fusarium wilt resistance gene. Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini, is a devastating disease in flax. Genetic resistance can counteract this disease and limit its spread. To map major genes for Fusarium wilt resistance, a recombinant inbred line population of more than 700 individuals derived from a cross between resistant cultivar 'Bison' and susceptible cultivar 'Novelty' was phenotyped in Fusarium wilt nurseries at two sites for two and three years, respectively. The population was genotyped with 4487 single nucleotide polymorphism (SNP) markers. Twenty-four QTLs were identified with IciMapping, 18 quantitative trait nucleotides with 3VmrMLM and 108 linkage disequilibrium blocks with RTM-GWAS. All models identified a major QTL on chromosome 1 that explained 20-48% of the genetic variance for Fusarium wilt resistance. The locus was estimated to span ~ 867 Kb but included a ~ 400 Kb unresolved region. Whole-genome sequencing of 'CDC Bethune', 'Bison' and 'Novelty' produced ~ 450 Kb continuous sequences of the locus. Annotation revealed 110 genes, of which six were considered candidate genes. Fine-mapping with 12 SNPs and 15 Kompetitive allele-specific PCR (KASP) markers narrowed down the interval to ~ 69 Kb, which comprised the candidate genes Lus10025882 and Lus10025891. The latter, a G-type S-lectin receptor-like kinase (SRLK) is the most likely resistance gene because it is the only polymorphic one. In addition, Fusarium wilt resistance genes previously isolated in tomato and Arabidopsis belonged to the SRLK class. The robust KASP markers can be used in marker-assisted breeding to select for this major Fusarium wilt resistance locus., (© 2024. Crown.)
- Published
- 2024
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27. Heat-moisture treatment to modify structure and functionality and reduce digestibility of wrinkled and round pea starches.
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Cheng F, Ren Y, Warkentin TD, and Ai Y
- Subjects
- Pisum sativum chemistry, Starch chemistry, Temperature, Amylose chemistry, Hot Temperature
- Abstract
Heat-moisture treatment (HMT) was employed to modify wrinkled pea (74.2 % and 76.5 % amylose) and round pea starches (35.9 % and 34.8 % amylose) at 35.0 % moisture, 110 or 130 °C, and 6 h. HMT increased the gelatinization temperatures and decreased the gelatinization enthalpy changes, reduced the pasting viscosities and gel hardness, and enhanced the enzymatic resistance of the pea starches in comparison with the native counterparts, with greater extents of changes observed for HMT at 130 °C overall. Although HMT decreased the relative crystallinity and elevated the proportion of amorphous conformation, the remaining double-helical crystallites in the modified samples showed improved thermal stability as revealed by differential scanning calorimetry (DSC). More importantly, the HMT-modified pea starches required a higher heating temperature of 120 °C, rather than 95 °C, in Rapid Visco Analyser to provide greater pasting viscosities and develop firmer gels, suggesting that the modified samples had stronger molecular entanglement than the native counterparts. Such molecular entanglement could also reduce enzymatic digestion of HMT-modified starches after boiling in water. With more diverse functional profiles and increased resistant starch (RS) contents (particularly for the HMT-modified wrinkled pea starches having 22.7-29.9 % RS), the HMT-modified pea starches could be promising new ingredients for food applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)
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- 2024
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28. Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69.
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Li Y, Wei ZZ, Sela H, Govta L, Klymiuk V, Roychowdhury R, Chawla HS, Ens J, Wiebe K, Bocharova V, Ben-David R, Pawar PB, Zhang Y, Jaiwar S, Molnár I, Doležel J, Coaker G, Pozniak CJ, and Fahima T
- Subjects
- Chromosome Mapping, Cloning, Molecular, Multigene Family, Triticum genetics, Genes, Plant genetics
- Abstract
Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2024
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29. Genome scans capture key adaptation and historical hybridization signatures in tetraploid wheat.
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Sertse D, Haile JK, Sari E, Klymiuk V, N'Diaye A, Pozniak CJ, Cloutier S, and Kagale S
- Abstract
Tetraploid wheats (Triticum turgidum L.), including durum wheat (T. turgidum ssp. durum (Desf.) Husn.), are important crops with high nutritional and cultural values. However, their production is constrained by sensitivity to environmental conditions. In search of adaptive genetic signatures tracing historical selection and hybridization events, we performed genome scans on two datasets: (1) Durum Global Diversity Panel comprising a total of 442 tetraploid wheat and wild progenitor accessions including durum landraces (n = 286), domesticated emmer (T. turgidum ssp. dicoccum (Schrank) Thell.; n = 103) and wild emmer (T. turgidum ssp. dicoccoides (Korn. ex Asch. & Graebn.) Thell.; n = 53) wheats genotyped using the 90K single nucleotide polymorphism (SNP) array, and (2) a second dataset comprising a total 121 accessions of nine T. turgidum subspecies including wild emmer genotyped with >100 M SNPs from whole-genome resequencing. The genome scan on the first dataset detected six outlier loci on chromosomes 1A, 1B, 3A (n = 2), 6A, and 7A. These loci harbored important genes for adaptation to abiotic stresses, phenological responses, such as seed dormancy, circadian clock, flowering time, and key yield-related traits, including pleiotropic genes, such as HAT1, KUODA1, CBL1, and ZFN1. The scan on the second dataset captured a highly differentiated region on chromosome 2B that shows significant differentiation between two groups: one group consists of Georgian (T. turgidum ssp. paleocolchicum A. Love & D. Love) and Persian (T. turgidum ssp. carthlicum (Nevski) A. Love & D. Love) wheat accessions, while the other group comprises all the remaining tetraploids including wild emmer. This is consistent with a previously reported introgression in this genomic region from T. timopheevii Zhuk. which naturally cohabit in the Georgian and neighboring areas. This region harbored several adaptive genes, including the thermomorphogenesis gene PIF4, which confers temperature-resilient disease resistance and regulates other biological processes. Genome scans can be used to fast-track germplasm housed in gene banks and in situ; which helps to identify environmentally resilient accessions for breeding and/or to prioritize them for conservation., (© 2023 National Research Council Canada and The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America. Reproduced with the permission of the Minister of Innovation, Science and Industry.)
