127 results on '"Noel Ellis"'
Search Results
2. An Integrated Linkage Map of Three Recombinant Inbred Populations of Pea (Pisum sativum L.)
- Author
-
Chie Sawada, Carol Moreau, Gabriel H. J. Robinson, Burkhard Steuernagel, Luzie U. Wingen, Jitender Cheema, Ellen Sizer-Coverdale, David Lloyd, Claire Domoney, and Noel Ellis
- Subjects
pea ,genetic map ,recombinant inbred population ,integrated map ,Genetics ,QH426-470 - Abstract
Biparental recombinant inbred line (RIL) populations are sets of genetically stable lines and have a simple population structure that facilitates the dissection of the genetics of interesting traits. On the other hand, populations derived from multiparent intercrosses combine both greater diversity and higher numbers of recombination events than RILs. Here, we describe a simple population structure: a three-way recombinant inbred population combination. This structure was easy to produce and was a compromise between biparental and multiparent populations. We show that this structure had advantages when analyzing cultivar crosses, and could achieve a mapping resolution of a few genes.
- Published
- 2022
- Full Text
- View/download PDF
3. NMR Metabolomics Defining Genetic Variation in Pea Seed Metabolites
- Author
-
Noel Ellis, Chie Hattori, Jitender Cheema, James Donarski, Adrian Charlton, Michael Dickinson, Giampaolo Venditti, Péter Kaló, Zoltán Szabó, György B. Kiss, and Claire Domoney
- Subjects
genetic map ,genetic variation ,pea ,seed ,metabolite ,nuclear magnetic resonance ,Plant culture ,SB1-1110 - Abstract
Nuclear magnetic resonance (NMR) spectroscopy profiling was used to provide an unbiased assessment of changes to the metabolite composition of seeds and to define genetic variation for a range of pea seed metabolites. Mature seeds from recombinant inbred lines, derived from three mapping populations for which there is substantial genetic marker linkage information, were grown in two environments/years and analyzed by non-targeted NMR. Adaptive binning of the NMR metabolite data, followed by analysis of quantitative variation among lines for individual bins, identified the main genomic regions determining this metabolic variability and the variability for selected compounds was investigated. Analysis by t-tests identified a set of bins with highly significant associations to genetic map regions, based on probability (p) values that were appreciably lower than those determined for randomized data. The correlation between bins showing high mean absolute deviation and those showing low p-values for marker association provided an indication of the extent to which the genetics of bin variation might be explained by one or a few loci. Variation in compounds related to aromatic amino acids, branched-chain amino acids, sucrose-derived metabolites, secondary metabolites and some unidentified compounds was associated with one or more genetic loci. The combined analysis shows that there are multiple loci throughout the genome that together impact on the abundance of many compounds through a network of interactions, where individual loci may affect more than one compound and vice versa. This work therefore provides a framework for the genetic analysis of the seed metabolome, and the use of genetic marker data in the breeding and selection of seeds for specific seed quality traits and compounds that have high commercial value.
- Published
- 2018
- Full Text
- View/download PDF
4. Genetic Variation Controlling Wrinkled Seed Phenotypes in Pisum: How Lucky Was Mendel?
- Author
-
Tracey Rayner, Carol Moreau, Mike Ambrose, Peter G. Isaac, Noel Ellis, and Claire Domoney
- Subjects
genetic markers ,myoinositol ,pea germplasm ,r and rb mutations ,seed phenotype ,seed coat (testa) metabolites ,wrinkled seeds ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
One of the traits studied by Mendel in pea (Pisum sativum L.) was the wrinkled-seeded phenotype, and the molecular basis for a mutation underlying this phenotype was discovered in the 1990s. Although the starch-branching enzyme gene mutation identified at the genetic locus r is most likely to be that in seeds available to Mendel in the mid-1800s, it has remained an open question as to whether or not additional natural mutations in this gene exist within Pisum germplasm collections. Here, we explore this question and show that all but two wrinkled-seeded variants in one such collection correspond to either the mutant allele described previously for the r locus or a mutation at a second genetic locus, rb, affecting the gene encoding the large subunit of Adenosine diphosphoglucose (ADP-glucose) pyrophosphorylase; the molecular basis for the rb mutation is described here. The genetic basis for the phenotype of one (JI 2110) of the two lines which are neither r nor rb has been studied in crosses with a round-seeded variant (JI 281); for which extensive genetic marker data were expected. In marked contrast to the trait studied by Mendel and the rb phenotype; the data suggest that the wrinkled-seeded phenotype in JI 2110 is maternally determined, controlled by two genetic loci, and the extent to which it is manifested is very sensitive to the environment. Metabolite analysis of the cotyledons of JI 2110 revealed a profile for sucrose and sucrose-derived compounds that was more similar to that of wild-type round-seeded, than that of wrinkled-seeded r, pea lines. However, the metabolite profile of the seed coat (testa) of JI 2110 was distinct from that of other round-seeded genotypes tested which, together with analysis of recombinant inbred progeny lines, suggests an explanation for the seed phenotype.
- Published
- 2017
- Full Text
- View/download PDF
5. The Taxonomic Status of Genera within the Fabeae (Vicieae), with a Special Focus on Pisum
- Author
-
T. H. Noel Ellis, Petr Smýkal, Nigel Maxted, Clarice J. Coyne, Claire Domoney, Judith Burstin, Yanis Bouchenak-Khelladi, and Noam Chayut
- Subjects
Leguminosae ,systematics ,phylogenetics ,Pisum sativum ,Lathyrus oleraceus ,nomenclature ,Biology (General) ,QH301-705.5 - Abstract
The taxonomy of the tribe Fabeae (Vicieae) has long been problematic, but an analysis by Schaefer et al. in 2012 gave an exceptionally clear view of the tribe and noted the possibility that some nomenclatural adjustments may be required at some future date. These authors suggested several options, expressing some preferences. However, there has been a recent change to formally accepted names, implementing one of these possibilities, but without any additional relevant information. This change seems unjustified and unhelpful. We therefore present an argument for the retention, or re-instatement, of the genera Pisum, Vavilovia, and Lens until such time as new data support this requirement and there is no nomenclatural solution that is both accurate and convenient.
- Published
- 2024
- Full Text
- View/download PDF
6. Mendel’s terminology and notation reveal his understanding of genetics
- Author
-
T. H. Noel Ellis and Peter J. van Dijk
- Subjects
Mendel ,Terminology ,Symbols ,Genetic nomenclatutre ,Olby ,Genetics ,QH426-470 - Abstract
Abstract We describe both the terminology and use of symbols introduced by Mendel in his 1866 paper and discuss some misconceptions concerning their interpretation.
- Published
- 2023
- Full Text
- View/download PDF
7. Mutation Breeding, Genetic Diversity and Crop Adaptation to Climate Change
- Author
-
Sobhana Sivasankar, Thomas Henry Noel Ellis, Ljupcho Jankuloski, Ivan Ingelbrecht and Sobhana Sivasankar, Thomas Henry Noel Ellis, Ljupcho Jankuloski, Ivan Ingelbrecht
- Published
- 2021
8. How did Mendel arrive at his discoveries?
- Author
-
Peter J. van Dijk, Adrienne P. Jessop, and T. H. Noel Ellis
- Subjects
Genetics - Published
- 2022
9. Gregor Mendel and the theory of species multiplication
- Author
-
van Dijk, Peter J, primary and Noel Ellis, T H, additional
- Published
- 2023
- Full Text
- View/download PDF
10. Gregor Mendel and the theory of species multiplication
- Author
-
Peter J van Dijk and T H Noel Ellis
- Subjects
Genetics - Abstract
According to the revisionist interpretation of Mendel’s pea crosses, his primary aim was not to study the inheritance of traits. Instead, he was interested in the question raised by Linnaeus as to whether new species could arise from the hybridization of existing species. The genetic interpretation is therefore seen as ahistorical by the revisionists. This view goes back to the 1979 article “Mendel no Mendelian?” by the historian of science R.C. Olby. A closer analysis shows that Olby implicitly assumed Mendel adhered to the unusual strictest species definition for Pisum. However, we argue that Mendel only mentions the hypothetical application of this strict definition in his 1866 paper. Like most of his contemporaries, Mendel accepted variation within species where the differences between varieties and species were a matter of degree. After researching variable hybrids in peas (Pisum; 1854–1863), Mendel also studied constant hybrids in hawkweeds (Hieracium; 1866–1873), which he considered to be new species. There is no debate about the latter, but the matter becomes muddled because Olby lumps Pisum and Hieracium together, despite their having completely different reproduction systems. Based on newly discovered historical sources, we also dispute several other assumptions made by Olby. We do not consider Olby’s claim that Mendel conducted the Pisum experiments to investigate species multiplication to be tenable.