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- 2023
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30. Prevalence and spatial distribution of cranberry fruit rot pathogens in British Columbia, Canada and potential fungicides for fruit rot management.
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Wood B, McBride E, Nabetani K, Griffin T, and Sabaratnam S
- Abstract
Twenty-eight cranberry farms in southwestern British Columbia were investigated for the prevalence and spatial distribution of fungal pathogens that contribute to fruit rot incidence. Farms were selected from six regions where most cranberry production is concentrated. Flowers, and green and ripe fruit (var. 'Stevens') samples, collected during two consecutive crop seasons, were analyzed for fruit rot pathogens. The most frequently isolated pathogens were identified as Allantophomopsis cytisporea , Botrytis cinerea , Coleophoma empetri , Colletotrichum fioriniae , Colletotrichum gloeosporioides , Fusicoccum putrefaciens , Glomerella sp., Phomopsis vaccinii , Phyllosticta elongata , Phyllosticta vaccinii and Physalospora vaccinii . The pathogens Allantophomopsis cytisporea , Phyllosticta spp., and Physalospora vaccinii were found at high incidence. These pathogens were present in all cranberry growing regions, although their mean percentage incidence varied from farm-to-farm and region-to-region. Amongst the pathogens from three phenological stages of cranberry crop examined, ripe fruit had the highest percentage incidence of fruit rot pathogens compared to that of flowers or green fruit; thus, indicating their presence at the early stages of crop development. The efficacy to inhibit the mycelial growth and spore germination of the fruit rot pathogens by twenty six fungicides, belonging to nine different modes of actions, were evaluated in vitro . The copper-based fungicides and captan of group M, flutriafol, triforine, difenoconazole, prothioconazole and propiconazole of group 3, benzovindiflupyr of group 7, and fosetyl-Al of group 33 demonstrated a high degree of efficacy in inhibiting the mycelial growth of all fruit rot pathogens. The fungicides chlorothalonil of group M, fenbuconazole of group 3, pyrimethanil and cyprodinil of group 9, and fludioxonil of group 12 also demonstrated activity against most fruit rot pathogens. The copper-based fungicides, chlorothalonil, captan, flutriafol, triforine, difenoconazole, prothioconazole, propiconazole, benzovindiflupyr, and fosetyl-Al effectively prevented the spore germination of most fruit rot pathogens. This demonstrated activity of the fungicides towards cranberry fruit rot pathogens should be assessed for efficacy in planta under field conditions. The current study identified the most critical fungal pathogens causing fruit rot of cranberry in British Columbia and potential fungicides that could be used in the management of fruit rot and to improve fruit quality and yield., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wood, McBride, Nabetani, Griffin and Sabaratnam.)
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- 2023
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31. Phylogenomic Insights on the Xanthomonas translucens Complex, and Development of a TaqMan Real-Time Assay for Specific Detection of pv. translucens on Barley.
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Tambong JT, Xu R, Fleitas MC, Wang L, Hubbard K, and Kutcher R
- Subjects
- Phylogeny, Commerce, Plant Diseases microbiology, Internationality, DNA, Hordeum microbiology, Xanthomonas genetics
- Abstract
The reemergence and spread of Xanthomonas translucens , the causal agent of bacterial leaf streak in cereal crops and wilt in turfgrass and forage species, is a concern to growers in the United States and Canada. The pathogen is seedborne and listed as an A2 quarantine organism by EPPO, making it a major constraint to international trade and exchange of germplasm. The pathovar concept of the X. translucens group is confusing due to overlapping of plant host ranges and specificity. Here, comparative genomics, phylogenomics, and 81 up-to-date bacterial core gene set (ubcg2) were used to assign the pathovars of X. translucens into three genetically and taxonomically distinct clusters. The study also showed that whole genome-based digital DNA-DNA hybridization unambiguously can differentiate the pvs. translucens and undulosa . Orthologous gene and proteome matrix analyses suggest that the cluster consisting of graminis , poae , arrhenatheri , phlei , and phleipratensis is very divergent. Whole-genome data were exploited to develop the first pathovar-specific TaqMan real-time PCR tool for detection of pv. translucen s on barley. Specificity of the TaqMan assay was validated using 62 Xanthomonas and non- Xanthomonas strains as well as growth chamber-inoculated and naturally infected barley leaves. Sensitivity levels of 0.1 pg (purified DNA) and 23 CFUs per reaction (direct culture) compared favorably with other previously reported real-time PCR assays. The phylogenomics data reported here suggest that the clusters could constitute novel taxonomic units or new species. Finally, the pathovar-specific diagnostic tool will have significant benefits to growers and facilitate international exchange of barley germplasm and trade., Competing Interests: The author(s) declare no conflict of interest.
- Published
- 2023
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32. Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles.