- Published
- 2023
11. Grasspea
- Author
-
Noel Ellis, M. Carlota Vaz Patto, Diego Rubiales, Jiří Macas, Petr Novák, Shiv Kumar, Xiaopeng Hao, Anne Edwards, Abhimanyu Sarkar, Peter Emmrich, Biotechnology and Biological Sciences Research Council (UK), John Innes Centre, Fundação para a Ciência e a Tecnologia (Portugal), Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Academy of Sciences of the Czech Republic, Templeton World Charity Foundation, and Agriculture Research System of China
- Abstract
Grasspea is an important food security crop, especially under severely adverse environmental conditions such as prolonged drought. The crop has a long history, but its cultivation has declined probably due to the presence of β-ODAP, a neurotoxin, which can cause a severe disease in people and domestic animals when grasspea is the main source of nutrition in an unbalanced diet. Grasspea, and the people who depend on it, can therefore benefit from the removal of this specific compound. A wide range of genetic and genomic tools are now available which can facilitate this development. The purpose of this article is to describe genetic and genomic resources and their specific features in grasspea., AE, NE, PE, and AS were supported by the John Innes Centre Institute Development Grant, the Biotechnology and Biological Sciences Research Council (BBSRC) Detox Grass pea project (BB/L011719/1), the BBSRC SASSA UPGRADE project (BB/R020604/1), and the BBSRC Institute Strategic Programme (BBS/E/J/000PR9799). NE gratefully acknowledges the support of an Institute Strategic Fellowship from The John Innes Centre. These authors thank Cathie Martin for her support and many useful discussions. MCVP would like to acknowledge financial support by Fundação para a Ciência e Tecnologia (FCT), Portugal, through the research unit GREEN-IT (UID/04551/2020). DR was supported by AEI projects AGL2017-82907-R and PID2020-11468RB-100. JM and PN were financially supported by the Czech Academy of Science (RVO: 60077344). SK acknowledges support of the BBSRC SASSA UPGRADE project (BB/R020604/1) and a grant from Templeton World Charity Foundation, Inc. XH acknowledges support from the China Agriculture Research System of MOF and MARA-Food Legumes (CARS-08-Z4).
- Published
- 2022
12. THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps.
- Author
-
Jitender Cheema, T. H. Noel Ellis, and Jo L. Dicks
- Published
- 2010
- Full Text
- View/download PDF
13. Mendel’s pea crosses: varieties, traits and statistics
- Author
-
T. H. Noel Ellis, Martin T. Swain, Julie M.I. Hofer, and Peter J. van Dijk
- Subjects
0106 biological sciences ,Genotype ,lcsh:QH426-470 ,Statistical controversy ,Biology ,010603 evolutionary biology ,01 natural sciences ,RA Fisher ,Normal distribution ,03 medical and health sciences ,Quantitative Trait, Heritable ,Statistics ,Genetics ,Statistical analysis ,Letter to the Editor ,Crosses, Genetic ,030304 developmental biology ,0303 health sciences ,Models, Genetic ,Gregor Mendel ,Peas ,Genetic Variation ,General Medicine ,Plant Breeding ,lcsh:Genetics ,F2 population ,Pea varieties - Abstract
A controversy arose over Mendel’s pea crossing experiments after the statistician R.A. Fisher proposed how these may have been performed and criticised Mendel’s interpretation of his data. Here we re-examine Mendel’s experiments and investigate Fisher’s statistical criticisms of bias. We describe pea varieties available in Mendel’s time and show that these could readily provide all the material Mendel needed for his experiments; the characters he chose to follow were clearly described in catalogues at the time. The combination of character states available in these varieties, together with Eichling’s report of crosses Mendel performed, suggest that two of his F3 progeny test experiments may have involved the same F2 population, and therefore that these data should not be treated as independent variables in statistical analysis of Mendel’s data. A comprehensive re-examination of Mendel’s segregation ratios does not support previous suggestions that they differ remarkably from expectation. The χ2values for his segregation ratios sum to a value close to the expectation and there is no deficiency of extreme segregation ratios. Overall the χ values for Mendel’s segregation ratios deviate slightly from the standard normal distribution; this is probably because of the variance associated with phenotypic rather than genotypic ratios and because Mendel excluded some data sets with small numbers of progeny, where he noted the ratios “deviate not insignificantly” from expectation.
- Published
- 2019
14. An Integrated Linkage Map of Three Recombinant Inbred Populations of Pea (
- Author
-
Chie, Sawada, Carol, Moreau, Gabriel H J, Robinson, Burkhard, Steuernagel, Luzie U, Wingen, Jitender, Cheema, Ellen, Sizer-Coverdale, David, Lloyd, Claire, Domoney, and Noel, Ellis
- Subjects
Phenotype ,Genetic Linkage ,Quantitative Trait Loci ,Peas ,Chromosome Mapping - Abstract
Biparental recombinant inbred line (RIL) populations are sets of genetically stable lines and have a simple population structure that facilitates the dissection of the genetics of interesting traits. On the other hand, populations derived from multiparent intercrosses combine both greater diversity and higher numbers of recombination events than RILs. Here, we describe a simple population structure: a three-way recombinant inbred population combination. This structure was easy to produce and was a compromise between biparental and multiparent populations. We show that this structure had advantages when analyzing cultivar crosses, and could achieve a mapping resolution of a few genes.
- Published
- 2021
15. Recombinant inbred lines derived from cultivars of pea for understanding the genetic basis of variation in breeders' traits
- Author
-
Claire Domoney, Jane Thomas, Steve Belcher, Haidee Philpott, Keith Fox, Tracey Rayner, Noel Ellis, Lynda Turner, Carol Moreau, and M. R. Knox
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Genetics ,Candidate gene ,Locus (genetics) ,Plant Science ,Quantitative trait locus ,Biology ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Inbred strain ,Genotype ,Cultivar ,Agronomy and Crop Science ,Legume ,010606 plant biology & botany - Abstract
In order to gain an understanding of the genetic basis of traits of interest to breeders, the pea varieties Brutus, Enigma and Kahuna were selected, based on measures of their phenotypic and genotypic differences, for the construction of recombinant inbred populations. Reciprocal crosses were carried out for each of the three pairs, and over 200 F2 seeds from each cross advanced to F13. Bulked F7 seeds were used to generate F8–F11 bulks, which were grown in triplicated plots within randomized field trials and used to collect phenotypic data, including seed weight and yield traits, over a number of growing seasons. Genetic maps were constructed from the F6 generation to support the analysis of qualitative and quantitative traits and have led to the identification of four major genetic loci involved in seed weight determination and at least one major locus responsible for variation in yield. Three of the seed weight loci, at least one of which has not been described previously, were associated with the marrowfat seed phenotype. For some of the loci identified, candidate genes have been identified. The F13 single seed descent lines are available as a germplasm resource for the legume and pulse crop communities.
- Published
- 2018
16. Retrotransposons and the Evolution of Genome Size in
- Author
-
T H Noel, Ellis and Alexander V, Vershinin
- Abstract
Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of pea LTR-containing retrotransposons have the frequency and age distributions consistent with the behavior of neutral alleles and whether these parameters can explain the rate of change of genome size in legumes. (2) We used the recently assembled v1a pea genome sequence to obtain data on LTR-LTR divergence from which their age can be estimated. We coupled these data to prior information on the distribution of insertion site alleles. (3) We found that the age and frequency distribution data are consistent with the neutral theory. (4) We concluded that demographic processes are the underlying cause of genome size variation in legumes.