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Holden S, Bakkeren G, Hubensky J, Bamrah R, Abbasi M, Qutob D, de Graaf ML, Kim SH, Kutcher HR, McCallum BD, Randhawa HS, Iqbal M, Uloth K, Burlakoti RR, and Brar GS
- Subjects
- Alleles, Canada, Recombination, Genetic, Europe, Plant Diseases genetics, Plant Diseases microbiology, Basidiomycota genetics
- Abstract
Background: The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the emergence of novel lineages has the potential to cause serious epidemics such as the one caused by the 'Warrior' lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and the origin of foreign incursions was not known. Additionally, while some Pst mating type genes have been identified in published genomes, there has been no rigorous assessment of mating type diversity and distribution across the species., Results: We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in their global context and evidence tracing foreign incursions. More importantly: for the first time ever, we identified nine alleles of the homeodomain mating type locus in the worldwide Pst population and show that previously identified lineages exhibit a single pair of these alleles. Consistently with the literature, we find only two pheromone receptor mating type alleles. We show that the recent population shift from the 'PstS1' lineage to the 'PstS1-related' lineage is also associated with the introduction of a novel mating type allele (Pst-b3-HD) to the Canadian population. We also show evidence for high levels of mating type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as 'PstPr' (probable recombinant) which we identify as a foreign incursion, most closely related to isolates sampled from China circa 2015., Conclusions: These data describe a recent shift in the population of Canadian Pst field isolates and characterize homeodomain-locus mating type alleles in the global Pst population which can now be utilized in testing several research questions and hypotheses around sexuality and hybridization in rust fungi., (© 2023. BioMed Central Ltd., part of Springer Nature.)
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- 2023
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33. Multi-locus genome-wide association studies reveal the genetic architecture of Fusarium head blight resistance in durum wheat.
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Haile JK, Sertse D, N'Diaye A, Klymiuk V, Wiebe K, Ruan Y, Chawla HS, Henriquez MA, Wang L, Kutcher HR, Steiner B, Buerstmayr H, and Pozniak CJ
- Abstract
Durum wheat is more susceptible to Fusarium head blight (FHB) than other types or classes of wheat. The disease is one of the most devastating in wheat; it reduces yield and end-use quality and contaminates the grain with fungal mycotoxins such as deoxynivalenol (DON). A panel of 265 Canadian and European durum wheat cultivars, as well as breeding and experimental lines, were tested in artificially inoculated field environments (2019-2022, inclusive) and two greenhouse trials (2019 and 2020). The trials were assessed for FHB severity and incidence, visual rating index, Fusarium -damaged kernels, DON accumulation, anthesis or heading date, maturity date, and plant height. In addition, yellow pigment and protein content were analyzed for the 2020 field season. To capture loci underlying FHB resistance and related traits, GWAS was performed using single-locus and several multi-locus models, employing 13,504 SNPs. Thirty-one QTL significantly associated with one or more FHB-related traits were identified, of which nine were consistent across environments and associated with multiple FHB-related traits. Although many of the QTL were identified in regions previously reported to affect FHB, the QTL QFhb-3B.2 , associated with FHB severity, incidence, and DON accumulation, appears to be novel. We developed KASP markers for six FHB-associated QTL that were consistently detected across multiple environments and validated them on the Global Durum Panel (GDP). Analysis of allelic diversity and the frequencies of these revealed that the lines in the GDP harbor between zero and six resistance alleles. This study provides a comprehensive assessment of the genetic basis of FHB resistance and DON accumulation in durum wheat. Accessions with multiple favorable alleles were identified and will be useful genetic resources to improve FHB resistance in durum breeding programs through marker-assisted recurrent selection and gene stacking., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Haile, Sertse, N’Diaye, Klymiuk, Wiebe, Ruan, Chawla, Henriquez, Wang, Kutcher, Steiner, Buerstmayr and Pozniak.)
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- 2023
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34. Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression.
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Zhang J, Xiong H, Burguener GF, Vasquez-Gross H, Liu Q, Debernardi JM, Akhunova A, Garland-Campbell K, Kianian SF, Brown-Guedira G, Pozniak C, Faris JD, Akhunov E, and Dubcovsky J
- Subjects
- Biological Assay, Gene Expression, Mutation, Triticum genetics, Promoter Regions, Genetic
- Abstract
Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.
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- 2023
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35. Differential gene expression provides leads to environmentally regulated soybean seed protein content.
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Hooker JC, Smith M, Zapata G, Charette M, Luckert D, Mohr RM, Daba KA, Warkentin TD, Hadinezhad M, Barlow B, Hou A, Lefebvre F, Golshani A, Cober ER, and Samanfar B
- Abstract
Soybean is an important global source of plant-based protein. A persistent trend has been observed over the past two decades that soybeans grown in western Canada have lower seed protein content than soybeans grown in eastern Canada. In this study, 10 soybean genotypes ranging in average seed protein content were grown in an eastern location (control) and three western locations (experimental) in Canada. Seed protein and oil contents were measured for all lines in each location. RNA-sequencing and differential gene expression analysis were used to identify differentially expressed genes that may account for relatively low protein content in western-grown soybeans. Differentially expressed genes were enriched for ontologies and pathways that included amino acid biosynthesis, circadian rhythm, starch metabolism, and lipid biosynthesis. Gene ontology, pathway mapping, and quantitative trait locus (QTL) mapping collectively provide a close inspection of mechanisms influencing nitrogen assimilation and amino acid biosynthesis between soybeans grown in the East and West. It was found that western-grown soybeans had persistent upregulation of asparaginase (an asparagine hydrolase) and persistent downregulation of asparagine synthetase across 30 individual differential expression datasets. This specific difference in asparagine metabolism between growing environments is almost certainly related to the observed differences in seed protein content because of the positive correlation between seed protein content at maturity and free asparagine in the developing seed. These results provided pointed information on seed protein-related genes influenced by environment. This information is valuable for breeding programs and genetic engineering of geographically optimized soybeans., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Hooker, Smith, Zapata, Charette, Luckert, Mohr, Daba, Warkentin, Hadinezhad, Barlow, Hou, Lefebvre, Golshani, Cober and Samanfar.)
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- 2023
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36. Identification of Fusarium head blight sources of resistance and associated QTLs in historical and modern Canadian spring wheat.
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Semagn K, Henriquez MA, Iqbal M, Brûlé-Babel AL, Strenzke K, Ciechanowska I, Navabi A, N'Diaye A, Pozniak C, and Spaner D
- Abstract
Fusarium head blight (FHB) is one the most globally destructive fungal diseases in wheat and other small grains, causing a reduction in grain yield by 10-70%. The present study was conducted in a panel of historical and modern Canadian spring wheat ( Triticum aestivum L.) varieties and lines to identify new sources of FHB resistance and map associated quantitative trait loci (QTLs). We evaluated 249 varieties and lines for reaction to disease incidence, severity, and visual rating index (VRI) in seven environments by artificially spraying a mixture of four Fusarium graminearum isolates. A subset of 198 them were genotyped with the Wheat 90K iSelect single nucleotide polymorphisms (SNPs) array. Genome-wide association mapping performed on the overall best linear unbiased estimators (BLUE) computed from all seven environments and the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map of 26,449 polymorphic SNPs out of the 90K identified sixteen FHB resistance QTLs that individually accounted for 5.7-10.2% of the phenotypic variance. The positions of two of the FHB resistance QTLs overlapped with plant height and flowering time QTLs. Four of the QTLs ( QFhb.dms-3B.1 , QFhb.dms-5A.5 , QFhb.dms-5A.7 , and QFhb.dms-6A.4 ) were simultaneously associated with disease incidence, severity, and VRI, which accounted for 27.0-33.2% of the total phenotypic variance in the combined environments. Three of the QTLs ( QFhb.dms-2A.2 , QFhb.dms-2D.2 , and QFhb.dms-5B.8 ) were associated with both incidence and VRI and accounted for 20.5-22.1% of the total phenotypic variance. In comparison with the VRI of the checks, we identified four highly resistant and thirty-three moderately resistant lines and varieties. The new FHB sources of resistance and the physical map of the associated QTLs would provide wheat breeders valuable information towards their efforts in developing improved varieties in western Canada., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Semagn, Henriquez, Iqbal, Brûlé-Babel, Strenzke, Ciechanowska, Navabi, N’Diaye, Pozniak and Spaner.)
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- 2023
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37. Alleviation of chromium stress in plants using metal and metal oxide nanoparticles.
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Soni S, Jha AB, Dubey RS, and Sharma P
- Subjects
- Humans, Oxides analysis, Chromium chemistry, Plants, Soil chemistry, Soil Pollutants analysis, Metal Nanoparticles
- Abstract
Chromium (Cr), one of the hazardous pollutants, exists predominantly as Cr(VI) and Cr(III) in the environment. Cr(VI) is more toxic than Cr(III) due to its high mobility and solubility. Elevated levels of Cr in agricultural soil due to various anthropogenic activities cause Cr accumulation in plants, resulting in a significant reduction in plant yield and quality due to Cr-induced physiological, biochemical and molecular alterations. It can infiltrate the food chain through crop plants and cause harmful effects in humans via biomagnification. Cr(VI) is linked to cancer in humans. Therefore, mitigation strategies are required to remediate Cr-polluted soils and limit its accumulation in plants for safe food production. Recent research on metal and metal oxide nanoparticles (NPs) has shown that they can effectively reduce Cr accumulation and phytotoxicity. The effects of these NPs are influenced by their type and dose, exposure method, plant species and experimental settings. In this review, we present an up-to-date compilation and comprehensive analysis of the existing literature regarding the process of uptake and distribution of Cr and impact and potential mechanisms of metal and metal oxide nanoparticles led mitigation of Cr-induced stress in plants. We have also discussed recent developments, existing research gaps and future research directions in the field of Cr stress mitigation by NPs in plants. Overall, this review can provide valuable insights in reducing Cr accumulation and toxicity using metal and metal oxide nanoparticles, thereby promoting safe and sustainable cultivation of food and phytostabilization of Cr-polluted soil., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
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- 2023
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38. Low phytic acid pea supplementation as an approach to combating iron deficiency in female runners: A randomized control trial.
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Shaw KA, Chilibeck PD, Lindsay DL, Warkentin TD, Ko J, and Zello GA
- Abstract
Background: Iron deficiency (ID) is the most prevalent micronutrient deficiency in the world and the leading cause of anemia globally. Female athletes are at a disproportionate risk for ID due to blood loss through menstruation and decreased iron absorption secondary to exercise. Field peas are a rich source of iron but, similar to iron from other plant-based sources, the iron has limited bioavailability due to high levels of phytic acid, an inherent compound that binds to cations, creating a salt (phytate), which limits absorption during digestion. Aim: The purpose of our research was to investigate the effect of a field pea variety bred to have low levels of phytic acid on plasma ferritin, exercise performance, and body composition in female runners. Methods: Twenty-eight female runners (age:34.6 ± 9.7 years; weight: 65.1 ± 8.1 kg; VO
2 max: 50.7 ± 8.9 ml/kg/min) underwent measures of ferritin, exercise performance, and body composition before and after being randomly assigned to consume a powder derived from regular peas, low phytic acid peas, or a non-pea control (maltodextrin), plus vitamin C for 8 weeks. Results: The regular pea and low phytic acid pea groups had a 14.4% and 5.1% increase in plasma ferritin, respectively, while the maltodextrin group had a decrease of 2.2%; however, the difference in changes between groups was not statistically significant. No differences between groups were evident in any of the other measures. Conclusion: Larger doses or longer duration of pea supplementation may be necessary to induce meaningful changes in iron status. This trial was registered at ClinicalTrials.gov (NCT04872140).- Published
- 2023
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39. Optimization of Ustilago nuda Inoculum Concentration for Screening Un8 -Mediated Loose Smut Resistance in Barley Reveals a Resistance Reaction that Disrupts Seed Germination and Suggests a Role for Abscisic Acid in Disease Development.