- Published
- 2020
17. A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume
- Author
-
Jonathan D. Moore, Shiv Kumar, Janet Higgins, Anne Edwards, Cathie Martin, Anne Webb, Martin Trick, Jane Thomas, Darren Waite, Rosa Caiazzo, Abhimanyu Sarkar, Darren Heavens, Trevor L. Wang, Gemy Kaithakottil, David Swarbreck, Isaac Njaci, Noel Ellis, Sagadevan G. Mundree, Jitender Cheema, Matthew Loose, Christopher I. Moore, Peter M. F. Emmrich, and Levi Yant
- Subjects
0106 biological sciences ,Genetics ,0303 health sciences ,Contig ,biology ,food and beverages ,biology.organism_classification ,01 natural sciences ,Genome ,03 medical and health sciences ,Sativum ,Lathyrus ,Nanopore sequencing ,Ploidy ,Genome size ,Gene ,030304 developmental biology ,010606 plant biology & botany - Abstract
We have sequenced the genome of grass pea (Lathyrus sativus), a resilient diploid (2n=14) legume closely related to pea (Pisum sativum). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp. We generated two assemblies of this genome, i) EIv1 using Illumina PCR-free paired-end sequencing and assembly followed by long-mate-pair scaffolding and ii) Rbp using Oxford Nanopore Technologies long-read sequencing and assembly followed by polishing with Illumina paired-end data. EIv1 has a total length of 8.12 Gbp (including 1.9 billion Ns) and scaffold N50 59,7 kbp. Annotation has identified 33,819 high confidence genes in the assembly. Rbp has a total length of 6.2 Gbp (with no Ns) and a contig N50 of 155.7 kbp. Gene space assessment using the eukaryote BUSCO database showed completeness scores of 82.8 % and 89.8%, respectively.
- Published
- 2020
18. Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement
- Author
-
Jens Berger, Lenka Zablatzká, Petr Smýkal, Robert Redden, T. H. Noel Ellis, Edward Marques, Shiv Kumar, Eric von Wettberg, Clarice J. Coyne, and Jan Brus
- Subjects
Genetic diversity ,Resistance (ecology) ,fungi ,introgression ,food and beverages ,Climate change ,Introgression ,genetic diversity ,Plant Science ,lcsh:Plant culture ,Biology ,lentil ,crop wild relatives ,Crop ,climate change ,Agronomy ,chickpea ,lcsh:SB1-1110 ,Food Science - Abstract
Legumes represent the second most important family of crop plants after grasses, accounting for approximately 27% of the world's crop production. Past domestication processes resulted in a high degree of relatedness between modern varieties of crops, leading to a narrower genetic base of cultivated germplasm prone to pests and diseases. Crop wild relatives (CWRs) harbor genetic diversity tested by natural selection in a range of environments. To fully understand and exploit local adaptation in CWR, studies in geographical centers of origin combining ecology, physiology, and genetics are needed. With the advent of modern genomics and computation, combined with systematic phenotyping, it is feasible to revisit wild accessions and landraces and prioritize their use for breeding, providing sources of disease resistances; tolerances of drought, heat, frost, and salinity abiotic stresses; nutrient densities across major and minor elements; and food quality traits. Establishment of hybrid populations with CWRs gives breeders a considerable benefit of a prebreeding tool for identifying and harnessing wild alleles and provides extremely valuable long‐term resources. There is a need of further collecting and both ex situ and in situ conservation of CWR diversity of these taxa in the face of habitat loss and degradation and climate change. In this review, we focus on three legume crops domesticated in the Fertile Crescent, pea, chickpea, and lentil, and summarize the current state and potential of their respective CWR taxa for crop improvement.
- Published
- 2020
19. Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.)
- Author
-
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
- Subjects
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.
- Published
- 2019
20. Diversity of Pod Shape in Pisum
- Author
-
Julie M.I. Hofer, Thomas Henry Noel Ellis, Eleni Vikeli, Luzie U. Wingen, Noam Chayut, Paola Higuera-Poveda, and Mike Ambrose
- Subjects
0106 biological sciences ,Germplasm ,QH301-705.5 ,Range (biology) ,pea ,Population structure ,Morphological variation ,Reproductive strategy ,Width ratio ,01 natural sciences ,Pisum ,03 medical and health sciences ,cv Afghanistan ,Pisum sativum ,Biology (General) ,030304 developmental biology ,Nature and Landscape Conservation ,0303 health sciences ,Ecology ,biology ,Ecological Modeling ,food and beverages ,germplasm ,Pisum fulvum ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,negative regulators of growth ,Horticulture ,Point of delivery ,pod ,010606 plant biology & botany - Abstract
The seed-containing pod is the defining structure of plants in the legume family, yet pods exhibit a wide range of morphological variation. Within a species pod characters are likely to be correlated with reproductive strategy, and within cultivated forms will correspond to aspects of yield determination and/or end use. Here variation in pod size, described as pod length: pod width ratio, has been analyzed in pea germplasm represented by 597 accessions. This pod size variation is discussed with respect to population structure and to known classical pod morphology mutants. Variability of the pod length: width ratio can be explained by allelic variation at two genetic loci that may correspond to organ-specific negative regulators of growth.
- Published
- 2021
21. The Full Breadth of Mendel’s Genetics
- Author
-
Peter J. van Dijk and T. H. Noel Ellis
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,constant hybrids ,Hieracium ,Centennial ,Gregor Mendel ,History, 19th Century ,Biology ,biology.organism_classification ,01 natural sciences ,Correspondence as Topic ,03 medical and health sciences ,030104 developmental biology ,Apomixis ,apomixis ,010606 plant biology & botany ,Perspectives - Abstract
Gregor Mendel’s “Experiments on Plant Hybrids” (1865/1866), published 150 years ago, is without doubt one of the most brilliant works in biology. Curiously, Mendel’s later studies on Hieracium (hawkweed) are usually seen as a frustrating failure, because it is assumed that they were intended to confirm the segregation ratios he found in Pisum. Had this been his intention, such a confirmation would have failed, since, unknown to Mendel, Hieracium species mostly reproduce by means of clonal seeds (apomixis). Here we show that this assumption arises from a misunderstanding that could be explained by a missing page in Mendel’s first letter to Carl Nägeli. Mendel’s writings clearly indicate his interest in “constant hybrids,” hybrids which do not segregate, and which were “essentially different” from “variable hybrids” such as in Pisum. After the Pisum studies, Mendel worked mainly on Hieracium for 7 years where he found constant hybrids and some great surprises. He also continued to explore variable hybrids; both variable and constant hybrids were of interest to Mendel with respect to inheritance and to species evolution. Mendel considered that their similarities and differences might provide deep insights and that their differing behaviors were “individual manifestations of a higher more fundamental law.”
- Published
- 2016
22. Evidence for the presence of hairpin chloroplast DNA molecules in barley cultivars
- Author
-
Collin, Sylvie and Noel Ellis, T. H.
- Published
- 1991
- Full Text
- View/download PDF
23. Retrotransposons and the Evolution of Genome Size in Pisum
- Author
-
Alexander V. Vershinin and T. H. Noel Ellis
- Subjects
0106 biological sciences ,0301 basic medicine ,legumes ,pea ,Biomedical Engineering ,Bioengineering ,Retrotransposon ,Biology ,01 natural sciences ,Applied Microbiology and Biotechnology ,Biochemistry ,Genome ,03 medical and health sciences ,Genetic drift ,Plant population genetics ,Allele ,Genome size ,Whole genome sequencing ,fungi ,food and beverages ,retrotransposons ,030104 developmental biology ,Evolutionary biology ,genome size ,Neutral theory of molecular evolution ,010606 plant biology & botany ,Biotechnology - Abstract
Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of pea LTR-containing retrotransposons have the frequency and age distributions consistent with the behavior of neutral alleles and whether these parameters can explain the rate of change of genome size in legumes. (2) We used the recently assembled v1a pea genome sequence to obtain data on LTR-LTR divergence from which their age can be estimated. We coupled these data to prior information on the distribution of insertion site alleles. (3) We found that the age and frequency distribution data are consistent with the neutral theory. (4) We concluded that demographic processes are the underlying cause of genome size variation in legumes.
- Published
- 2020
24. Methylated and undermethylated rDNA repeats are interspersed at random in two higher plant species
- Author
-
Noel Ellis, T. H., Delseny, Michel, Lee, David, and Burcham, Kenneth W. G.