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Zang W, Zhang XM, Eckstein PE, Yang F, Colin M, and Beattie AD
- Subjects
- Germination genetics, Abscisic Acid, Seeds, Plant Diseases, Seedlings genetics, Plant Growth Regulators, Hordeum genetics, Ustilaginales
- Abstract
Barley loose smut has been effectively controlled for decades through resistance conferred by the Un8 gene. However, evaluation of loose smut reaction using floret inoculation at the standard inoculum concentration is associated with the production of small, discolored seeds in Un8 carriers and susceptible genotypes. Interestingly, Un8 carriers also displayed significantly poorer germination than susceptible genotypes and produce short-lived seedlings following inoculation. To understand these observations, a Un8 carrier (TR11698) and susceptible non- Un8 carrier (CDC Austenson) were assessed for seed traits, Ustilago nuda biomass in the seed, infection rate, and phytohormone profile across a range of lower inoculum concentrations. At lower inoculum concentrations, seed appearance and weight improved in both genotypes, and infection rate increased in CDC Austenson. Pathogen load in the seed was similar in both genotypes and was positively correlated with the CDC Austenson infection rate. No infection was ever observed in TR11698. Significantly, germination rate improved in CDC Austenson, whereas the very low germination rate and short-lived seedlings remained associated with TR11698. It appears that poor seed appearance in both genotypes and low germination rate in the susceptible genotype can be improved by lowering the inoculum concentration. However, the very low germination rates and seedling death associated with the Un8 carrier TR11698 are indicative of Un8 -mediated resistance to loose smut. Finally, profiling of 38 phytohormones revealed that larger seeds observed at some inoculum concentrations compared with mock inoculation had higher abscisic acid concentrations. This could represent a pathogen survival strategy by ensuring better growth of the host., Competing Interests: The author(s) declare no conflict of interest.
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- 2023
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40. Wheat doubled haploids have a marked prevalence of chromosomal aberrations.
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Shrestha S, Koo DH, Evers B, Wu S, Walkowiak S, Hucl P, Pozniak C, Fritz A, and Poland J
- Subjects
- Haploidy, Prevalence, Chromosome Aberrations, Triticum genetics, Plant Breeding
- Abstract
Double haploid (DH) population development is widely used in many crops, including wheat (Triticum aestivum L.), to rapidly produce fixed germplasm for breeding and genetic studies. The genome shock that takes place during DH induction could induce chromosomal aberrations that can impact genome integrity and subsequently plant fitness and agronomic performance. To evaluate the extent of chromosomal aberrations that exist as a result of the DH process, we studied two wheat DH populations: CDC Stanley×CDC Landmark and KS13H9×SYMonument. We utilized high-throughput skim sequencing to construct digital karyotypes of these populations to quantify deletions and aneuploidy with high resolution and accuracy, which was confirmed in selected plants by cytological analysis. The two populations studied showed high proportion of abnormal primary DH lines, 55 and 45%, respectively, based on at least one abnormality per progeny. The chromosomal abnormalities are genetically unstable and were observed segregating in the subsequent generations. These observations have important implications for the use of DH lines in genetics and breeding., (© 2023 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)
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- 2023
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41. Inoculum dose-disease response relationships for the pea root rot pathogen, Aphanomyces euteiches , are dependent on soil type and other pathogens.
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Chatterton S, Schwinghamer TD, Pagé A, Davidson RB, Harding MW, and Banniza S
- Abstract
The oomycete pathogen, Aphanomyces euteiches , was implicated for the first time in pea and lentil root rot in Saskatchewan and Alberta in 2012 and 2013. Subsequent surveys from 2014 to 2017 revealed that Aphanomyces root rot (ARR) was widespread across the Canadian prairies. The absence of effective chemical, biological, and cultural controls and lack of genetic resistance leave only one management option: avoidance. The objectives of this study were to relate oospore levels in autoclaved and non-autoclaved soils to ARR severity across soil types from the vast prairie landscape and to determine the relationship of measured DNA quantity of A. euteiches using droplet digital PCR or quantitative PCR to the initial oospore inoculum dose in soils. These objectives support a future end goal of creating a rapid assessment method capable of categorizing root rot risk in field soil samples to aid producers with pulse crop field selection decisions. The ARR severity to oospore dose relationship was statistically significantly affected by the soil type and location from which soils were collected and did not show a linear relationship. For most soil types, ARR did not develop at oospore levels below 100/g soil, but severity rose above this level, confirming a threshold level of 100 oospores/g soil for disease development. For most soil types, ARR severity was significantly higher in non-autoclaved compared to autoclaved treatments, demonstrating the role that other pathogens play in increasing disease severity. There was a significant linear relationship between DNA concentrations measured in soil and oospore inoculum concentration, although the strength of the relationship was better for some soil types, and in some soil types, DNA measurement results underestimated the number of oospores. This research is important for developing a root rot risk assessment system for the Canadian prairies based on soil inoculum quantification, following field validation of soil quantification and relationship to root rot disease severity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Chatterton, Schwinghamer, Pagé, Davidson, Harding and Banniza.)
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- 2023
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42. Historical Selection, Adaptation Signatures, and Ambiguity of Introgressions in Wheat.