- Published
- 1990
- Full Text
- View/download PDF
25. NMR Metabolomics Defining Genetic Variation in Pea Seed Metabolites
- Author
-
Adrian J. Charlton, Michael Dickinson, Giampaolo Venditti, Noel Ellis, Zoltán Szabó, James Donarski, Jitender Cheema, Claire Domoney, György B. Kiss, Chie Hattori, and Péter Kaló
- Subjects
0106 biological sciences ,0301 basic medicine ,Metabolite ,pea ,metabolite ,Genomics ,Plant Science ,Biology ,lcsh:Plant culture ,01 natural sciences ,Genetic analysis ,03 medical and health sciences ,chemistry.chemical_compound ,Metabolomics ,Gene mapping ,Genetic variation ,Metabolome ,genetic map ,lcsh:SB1-1110 ,Original Research ,2. Zero hunger ,Genetics ,food and beverages ,nuclear magnetic resonance ,030104 developmental biology ,chemistry ,Genetic marker ,genetic variation ,seed ,010606 plant biology & botany - Abstract
Nuclear magnetic resonance (NMR) spectroscopy profiling was used to provide an unbiased assessment of changes to the metabolite composition of seeds and to define genetic variation for a range of pea seed metabolites. Mature seeds from recombinant inbred lines, derived from three mapping populations for which there is substantial genetic marker linkage information, were grown in two environments/years and analyzed by non-targeted NMR. Adaptive binning of the NMR metabolite data, followed by analysis of quantitative variation among lines for individual bins, identified the main genomic regions determining this metabolic variability and the variability for selected compounds was investigated. Analysis by t-tests identified a set of bins with highly significant associations to genetic map regions, based on probability (p) values that were appreciably lower than those determined for randomized data. The correlation between bins showing high mean absolute deviation and those showing low p-values for marker association provided an indication of the extent to which the genetics of bin variation might be explained by one or a few loci. Variation in compounds related to aromatic amino acids, branched-chain amino acids, sucrose-derived metabolites, secondary metabolites and some unidentified compounds was associated with one or more genetic loci. The combined analysis shows that there are multiple loci throughout the genome that together impact on the abundance of many compounds through a network of interactions, where individual loci may affect more than one compound and vice versa. This work therefore provides a framework for the genetic analysis of the seed metabolome, and the use of genetic marker data in the breeding and selection of seeds for specific seed quality traits and compounds that have high commercial value.
- Published
- 2018
- Full Text
- View/download PDF
26. How Mendel's Interest in Inheritance Grew out of Plant Improvement
- Author
-
Peter J. van Dijk, Franz J. Weissing, T. H. Noel Ellis, and Weissing group
- Subjects
0301 basic medicine ,Genetics ,media_common.quotation_subject ,Gregor Mendel ,horticulture ,History, 19th Century ,Biology ,Genealogy ,03 medical and health sciences ,Plant Breeding ,030104 developmental biology ,MENDEL ,MYTH-CONCEPTIONS ,inheritance ,GREGOR ,Plant breeding ,Inheritance ,MENDEL,GREGOR ,media_common ,Plant Diseases ,Perspectives - Abstract
Gregor Mendel’s crossing experiments in pea are the foundation of classical genetics, but since the importance of his 1866 paper was not understood until after long after his notebooks were burned, we know little..., Despite the fact that Gregor Mendel is generally respected as the founder of genetics, little is known about the origin of and motivation for his revolutionary work. No primary sources are known that discuss his work during the period of his pea crossing experiments. Here, we report on two previously unknown interconnected local newspaper articles about Mendel’s work that predate his famous Pisum lectures by 4 years. These articles describe Mendel as a plant breeder and a horticulturist. We argue that Mendel’s initial interests concerned crop improvement, but that with time he became more interested in fundamental questions about inheritance, fertilization, and natural hybridization.
- Published
- 2018
27. Identification of Stipules reduced, a leaf morphology gene in pea (Pisum sativum)
- Author
-
Matthew J. Hegarty, Andrey A. Sinjushin, Martin T. Swain, Cristina Ferrándiz, Julie Margareth Hofer, Kirsten P. Skøt, Vicente Balanzà, Mike Ambrose, Carol Moreau, Morgane P Eléouët, Tina Blackmore, and T. H. Noel Ellis
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Mutant ,pea ,Plant Science ,Biology ,RAD sequencing ,Genes, Plant ,01 natural sciences ,Stipule ,DNA sequencing ,Plant Epidermis ,Pisum ,stipule ,03 medical and health sciences ,Sativum ,Gene Expression Regulation, Plant ,Medicago ,Tendril ,Fast Neutron ,mutant ,Gene ,Genetic Association Studies ,Phylogeny ,Pisum sativum ,Plant Proteins ,Genetics ,leaf ,Peas ,food and beverages ,biology.organism_classification ,Plant Leaves ,Restriction site ,Phenotype ,030104 developmental biology ,C2H2 zinc finger ,Mutation ,010606 plant biology & botany - Abstract
Pea (Pisum sativum) is one of relatively few genetically amenable plant species with compound leaves. Pea leaves have a variety of specialized organs: leaflets, tendrils, pulvini and stipules, which enable the identification of mutations that transform or affect distinct parts of the leaf. Characterization of these mutations offers insights into the development and evolution of novel leaf traits. The previously characterized morphological gene Cochleata, conferring stipule identity, was known to interact with Stipules reduced (St), which conditions stipule size in pea, but the St gene remained unknown. Here we analysed Fast Neutron irradiated pea mutants by restriction site associated DNA sequencing. We identified St as a gene encoding a C2H2 zinc finger transcription factor that is regulated by Cochleata. St regulates both cell division and cell expansion in the stipule. Our approach shows how systematic genome-wide screens can be used successfully for the analysis of traits in species for which whole genome sequences are not available.
- Published
- 2018
28. Translational Genomics in Agriculture: Some Examples in Grain Legumes
- Author
-
Abhishek Bohra, Lekha T. Pazhamala, Himabindu Kudapa, Asnake Fikre, Pasupuleti Janila, Noel Ellis, Paul Kimurto, Mahendar Thudi, Rajeev K. Varshney, Pooran M. Gaur, and Annapurna Chitikineni
- Subjects
Oryza sativa ,Agroforestry ,business.industry ,Genomics ,Plant Science ,Biology ,Private sector ,Genome ,Agronomy ,Agriculture ,Translational genomics ,Legume crops ,business ,Hectare - Abstract
Recent advances in genomics and associated disciplines like bioinformatics have made it possible to develop genomic resources, such as large-scale sequence data for any crop species. While these datasets have been proven very useful for the understanding of genome architecture and dynamics as well as facilitating the discovery of genes, an obligation for, and challenge to the scientific community is to translate genome information to develop products, i.e. superior lines for trait(s) of interest. We call this approach, “translational genomics in agriculture” (TGA). TGA is currently in practice for cereal crops, such as maize (Zea mays) and rice (Oryza sativa), mainly in developed countries and by the private sector; progress has been slow for legume crops. Grown globally on 62.8 million ha with a production of 53.2 million tons and a value of nearly 24.2 billion dollars, the majority of these legumes have low crop productivity (
- Published
- 2014
29. Genetic Variation Controlling Wrinkled Seed Phenotypes in Pisum: How Lucky Was Mendel?
- Author
-
Mike Ambrose, Claire Domoney, Peter Isaac, Tracey Rayner, Noel Ellis, and Carol Moreau
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Glucose-1-Phosphate Adenylyltransferase ,01 natural sciences ,lcsh:Chemistry ,Genotype ,myoinositol ,lcsh:QH301-705.5 ,Spectroscopy ,seed coat (testa) metabolites ,Plant Proteins ,2. Zero hunger ,Genetics ,biology ,food and beverages ,General Medicine ,Phenotype ,Computer Science Applications ,Seeds ,seed phenotype ,Locus (genetics) ,pea germplasm ,Genes, Plant ,Catalysis ,Article ,Pisum ,Inorganic Chemistry ,wrinkled seeds ,03 medical and health sciences ,genetic markers ,r and rb mutations ,Genetic variation ,Physical and Theoretical Chemistry ,Molecular Biology ,Gene ,Alleles ,Organic Chemistry ,Peas ,Genetic Variation ,biology.organism_classification ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Genetic marker ,Genetic Loci ,Mutation ,010606 plant biology & botany - Abstract
One of the traits studied by Mendel in pea (Pisum sativum L.) was the wrinkled-seeded phenotype, and the molecular basis for a mutation underlying this phenotype was discovered in the 1990s. Although the starch-branching enzyme gene mutation identified at the genetic locus r is most likely to be that in seeds available to Mendel in the mid-1800s, it has remained an open question as to whether or not additional natural mutations in this gene exist within Pisum germplasm collections. Here, we explore this question and show that all but two wrinkled-seeded variants in one such collection correspond to either the mutant allele described previously for the r locus or a mutation at a second genetic locus, rb, affecting the gene encoding the large subunit of Adenosine diphosphoglucose (ADP-glucose) pyrophosphorylase; the molecular basis for the rb mutation is described here. The genetic basis for the phenotype of one (JI 2110) of the two lines which are neither r nor rb has been studied in crosses with a round-seeded variant (JI 281); for which extensive genetic marker data were expected. In marked contrast to the trait studied by Mendel and the rb phenotype; the data suggest that the wrinkled-seeded phenotype in JI 2110 is maternally determined, controlled by two genetic loci, and the extent to which it is manifested is very sensitive to the environment. Metabolite analysis of the cotyledons of JI 2110 revealed a profile for sucrose and sucrose-derived compounds that was more similar to that of wild-type round-seeded, than that of wrinkled-seeded r, pea lines. However, the metabolite profile of the seed coat (testa) of JI 2110 was distinct from that of other round-seeded genotypes tested which, together with analysis of recombinant inbred progeny lines, suggests an explanation for the seed phenotype.
- Published
- 2017
30. Developmental specialisations in the legume family
- Author
-
T. H. Noel Ellis and Julie M.I. Hofer
- Subjects
Models, Genetic ,Phylogenetic tree ,Ecology ,Gene Expression Regulation, Developmental ,Fabaceae ,Flowers ,Plant Science ,Biology ,Genes, Plant ,Models, Biological ,Plant Roots ,Plant Leaves ,Plant development ,Data sequences ,Taxon ,Developmental genetics ,Gene Expression Regulation, Plant ,Phylogenetic Pattern - Abstract
The legume family is astonishingly diverse; inventiveness in the form of novel organs, modified organs and additional meristems, is rife. Evolutionary changes can be inferred from the phylogenetic pattern of this diversity, but a full understanding of the origin of these 'hopeful monsters' of meristematic potential requires clear phylogenetic reconstructions and extensive, species-rich, sequence data. The task is large, but rapid progress is being made in both these areas. Here we review specialisations that have been characterised in a subset of intensively studied papilionoid legume taxa at the vanguard of developmental genetic studies.
- Published
- 2014
31. NODULE ROOT and COCHLEATA Maintain Nodule Development and Are Legume Orthologs of Arabidopsis BLADE-ON-PETIOLE Genes
- Author
-
Julie M.I. Hofer, Ghada Abu el Heba, Jiangqi Wen, Million Tadege, Mike Ambrose, Vladimir A. Zhukov, Kirankumar S. Mysore, Samuel Mondy, Igor A. Tikhonovich, Pascal Ratet, T. H. Noel Ellis, Alexei Y. Borisov, Jean-Malo Couzigou, Viviane Cosson, Joanna Putterill, Institut des sciences du végétal (ISV), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0106 biological sciences ,Recombinant Fusion Proteins ,[SDV]Life Sciences [q-bio] ,Molecular Sequence Data ,Arabidopsis ,Flowers ,Plant Science ,Plant Roots ,01 natural sciences ,Petiole (botany) ,Rhizobia ,Pisum ,03 medical and health sciences ,Symbiosis ,Gene Expression Regulation, Plant ,Nitrogen Fixation ,Medicago truncatula ,Botany ,Arabidopsis thaliana ,Phylogeny ,Research Articles ,ComputingMilieux_MISCELLANEOUS ,Plant Proteins ,030304 developmental biology ,0303 health sciences ,Sinorhizobium meliloti ,Base Sequence ,biology ,fungi ,Peas ,food and beverages ,Sequence Analysis, DNA ,Cell Biology ,biology.organism_classification ,Protein Structure, Tertiary ,Plant Leaves ,Phenotype ,Mutation ,Root Nodules, Plant ,010606 plant biology & botany - Abstract
During their symbiotic interaction with rhizobia, legume plants develop symbiosis-specific organs on their roots, called nodules, that house nitrogen-fixing bacteria. The molecular mechanisms governing the identity and maintenance of these organs are unknown. Using Medicago truncatula nodule root (noot) mutants and pea (Pisum sativum) cochleata (coch) mutants, which are characterized by the abnormal development of roots from the nodule, we identified the NOOT and COCH genes as being necessary for the robust maintenance of nodule identity throughout the nodule developmental program. NOOT and COCH are Arabidopsis thaliana BLADE-ON-PETIOLE orthologs, and we have shown that their functions in leaf and flower development are conserved in M. truncatula and pea. The identification of these two genes defines a clade in the BTB/POZ-ankyrin domain proteins that shares conserved functions in eudicot organ development and suggests that NOOT and COCH were recruited to repress root identity in the legume symbiotic organ.
- Published
- 2012
32. Conserved genetic determinant of motor organ identity in Medicago truncatula and related legumes
- Author
-
Carol Moreau, Rujin Chen, Julie M.I. Hofer, Masayoshi Kawaguchi, Jianghua Chen, Noel Ellis, and Yu Liu
- Subjects
0106 biological sciences ,DNA, Complementary ,Movement ,Molecular Sequence Data ,Lotus japonicus ,Mutant ,Genes, Plant ,Real-Time Polymerase Chain Reaction ,01 natural sciences ,Pisum ,03 medical and health sciences ,Species Specificity ,Commentaries ,Medicago truncatula ,Pulvinus ,Cloning, Molecular ,Gene ,In Situ Hybridization ,030304 developmental biology ,Cloning ,Genetics ,0303 health sciences ,Multidisciplinary ,Base Sequence ,biology ,fungi ,Chromosome Mapping ,food and beverages ,Sequence Analysis, DNA ,biology.organism_classification ,Microscopy, Electron, Scanning ,Ectopic expression ,Transcription Factors ,010606 plant biology & botany - Abstract
Plants exhibit various kinds of movements that have fascinated scientists and the public for centuries. Physiological studies in plants with the so-called motor organ or pulvinus suggest that cells at opposite sides of the pulvinus mediate leaf or leaflet movements by swelling and shrinking. How motor organ identity is determined is unknown. Using a genetic approach, we isolated a mutant designated elongated petiolule1 ( elp1 ) from Medicago truncatula that fails to fold its leaflets in the dark due to loss of motor organs. Map-based cloning indicated that ELP1 encodes a putative plant-specific LOB domain transcription factor. RNA in situ analysis revealed that ELP1 is expressed in primordial cells that give rise to the motor organ. Ectopic expression of ELP1 resulted in dwarf plants with petioles and rachises reduced in length, and the epidermal cells gained characteristics of motor organ epidermal cells. By identifying ELP1 orthologs from other legume species, namely pea ( Pisum sativum ) and Lotus japonicus , we show that this motor organ identity is regulated by a conserved molecular mechanism.