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Sertse D, You FM, Klymiuk V, Haile JK, N'Diaye A, Pozniak CJ, Cloutier S, and Kagale S
- Subjects
- Plant Breeding, Ploidies, Acclimatization, Polymorphism, Single Nucleotide, Genome, Plant, Triticum genetics
- Abstract
Wheat was one of the crops domesticated in the Fertile Crescent region approximately 10,000 years ago. Despite undergoing recent polyploidization, hull-to-free-thresh transition events, and domestication bottlenecks, wheat is now grown in over 130 countries and accounts for a quarter of the world's cereal production. The main reason for its widespread success is its broad genetic diversity that allows it to thrive in different environments. To trace historical selection and hybridization signatures, genome scans were performed on two datasets: approximately 113K SNPs from 921 predominantly bread wheat accessions and approximately 110K SNPs from about 400 wheat accessions representing all ploidy levels. To identify environmental factors associated with the loci, a genome-environment association (GEA) was also performed. The genome scans on both datasets identified a highly differentiated region on chromosome 4A where accessions in the first dataset were dichotomized into a group (n = 691), comprising nearly all cultivars, wild emmer, and most landraces, and a second group (n = 230), dominated by landraces and spelt accessions. The grouping of cultivars is likely linked to their potential ancestor, bread wheat cv. Norin-10. The 4A region harbored important genes involved in adaptations to environmental conditions. The GEA detected loci associated with latitude and temperature. The genetic signatures detected in this study provide insight into the historical selection and hybridization events in the wheat genome that shaped its current genetic structure and facilitated its success in a wide spectrum of environmental conditions. The genome scans and GEA approaches applied in this study can help in screening the germplasm housed in gene banks for breeding, and for conservation purposes.
- Published
- 2023
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43. Systematic Characterization of Multi-Rust Resistance Genes from a 'Parula × Thatcher' Population with a High-Density Genetic Map.
- Author
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Zhang W, Boyle K, Gao P, Polley B, Brost JM, Francis T, Sidebottom C, McCallum BD, Kutcher HR, Randhawa H, Fetch TG, Ferrie AMR, and Fobert PR
- Subjects
- Chromosome Mapping, Canada, Quantitative Trait Loci genetics, Disease Resistance genetics, Plant Diseases genetics, Basidiomycota genetics
- Abstract
Pyramiding multiple resistant genes has been proposed as the most effective way to control wheat rust diseases globally. Identifying the most effective pyramids is challenged by the large pool of rust resistance genes and limited information about their mechanisms of resistance and interactions. Here, using a high-density genetic map, a double haploid population, and multi-rust field testing, we aimed to systematically characterize the most effective gene pyramids for rust resistance from the durable multi-rust resistant CIMMYT cultivar Parula. We revealed that the Parula resistance gene pyramid contains Lr34/Yr18/Sr57 ( Lr34 ), Lr46/Yr29/Sr58 ( Lr46 ), Lr27/Yr30/Sr2 ( Sr2 ), and Lr68 . The efficacy, magnitude of effect, and interactions varied for the three rust diseases. A subpopulation mapping approach was applied to characterize the complex interactions of the resistance genes by controlling for the effect of Lr34 . Using this approach, we found that Lr34 and Lr68 have a strong additive effect for leaf rust, whereas no additive effects were observed for any rusts between Lr34 and Lr46 . Lr34 combined synergistically with Sr12 from Thatcher for stem rust, whereas the additive effect of Lr34 and Sr2 was dependent on the type of rust and environment. Two novel leaf rust quantitative trait loci (QTLs) from Parula were identified in this study, a stable QTL QLr-7BS and QLr-5AS , which showed Lr34 dependent expression. With these findings, we propose combining two to three high-value genes from Canadian wheat (e.g., Sr12 from Thatcher) with a foundational multi-adult plant resistance cassette for desirable and durable resistance to all three rusts in Canadian wheat., Competing Interests: The author(s) declare no conflict of interest.
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- 2023
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44. Interaction and association analysis of malting related traits in barley.
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Iqbal I, Desta ZA, Tripathi RK, Beattie A, Badea A, and Singh J
- Subjects
- Humans, Chromosome Mapping, Phenotype, Quantitative Trait Loci genetics, Polymorphism, Single Nucleotide, Hordeum genetics, Hordeum chemistry
- Abstract
Barley is considered as a foundation of the brewing and malting industry. Varieties with superior malt quality traits are required for efficient brewing and distillation processes. Among these, the Diastatic Power (DP), wort-Viscosity (VIS), β-glucan content (BG), Malt Extract (ME) and Alpha-Amylase (AA) are controlled by several genes linked to numerous quantitative trait loci (QTL), identified for barley malting quality. One of the well-known QTL, QTL2, associated with barley malting trait present on chromosome 4H harbours a key gene, called as HvTLP8 that has been identified for influencing the barley malting quality through its interaction with β-glucan in a redox-dependent manner. In this study, we examined to develop a functional molecular marker for HvTLP8 in the selection of superior malting cultivars. We first examined the expression of HvTLP8 and HvTLP17 containing carbohydrate binding domains in barley malt and feed varieties. The higher expression of HvTLP8 prompted us to further investigate its role as a marker for malting trait. By exploring the 1000 bp downstream 3' UTR region of HvTLP8, we found single nucleotide polymorphism (SNP) in between Steptoe (feed variety) and Morex (malt variety), which was further validated by Cleaved Amplified Polymorphic Sequence (CAPS) marker assay. Analysis of 91 individuals from the Steptoe x Morex doubled haploid (DH) mapping population revealed CAPS polymorphism in HvTLP8. Highly significant (p<0.001) correlations among ME, AA and DP malting traits were observed. The correlation coefficient (r) between these traits ranged from 0.53 to 0.65. However, the polymorphism in HvTLP8 did not correlate effectively with ME, AA, and DP. Altogether, these findings will help us to further design the experiment regarding the HvTLP8 variation and its association with other desirable traits., Competing Interests: The authors declare that they have no competing interests., (Copyright: © 2023 Iqbal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
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45. The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat.