- Published
- 2012
33. The b Gene of Pea Encodes a Defective Flavonoid 3′,5′-Hydroxylase, and Confers Pink Flower Color
- Author
-
Julie M.I. Hofer, Lynda Turner, Lionel Hill, Noel Ellis, Carol Moreau, and Mike Ambrose
- Subjects
DNA, Plant ,Physiology ,Molecular Sequence Data ,Mutant ,Population ,Color ,Flowers ,Plant Science ,Genes, Plant ,Hydroxylation ,Pisum ,Anthocyanins ,chemistry.chemical_compound ,Cytochrome P-450 Enzyme System ,Gene mapping ,Petunidin ,Genetics, Genomics, and Molecular Evolution ,Genetics ,Amino Acid Sequence ,Allele ,education ,Gene ,Alleles ,Crosses, Genetic ,Phylogeny ,Plant Proteins ,education.field_of_study ,biology ,Pigmentation ,fungi ,Peas ,food and beverages ,biology.organism_classification ,Phenotype ,Biochemistry ,chemistry ,Delphinidin ,Gene Deletion - Abstract
The inheritance of flower color in pea (Pisum sativum) has been studied for more than a century, but many of the genes corresponding to these classical loci remain unidentified. Anthocyanins are the main flower pigments in pea. These are generated via the flavonoid biosynthetic pathway, which has been studied in detail and is well conserved among higher plants. A previous proposal that the Clariroseus (B) gene of pea controls hydroxylation at the 5′ position of the B ring of flavonoid precursors of the anthocyanins suggested to us that the gene encoding flavonoid 3′,5′-hydroxylase (F3′5′H), the enzyme that hydroxylates the 5′ position of the B ring, was a good candidate for B. In order to test this hypothesis, we examined mutants generated by fast neutron bombardment. We found allelic pink-flowered b mutant lines that carried a variety of lesions in an F3′5′H gene, including complete gene deletions. The b mutants lacked glycosylated delphinidin and petunidin, the major pigments present in the progenitor purple-flowered wild-type pea. These results, combined with the finding that the F3′5′H gene cosegregates with b in a genetic mapping population, strongly support our hypothesis that the B gene of pea corresponds to a F3′5′H gene. The molecular characterization of genes involved in pigmentation in pea provides valuable anchor markers for comparative legume genomics and will help to identify differences in anthocyanin biosynthesis that lead to variation in pigmentation among legume species.
- Published
- 2012
34. Mendel, 150 years on
- Author
-
Gail M. Timmerman-Vaughan, T. H. Noel Ellis, Julie M.I. Hofer, Clarice J. Coyne, and Roger P. Hellens
- Subjects
Genetics ,Transposable element ,biology ,Genetic Linkage ,Pigmentation ,Alternative splicing ,food and beverages ,History, 19th Century ,Flowers ,Plant Science ,Quantitative trait locus ,History, 18th Century ,biology.organism_classification ,Pisum ,Quantitative Trait, Heritable ,Sativum ,Genes ,Genetic linkage ,Missense mutation ,Gene - Abstract
Mendel's paper 'Versuche über Pflanzen-Hybriden' is the best known in a series of studies published in the late 18th and 19th centuries that built our understanding of the mechanism of inheritance. Mendel investigated the segregation of seven gene characters of pea (Pisum sativum), of which four have been identified. Here, we review what is known about the molecular nature of these genes, which encode enzymes (R and Le), a biochemical regulator (I) and a transcription factor (A). The mutations are: a transposon insertion (r), an amino acid insertion (i), a splice variant (a) and a missense mutation (le-1). The nature of the three remaining uncharacterized characters (green versus yellow pods, inflated versus constricted pods, and axial versus terminal flowers) is discussed.
- Published
- 2011
35. Natural Variation in Host-Specific Nodulation of Pea Is Associated with a Haplotype of the SYM37 LysM-Type Receptor-Like Kinase
- Author
-
Ronghui Li, Bridget V. Hogg, Gehong Wei, J. Allan Downie, Anne Edwards, T. H. Noel Ellis, and M. R. Knox
- Subjects
Physiology ,Molecular Sequence Data ,Quantitative Trait Loci ,Mutant ,Locus (genetics) ,Quantitative trait locus ,Biology ,Genes, Plant ,medicine.disease_cause ,Rhizobium leguminosarum ,Gene mapping ,Nitrogen Fixation ,Genetic variation ,medicine ,Amino Acid Sequence ,Gene ,Genetics ,Sequence Homology, Amino Acid ,Haplotype ,Peas ,Genetic Variation ,Receptor Protein-Tyrosine Kinases ,food and beverages ,General Medicine ,Haplotypes ,Agronomy and Crop Science - Abstract
Rhizobium leguminosarum bv. viciae, which nodulates pea and vetch, makes a mixture of secreted nodulation signals (Nod factors) carrying either a C18:4 or a C18:1 N-linked acyl chain. Mutation of nodE blocks the formation of the C18:4 acyl chain, and nodE mutants, which produce only C18:1-containing Nod factors, are less efficient at nodulating pea. However, there is significant natural variation in the levels of nodulation of different pea cultivars by a nodE mutant of R. leguminosarum bv. viciae. Using recombinant inbred lines from two pea cultivars, one which nodulated relatively well and one very poorly by the nodE mutant, we mapped the nodE-dependent nodulation phenotype to a locus on pea linkage group I. This was close to Sym37 and PsK1, predicted to encode LysM-domain Nod-factor receptor-like proteins; the Sym2 locus that confers Nod-factor-specific nodulation is also in this region. We confirmed the map location using an introgression line carrying this region. Our data indicate that the nodE-dependent nodulation is not determined by the Sym2 locus. We identified several pea lines that are nodulated very poorly by the R. leguminosarum bv. viciae nodE mutant, sequenced the DNA of the predicted LysM-receptor domains of Sym37 and PsK1, and compared the sequences with those derived from pea cultivars that were relatively well nodulated by the nodE mutant. This revealed that one haplotype (encoding six conserved polymorphisms) of Sym37 is associated with very poor nodulation by the nodE mutant. There was no such correlation with polymorphisms at the PsK1 locus. We conclude that the natural variation in nodE-dependent nodulation in pea is most probably determined by the Sym37 haplotype.
- Published
- 2011
36. Phylogeny, phylogeography and genetic diversity of the Pisum genus
- Author
-
Petr Smýkal, Rebecca Ford, Oleg E. Kosterin, Robert Redden, Gregory Kenicer, Jukka Corander, Clarice J. Coyne, Mike Ambrose, Andrew J. Flavell, Noel Ellis, and Nigel Maxted
- Subjects
Germplasm ,Fabeae ,Genetic diversity ,biology ,Introgression ,Plant Science ,biology.organism_classification ,Vicia ,Botany ,Genetics ,Lathyrus ,Vavilovia ,Domestication ,Agronomy and Crop Science - Abstract
The tribeFabeae(formerlyVicieae) contains some of humanity's most important grain legume crops, namelyLathyrus(grass pea/sweet pea/chickling vetches; about 160 species);Lens(lentils; 4 species);Pisum(peas; 3 species);Vicia(vetches; about 140 species); and the monotypic genusVavilovia.Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positionedPisumgenetically betweenViciaandLathyrusand shows it to be closely allied toVavilovia.A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429Pisumaccessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishingPisum fulvum,P. elatiusandP. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining globalPisumgermplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.
- Published
- 2010
37. Do Transcription Factors Play Special Roles in Adaptive Variation?
- Author
-
Cathie Martin, Fred Rook, and Noel Ellis
- Subjects
Genetics ,Physiology ,RNA ,lac operon ,Plant Science ,Biology ,Start point ,Evolutionary biology ,Gene expression ,bacteria ,Adaptation ,Control (linguistics) ,Gene ,Transcription factor - Abstract
Ever since the work by Jacob and Monod on the Lac operon, scientists have appreciated that the control of gene expression is one of the most important points of regulation in biology. Although many other layers of regulation exist, the possibility of control at the start point of production of RNA
- Published
- 2010
38. THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps
- Author
-
Jo Dicks, Jitender Cheema, and T. H. Noel Ellis
- Subjects
Genetics ,Internet ,Web server ,Genetic Linkage ,business.industry ,Visual comparison ,Chromosome Mapping ,Computational Biology ,Articles ,Thread (computing) ,Biology ,computer.software_genre ,Computer graphics ,Data set ,Software ,Computer Graphics ,The Internet ,Data mining ,business ,computer ,Studio - Abstract
The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http:// cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets.
- Published
- 2010
39. Pea
- Author
-
Thomas D. Warkentin, Petr Smýkal, Clarice J. Coyne, Norman Weeden, Claire Domoney, Deng-Jin Bing, Antonio Leonforte, Zong Xuxiao, Girish Prasad Dixit, Lech Boros, Kevin E. McPhee, Rebecca J. McGee, Judith Burstin, and Thomas Henry Noel Ellis
- Published
- 2015
40. Genetic and genomic analysis of legume flowers and seeds
- Author
-
Karine Gallardo, Christian Firnhaber, Gérard Duc, Claire Domoney, Christophe Salon, Helge Küster, Franciso Madueño, Richard D. Thompson, Joachim Kopka, Klaus F. X. Mayer, Julie M.I. Hofer, Nathalie G. Munier-Jolain, Michael K. Udvardi, T. H. Noel Ellis, Cristina Ferrándiz, John Innes Centre, 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, Universitat Politècnica de València (UPV), Universität Bielefeld = Bielefeld University, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, and German Research Center for Environmental Health - Helmholtz Center München (GmbH)
- Subjects
0106 biological sciences ,2. Zero hunger ,0303 health sciences ,business.industry ,Genomics ,Plant Science ,15. Life on land ,Biology ,01 natural sciences ,GENOMIQUE ,Biotechnology ,03 medical and health sciences ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,GENETIQUE VEGETALE ,DNA microarray ,business ,Legume ,030304 developmental biology ,010606 plant biology & botany - Abstract
International audience; New tools, such as ordered mutant libraries, microarrays and sequence based comparative maps, are available for genetic and genomic studies of legumes that are being used to shed light on seed production, the objective of most arable farming. The new information and understanding brought by these tools are revealing the biological processes that underpin and impact on seed production.
- Published
- 2006
41. Conservation of Arabidopsis Flowering Genes in Model Legumes
- Author
-
Noel Ellis, Fabrice Foucher, Valérie Hecht, Richard C. Macknight, José Pío Beltrán, Catherine Rameau, Cristina Santamaría Navarro, Cristina Ferrándiz, Julie Morin, Megan E. Vardy, James L. Weller, School of Plant Science, University of Tasmania [Hobart, Australia] (UTAS), Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), Universitat Politècnica de València (UPV), Department of Biochemistry, Hôpital Lapeyronie, Department of Crop Genetics, and John Innes Centre [Norwich]
- Subjects
0106 biological sciences ,Physiology ,Lotus ,Lotus japonicus ,Locus (genetics) ,Plant Science ,01 natural sciences ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,03 medical and health sciences ,Arabidopsis ,Flowering Locus C ,Botany ,Genetics ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,LOTUS JAPONICUS ,2. Zero hunger ,0303 health sciences ,Expressed sequence tag ,Medicago ,biology ,fungi ,ARABIDOPSIS THALIANA ,food and beverages ,BASE DE DONNEES ,biology.organism_classification ,Medicago truncatula ,PISUM SATIVUM ,010606 plant biology & botany - Abstract
The model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have provided a wealth of information about genes and genetic pathways controlling the flowering process, but little is known about the corresponding pathways in legumes. The garden pea (Pisum sativum) has been used for several decades as a model system for physiological genetics of flowering, but the lack of molecular information about pea flowering genes has prevented direct comparison with other systems. To address this problem, we have searched expressed sequence tag and genome sequence databases to identify flowering-gene-related sequences from Medicago truncatula, soybean (Glycine max), and Lotus japonicus, and isolated corresponding sequences from pea by degenerate-primer polymerase chain reaction and library screening. We found that the majority of Arabidopsis flowering genes are represented in pea and in legume sequence databases, although several gene families, including the MADS-box, CONSTANS, and FLOWERING LOCUS T/TERMINAL FLOWER1 families, appear to have undergone differential expansion, and several important Arabidopsis genes, including FRIGIDA and members of the FLOWERING LOCUS C clade, are conspicuously absent. In several cases, pea and Medicago orthologs are shown to map to conserved map positions, emphasizing the closely syntenic relationship between these two species. These results demonstrate the potential benefit of parallel model systems for an understanding of flowering phenology in crop and model legume species.
- Published
- 2005
42. Identification of markers tightly linked to sbm recessive genes for resistance to Pea seed-borne mosaic virus
- Author
-
Andrew J. Maule, Carole L. Thomas, S. Eyers, Z. Gao, and Noel Ellis
- Subjects
Genetic Markers ,DNA, Complementary ,food.ingredient ,Genetic Linkage ,Population ,food ,Mosaic Viruses ,Genetics ,Eukaryotic Initiation Factors ,Watermelon mosaic virus ,education ,Gene ,Crosses, Genetic ,DNA Primers ,Plant Diseases ,education.field_of_study ,biology ,Mosaic virus ,Potyviridae ,Peas ,Potyvirus ,Chromosome Mapping ,food and beverages ,Agriculture ,General Medicine ,Bean yellow mosaic virus ,biology.organism_classification ,Virology ,Blotting, Southern ,Phenotype ,Pea seed-borne mosaic virus ,Agronomy and Crop Science ,Polymorphism, Restriction Fragment Length ,Biotechnology - Abstract
Two virus resistance loci on linkage groups II and VI have provided the only sources of natural resistance against Pea seed-borne mosaic virus (PSbMV, Potyviridae) in the important crop plant Pisum sativum L. A combination of parallel approaches was used to collate linked markers, particularly for sbm-1 resistance on linkage group VI. We have identified sequences derived from the genes for the eukaryotic translation initiation factors eIF4E and eIF(iso)4E as being very tightly linked to the resistance gene clusters on linkage groups VI and II, respectively. In particular, no recombinants between sbm-1 and eIF4E were found amongst 500 individuals of an F2 cross between the BC4 resistant line (JI1405) and its recurrent susceptible parent 'Scout'. In a different mapping population, the gene eIF(iso)4E was also shown to be linked to sbm-2 on linkage group II. A parallel cDNA-AFLP comparison of pairs of resistant and susceptible lines also identified an expressed tag marker just 0.7 cM from sbm-1. eIF4E and eIF(iso)4E have been associated with resistance to related viruses in other hosts. This correlation strengthens the use of our markers as valuable tools to assist in breeding multiple virus resistances into peas, and identifies potential targets for resistance gene identification in pea.
- Published
- 2004
43. NMR profiling of transgenic peas
- Author
-
Adrian J. Charlton, Phil Mullineaux, Stephen Holmes, Sarah Oehlschlager, Samantha Bean, James Chisholm, Theo R. Allnutt, and Noel Ellis
- Subjects
Genetics ,biology ,Metabolite ,Transgene ,food and beverages ,Plant Science ,Nuclear magnetic resonance spectroscopy ,biology.organism_classification ,Pisum ,Genetically modified organism ,chemistry.chemical_compound ,Sativum ,chemistry ,Botany ,Proton NMR ,Transgenic lines ,Agronomy and Crop Science ,Biotechnology - Abstract
A high throughput proton nuclear magnetic resonance spectroscopy method for the metabolite fingerprinting of plants was applied to genetically modified peas (Pisum sativum) to determine whether biochemical changes, so called 'unintended effects', beyond those intended by incorporation of a transgene, were detectable. Multivariate analysis of 1H NMR (nuclear magnetic resonance) spectra obtained from uniformly grown glasshouse plants revealed differences between the transgenic and control group that exceeded the natural variation of the plants. When a larger data set of six related transgenic lines was analysed, including a null segregant in addition to the wild-type control, multivariate analysis showed that the distribution of metabolites in the transgenics was different from that of the null segregant. However, the profile obtained from the wild-type material was diverse in comparison with both the transgenics and the null segregant, suggesting that the primary cause of the observed differences was that the transformation process selects for a subset of individuals able to undergo the transformation and selection procedures, and that their descendants have a restricted variation in metabolite profile, rather than that the presence of the transgene itself generates these differences.
- Published
- 2004
44. PROLIFERATING INFLORESCENCE MERISTEM, a MADS-Box Gene That Regulates Floral Meristem Identity in Pea
- Author
-
T. H. Noel Ellis, Ian C. Murfet, John Sollinger, Scott A. Taylor, Susan R. Singer, Julie M.I. Hofer, and M. R. Knox
- Subjects
Genetics ,biology ,Physiology ,fungi ,Mutant ,food and beverages ,Plant Science ,Meristem ,biology.organism_classification ,ABC model of flower development ,Antirrhinum majus ,Inflorescence ,hemic and lymphatic diseases ,Arabidopsis ,Gene ,MADS-box - Abstract
SQUAMOSA and APETALA1 are floral meristem identity genes from snapdragon (Antirrhinum majus) and Arabidopsis, respectively. Here, we characterize the floral meristem identity mutation proliferating inflorescence meristem(pim) from pea (Pisum sativum) and show that it corresponds to a defect in the PEAM4 gene, a homolog of SQUAMOSA and APETALA1. ThePEAM4 coding region was deleted in thepim-1 allele, and this deletion cosegregated with thepim-1 mutant phenotype. The pim-2 allele carried a nucleotide substitution at a predicted 5′ splice site that resulted in mis-splicing of pim-2 mRNA. PCR products corresponding to unspliced and exon-skipped mRNA species were observed. The pim-1 and pim-2 mutations delayed floral meristem specification and altered floral morphology significantly but had no observable effect on vegetative development. These floral-specific mutant phenotypes and the restriction ofPIM gene expression to flowers contrast with other known floral meristem genes in pea that additionally affect vegetative development. The identification of PIM provides an opportunity to compare pathways to flowering in species with different inflorescence architectures.