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Jiang Y, N'Diaye A, Koh CS, Quilichini TD, Shunmugam ASK, Kirzinger MW, Konkin D, Bekkaoui Y, Sari E, Pasha A, Esteban E, Provart NJ, Higgins JD, Rozwadowski K, Sharpe AG, Pozniak CJ, and Kagale S
- Subjects
- Meiosis genetics, RNA, Messenger genetics, RNA, Untranslated genetics, Triticum genetics, Triticum metabolism, Transcriptome
- Abstract
Reproductive success hinges on precisely coordinated meiosis, yet our understanding of how structural rearrangements of chromatin and phase transitions during meiosis are transcriptionally regulated is limited. In crop plants, detailed analysis of the meiotic transcriptome could identify regulatory genes and epigenetic regulators that can be targeted to increase recombination rates and broaden genetic variation, as well as provide a resource for comparison among eukaryotes of different taxa to answer outstanding questions about meiosis. We conducted a meiotic stage-specific analysis of messenger RNA (mRNA), small non-coding RNA (sncRNA), and long intervening/intergenic non-coding RNA (lincRNA) in wheat (Triticum aestivum L.) and revealed novel mechanisms of meiotic transcriptional regulation and meiosis-specific transcripts. Amidst general repression of mRNA expression, significant enrichment of ncRNAs was identified during prophase I relative to vegetative cells. The core meiotic transcriptome was comprised of 9309 meiosis-specific transcripts, 48 134 previously unannotated meiotic transcripts, and many known and novel ncRNAs differentially expressed at specific stages. The abundant meiotic sncRNAs controlled the reprogramming of central metabolic pathways by targeting genes involved in photosynthesis, glycolysis, hormone biosynthesis, and cellular homeostasis, and lincRNAs enhanced the expression of nearby genes. Alternative splicing was not evident in this polyploid species, but isoforms were switched at phase transitions. The novel, stage-specific regulatory controls uncovered here challenge the conventional understanding of this crucial biological process and provide a new resource of requisite knowledge for those aiming to directly modulate meiosis to improve crop plants. The wheat meiosis transcriptome dataset can be queried for genes of interest using an eFP browser located at https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi?dataSource=Wheat_Meiosis., (© 2023 National Research Council Canada and The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. Reproduced with the permission of the Minister of Innovation, Science, and Economic Development.)
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- 2023
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46. Updated guidelines for gene nomenclature in wheat.
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Boden SA, McIntosh RA, Uauy C, Krattinger SG, Dubcovsky J, Rogers WJ, Xia XC, Badaeva ED, Bentley AR, Brown-Guedira G, Caccamo M, Cattivelli L, Chhuneja P, Cockram J, Contreras-Moreira B, Dreisigacker S, Edwards D, González FG, Guzmán C, Ikeda TM, Karsai I, Nasuda S, Pozniak C, Prins R, Sen TZ, Silva P, Simkova H, and Zhang Y
- Subjects
- Phenotype, Genes, Plant, Edible Grain genetics, Triticum genetics, Plant Breeding
- Abstract
Key Message: Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding., (© 2023. The Author(s).)
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- 2023
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47. Genetic architecture of rust resistance in a wheat ( Triticum turgidum ) diversity panel.
- Author
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Klymiuk V, Haile T, Ens J, Wiebe K, N'Diaye A, Fatiukha A, Krugman T, Ben-David R, Hübner S, Cloutier S, and Pozniak CJ
- Abstract
Introduction: Wheat rust diseases are widespread and affect all wheat growing areas around the globe. Breeding strategies focus on incorporating genetic disease resistance. However, pathogens can quickly evolve and overcome the resistance genes deployed in commercial cultivars, creating a constant need for identifying new sources of resistance., Methods: We have assembled a diverse tetraploid wheat panel comprised of 447 accessions of three Triticum turgidum subspecies and performed a genome-wide association study (GWAS) for resistance to wheat stem, stripe, and leaf rusts. The panel was genotyped with the 90K Wheat iSelect single nucleotide polymorphism (SNP) array and subsequent filtering resulted in a set of 6,410 non-redundant SNP markers with known physical positions., Results: Population structure and phylogenetic analyses revealed that the diversity panel could be divided into three subpopulations based on phylogenetic/geographic relatedness. Marker-trait associations (MTAs) were detected for two stem rust, two stripe rust and one leaf rust resistance loci. Of them, three MTAs coincide with the known rust resistance genes Sr13, Yr15 and Yr67, while the other two may harbor undescribed resistance genes., Discussion: The tetraploid wheat diversity panel, developed and characterized herein, captures wide geographic origins, genetic diversity, and evolutionary history since domestication making it a useful community resource for mapping of other agronomically important traits and for conducting evolutionary studies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Klymiuk, Haile, Ens, Wiebe, N’Diaye, Fatiukha, Krugman, Ben-David, Hübner, Cloutier and Pozniak.)
- Published
- 2023
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48. Quantitative trait loci associated with amino acid concentration and in vitro protein digestibility in pea ( Pisum sativum L.).