- Published
- 2002
45. Conservation and diversification of gene function in plant development
- Author
-
Julie M.I. Hofer and Noel Ellis
- Subjects
Transcription, Genetic ,Arabidopsis ,Plant Development ,MADS Domain Proteins ,Plant Science ,Biology ,Genome ,Gene Duplication ,Gene duplication ,Genetic variation ,Gene ,Leaf development ,Plant Proteins ,Arabidopsis Proteins ,Ecology ,fungi ,Genetic Variation ,food and beverages ,Plants ,biology.organism_classification ,Plant development ,Evolutionary biology ,Arabidopsis genome ,Flowering plant ,Plant Structures ,human activities ,Genome, Plant - Abstract
The Arabidopsis genome sequence has given us an inventory of the genes needed to specify a flowering plant. Plants are highly diverse in appearance and the mechanisms whereby this diversity has arisen need explanation. A fundamental question is to what extent diversity arises from remodelling of gene function or relocation of gene pathways, rather than from the gain or loss of genes. Similar types of genetic rewiring may be responsible for both intra- and inter-specific differences in developmental processes. Recent advances in the understanding of shoot, flower and leaf development provide insights to this question.
- Published
- 2002
46. [Untitled]
- Author
-
Noel Ellis, Lynda Turner, Tracey Welham, Claire Domoney, and Philippe Mozzanega
- Subjects
Genetics ,Trypsin inhibitor ,food and beverages ,Sequence alignment ,Locus (genetics) ,Plant Science ,General Medicine ,Biology ,genomic DNA ,Proteinase Inhibitor Gene ,Gene expression ,Agronomy and Crop Science ,Gene ,Peptide sequence - Abstract
Genes representative of three gene classes encoding proteinase inhibitor proteins, with distinct spatial expression patterns, were isolated and characterized from Pisum. Under standard plant growth conditions, one class is expressed exclusively in seeds, whereas the other two make minor contributions to seed inhibitor proteins but are also expressed in other organs, predominantly in root endodermal and floral reproductive tissues. Two of the gene classes contain few genes and are genetically linked at the Tri locus, whereas the third class displays complex hybridization patterns to genomic DNA and maps to diverse genetic loci. Expression analysis of this last class suggests that only a small number of these genes are expressed. The quantitative effect of the Tri locus on root and floral inhibitor gene expression was examined in near-isogenic lines of pea. The proteins encoded by the three classes are all members of the same family (Bowman-Birk) of enzyme inhibitors but are distinct in terms of overall sequence, active site sequences and inhibitor function.
- Published
- 2002
47. Germplasm resources in legumes
- Author
-
T. H. Noel Ellis
- Subjects
Germplasm ,business.industry ,Genetics ,Plant Science ,Biology ,business ,Agronomy and Crop Science ,Biotechnology - Abstract
The collected articles in this volume are discussed in their wider context.
- Published
- 2011
48. Genetic Control of Leaf Morphology: A Partial View
- Author
-
Julie M.I. Hofer, T. H. Noel Ellis, and Campbell W. Gourlay
- Subjects
fungi ,Botany ,Mutation (genetic algorithm) ,Mutant ,Shoot ,Morphological variation ,food and beverages ,Morphology (biology) ,Plant Science ,Biology - Abstract
The partial-shoot theory of the leaf was a controversial hypothesis revived by Arber and supported by her morphological and anatomical studies. This theory highlighted the parallels between leaves and shoots and contrasted with an alternative view that leaves, with their limited growth potential, are completely distinct from shoots. Pea morphological mutants with altered growth potential in their compound leaves are described. The unifoliata mutant has a limited growth potential relative to wild-type;cochleata, afila and insecatus have extended potentials. Characterization of theunifoliata mutation and gene expression patterns indicate that unifoliata is a common factor in pea compound leaf and floral shoot development, and so provides rudimentary support for the idea that some leaves have shoot-like characteristics. Tomato leaves are also considered to lend tentative support. The afila and insecatus leaf forms are described as bipinnate and weakly bipinnate, respectively. These and the tendril-less mutant are potential phenocopies of legume relatives, an idea based on Vavilov's law of homologous series of variation. Arber illustrated, but did not articulate in genetical terms, that morphological variation in structures within an individual plant can be interpreted as reiteration of design. Analogous with Vavilov's view, this can be considered a consequence of the same genetic programme in a different location.
- Published
- 2001
49. Association of dominant loci for resistance to Pseudomonas syringae pv. pisi with linkage groups II, VI and VII of Pisum sativum
- Author
-
Noel Ellis, P. J. Hunter, and J. D. Taylor
- Subjects
Genetics ,Locus (genetics) ,General Medicine ,Biology ,RAPD ,chemistry.chemical_compound ,Sativum ,Gene mapping ,chemistry ,Inbred strain ,Genetic linkage ,Molecular marker ,Pseudomonas syringae ,Agronomy and Crop Science ,Biotechnology - Abstract
Morphological characters, isoenzymes and recombinant inbred lines were employed to assign four loci for resistance to Pseudomonas syringae pv pisi to genetic linkage groups in Pisum sativum. A total of five morphological markers and 11 isoenzyme loci were screened in two independent F2 P. sativum populations: Vinco × Hurst’s Greenshaft (V×HGS) and Partridge × Early Onward (P×EO). Mapping was also carried out in two recombinant inbred populations, unrelated to the F2 populations. Previously reported linkage between resistance genes Ppi3 and Ppi4 was confirmed. Linkage was also detected between resistance gene Ppi2 and the isoenzyme locus Aldo (linkage group VII). The linked loci Ppi3 and Ppi4 were associated with a (linkage group II). A further resistance gene Ppi1 was associated with linkage group VI close to the hilum colour gene P1. RAPD markers tested in the cross P×EO were not well targeted; however, one marker, OPA-200.71, showed linkage to Ppi3.
- Published
- 2001
50. [Untitled]
- Author
-
Anthony J. Michael, T. H. Noel Ellis, Campbell W. Gourlay, and Julie M.I. Hofer
- Subjects
Regulation of gene expression ,biology ,fungi ,Mutant ,food and beverages ,Plant Science ,General Medicine ,Meristem ,biology.organism_classification ,Pisum ,Complementary DNA ,Gene expression ,Botany ,Genetics ,Homeobox ,Primordium ,Agronomy and Crop Science - Abstract
Differences in knotted1-like (knox) gene expression may account for some of the diversity of leaf forms seen in nature. Class 1 knox genes are expressed in the compound leaf primordia of tomato but not in the simple leaf primordia of a range of species examined so far. In order to test the hypothesis that all compound leaves differ from simple leaves in this way, we isolated a class 1 knox cDNA from pea, Pskn1 (Pisum sativum knotted1) and examined its expression pattern. The encoded homeodomain of Pskn1 shares 88% identical residues with KNOTTED1 from maize and an adjacent ELK domain is present. The protein sequence of PSKN1 is 69% identical to TKN2, its nearest related sequence in tomato. Unlike TKn2, Pskn1 was not expressed in newly initiated compound leaves. The expression pattern of Pskn1 resembled those of other class 1 knox genes described in maize and Arabidopsis. Transcripts were detected in the shoot apical meristem and developing vasculature of the vegetative shoot, but expression was not detected in newly initiated and developing compound leaf primordia. The same pattern of expression was observed in the afila mutant, which is characterised by highly ramified compound leaves. Our results suggest that tomato and pea use different developmental processes in the generation of their compound leaves.
- Published
- 2001
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.