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Zhou J, Wan Z, Gali KK, Jha AB, Nickerson MT, House JD, Tar'an B, and Warkentin TD
- Abstract
With the expanding interest in plant-based proteins in the food industry, increasing emphasis is being placed on breeding for protein concentration and quality. Two protein quality traits i.e., amino acid profile and protein digestibility, were assessed in replicated, multi-location field trials from 2019 to 2021 in pea recombinant inbred line population PR-25. This RIL population was targeted specifically for the research of protein related traits and its parents, CDC Amarillo and CDC Limerick, had distinct variations in the concentration of several amino acids. Amino acid profile was determined using near infrared reflectance analysis, and protein digestibility was through an in vitro method. Several essential amino acids were selected for QTL analysis, including lysine, one of the most abundant essential amino acids in pea, and methionine, cysteine, and tryptophan, the limiting amino acids in pea. Based on phenotypic data of amino acid profiles and in vitro protein digestibility of PR-25 harvested in seven location-years, three QTLs were associated with methionine + cysteine concentration, among which, one was located on chromosome 2 (R
2 = 17%, indicates this QTL explained 17% phenotypic variation of methionine + cysteine concentration within PR-25), and two were located on chromosome 5 (R2 = 11% and 16%). Four QTLs were associated with tryptophan concentration and are located on chromosome 1 (R2 = 9%), chromosome 3 (R2 = 9%), and chromosome 5 (R2 = 8% and 13%). Three QTLs were associated with lysine concentration, among which, one was located on chromosome 3 (R2 = 10%), the other two were located on chromosome 4 (R2 = 15% and 21%). Two QTLs were associated with in vitro protein digestibility, one each located on chromosomes 1 (R2 = 11%) and 2 (R2 = 10%). QTLs associated with in vitro protein digestibility, and methionine + cysteine concentration on chromosome 2 were identified to be co-localized with known QTL for total seed protein concentration in PR-25. QTLs associated with tryptophan and methionine + cysteine concentration co-localized on chromosome 5. The identification of QTLs associated with pea seed quality is an important step towards marker-assisted selection of breeding lines with improved nutritional quality, which will further boost the competitiveness of pea in plant-based protein markets., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zhou, Wan, Gali, Jha, Nickerson, House, Tar’an and Warkentin.)- Published
- 2023
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49. Genomic selection for agronomic traits in a winter wheat breeding program.
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Ficht A, Konkin DJ, Cram D, Sidebottom C, Tan Y, Pozniak C, and Rajcan I
- Subjects
- Phenotype, Genotype, Genomics methods, Selection, Genetic, Models, Genetic, Triticum genetics, Plant Breeding
- Abstract
Key Message: rAMP-seq based genomic selection for agronomic traits has been shown to be a useful tool for winter wheat breeding programs by increasing the rate of genetic gain. Genomic selection (GS) is an effective strategy to employ in a breeding program that focuses on optimizing quantitative traits, which results in the ability for breeders to select the best genotypes. GS was incorporated into a breeding program to determine the potential for implementation on an annual basis, with emphasis on selecting optimal parents and decreasing the time and costs associated with phenotyping large numbers of genotypes. The design options for applying repeat amplification sequencing (rAMP-seq) in bread wheat were explored, and a low-cost single primer pair strategy was implemented. A total of 1870 winter wheat genotypes were phenotyped and genotyped using rAMP-seq. The optimization of training to testing population size showed that the 70:30 ratio provided the most consistent prediction accuracy. Three GS models were tested, rrBLUP, RKHS and feed-forward neural networks using the University of Guelph Winter Wheat Breeding Program (UGWWBP) and Elite-UGWWBP populations. The models performed equally well for both populations and did not differ in prediction accuracy (r) for most agronomic traits, with the exception of yield, where RKHS performed the best with an r = 0.34 and 0.39 for each population, respectively. The ability to operate a breeding program where multiple selection strategies, including GS, are utilized will lead to higher efficiency in the program and ultimately lead to a higher rate of genetic gain., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
- Published
- 2023
- Full Text
- View/download PDF
50. Untargeted profiling of secondary metabolites and phytotoxins associated with stemphylium blight of lentil.
- Author
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Adobor S, Banniza S, Vandenberg A, and Purves RW
- Subjects
- Plant Breeding, Secondary Metabolism, Metabolomics, Lens Plant, Alkaloids
- Abstract
Main Conclusion: Stemphylium botryosum alters lentil secondary metabolism and differentially affects resistant and susceptible genotypes. Untargeted metabolomics identifies metabolites and their potential biosynthetic pathways that play a crucial role in resistance to S. botryosum. The molecular and metabolic processes that mediate resistance to stemphylium blight caused by Stemphylium botryosum Wallr. in lentil are largely unknown. Identifying metabolites and pathways associated with Stemphylium infection may provide valuable insights and novel targets to breed for enhanced resistance. The metabolic changes following infection of four lentil genotypes by S. botryosum were investigated by comprehensive untargeted metabolic profiling employing reversed-phase or hydrophilic interaction liquid chromatography (HILIC) coupled to a Q-Exactive mass spectrometer. At the pre-flowering stage, plants were inoculated with S. botryosum isolate SB19 spore suspension and leaf samples were collected at 24, 96 and 144 h post-inoculation (hpi). Mock-inoculated plants were used as negative controls. After analyte separation, high-resolution mass spectrometry data was acquired in positive and negative ionization modes. Multivariate modeling revealed significant treatment, genotype and hpi effects on metabolic profile changes that reflect lentil response to Stemphylium infection. In addition, univariate analyses highlighted numerous differentially accumulated metabolites. By contrasting the metabolic profiles of SB19-inoculated and mock-inoculated plants and among lentil genotypes, 840 pathogenesis-related metabolites were detected including seven S. botryosum phytotoxins. These metabolites included amino acids, sugars, fatty acids and flavonoids in primary and secondary metabolism. Metabolic pathway analysis revealed 11 significant pathways including flavonoid and phenylpropanoid biosynthesis, which were affected upon S. botryosum infection. This research contributes to ongoing efforts toward a comprehensive understanding of the regulation and reprogramming of lentil metabolism under biotic stress, which will provide targets for potential applications in breeding for enhanced disease resistance., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
- Published
- 2023
- Full Text
- View/download PDF
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