423 results on '"Doležel, Jaroslav'
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2. Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension
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Shan Yang, Petr Cápal, Jaroslav Doležel, Xueting Li, Wang Qian, Zhiqiang Wang, Kai Zeng, Peiting Li, Hongkai Zhou, Rui Xia, Muqing Zhang, and Zuhu Deng
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Plant Science ,Agronomy and Crop Science - Published
- 2022
3. Fine mapping of powdery mildew and stripe rust resistance genes Pm5V/Yr5V transferred from Dasypyrum villosum into wheat without yield penalty
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Ruiqi Zhang, Chuntian Lu, Xiangru Meng, Yali Fan, Jie Du, Runran Liu, Yigao Feng, Liping Xing, Petr Cápal, Kateřina Holušová, Jaroslav Doležel, Yiwei Wang, Huanqing Mu, Bingxiao Sun, Fu Hou, Ruonan Yao, Chuanxi Xiong, Yang Wang, Peidu Chen, and Aizhong Cao
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Plant Breeding ,Basidiomycota ,Genetics ,General Medicine ,Poaceae ,Agronomy and Crop Science ,Triticum ,Disease Resistance ,Plant Diseases ,Biotechnology - Abstract
The novel wheat powdery mildew and stripe rust resistance genes Pm5V/Yr5V are introgressed from Dasypyrum villosum and fine mapped to a narrowed region in 5VS, and their effects on yield-related traits were characterized. The powdery mildew and stripe rust seriously threaten wheat production worldwide. Dasypyrum villosum (2n = 2x = 14, VV), a relative of wheat, is a valuable resource of resistance genes for wheat improvement. Here, we describe a platform for rapid introgression of the resistance genes from D. villosum into the wheat D genome. A complete set of new wheat-D. villosum V (D) disomic substitution lines and 11 D/V Robertsonian translocation lines are developed and characterized by molecular cytogenetic method. A new T5DL·5V#5S line NAU1908 shows resistance to both powdery mildew and stripe rust, and the resistances associated with 5VS are confirmed to be conferred by seedling resistance gene Pm5V and adult-plant resistance gene Yr5V, respectively. We flow-sort chromosome arm 5VS and sequence it using the Illumina NovaSeq 6000 system that allows us to generate 5VS-specific markers for genetic mapping of Pm5V/Yr5V. Fine mapping shows that Pm5V and Yr5V are closely linked and the location is narrowed to an approximately 0.9 Mb region referencing the sequence of Chinese Spring 5DS. In this region, a NLR gene in scaffold 24,874 of 5VS orthologous to TraesCS5D02G044300 is the most likely candidate gene for Pm5V. Soft- and hard-grained T5DL·5V#5S introgressions confer resistance to both powdery mildew and stripe rust in diverse wheat genetic backgrounds without yield penalty. Meanwhile, significant decrease in plant height and increase in yield were observed in NIL-5DL·5V#5S compared with that in NIL-5DL·5DS. These results indicate that Pm5V/Yr5V lines might have the potential value to facilitate wheat breeding for disease resistance.
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- 2022
4. Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense Using Musa acuminata ssp. malaccensis
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Andrew Chen, Jiaman Sun, Altus Viljoen, Diane Mostert, Yucong Xie, Leroy Mangila, Sheryl Bothma, Rebecca Lyons, Eva Hřibová, Pavla Christelová, Brigitte Uwimana, Delphine Amah, Stephen Pearce, Ning Chen, Jacqueline Batley, David Edwards, Jaroslav Doležel, Peter Crisp, Alla F. Brown, Guillaume Martin, Nabila Yahiaou, Angelique D’Hont, Lachlan Coin, Ron Swennen, and Elizabeth A. B. Aitken
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Quantitative trait locus ,Fine mapping ,Subtropical race 4 ,Fusarium oxysporum f. sp. cubense ,Tropical race 4 ,Marker-assisted selection ,Musa acuminata ssp. malaccensis ,RNAseq ,Receptor-like kinase ,Fusarium wilt ,Resistance gene expression ,Banana - Abstract
Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. Cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. Malaccensis segregating populations, segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on chromosome 3 of ‘DHPahang’ reference assembly v4. Within this region, there was a cluster of pattern recognition receptors, namely leucine-rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell-wall-associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins, positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant progenies but not in the susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent ‘Ma850’ and a susceptible line ‘Ma848’, to show that the STR4 resistance co-segregated with marker ‘28820’ at this locus. Finally, an informative SNP marker 29730 allowed the locus-specific resistance to be assessed in a collection of diploid and polyploid banana plants. Of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4-resistant, such as ‘Pahang’, ‘SH-3362’, ‘SH-3217’, ‘Ma-ITC0250’, and ‘DH-Pahang/CIRAD 930’. Additional screening in the International Institute for Tropical Agriculture’s collection suggests that the dominant allele is common among the elite ‘Matooke’ NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine mapping and candidate gene identification will allow characterization of molecular mechanisms underlying the TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world. ispartof: Pathogens vol:12 issue:6 pages:820- ispartof: location:Switzerland status: Published online
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- 2023
5. Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense Using Musa acuminata ssp. malaccensis
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Aitken, Andrew Chen, Jiaman Sun, Altus Viljoen, Diane Mostert, Yucong Xie, Leroy Mangila, Sheryl Bothma, Rebecca Lyons, Eva Hřibová, Pavla Christelová, Brigitte Uwimana, Delphine Amah, Stephen Pearce, Ning Chen, Jacqueline Batley, David Edwards, Jaroslav Doležel, Peter Crisp, Allan F. Brown, Guillaume Martin, Nabila Yahiaoui, Angelique D’Hont, Lachlan Coin, Rony Swennen, and Elizabeth A. B.
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banana ,fine mapping ,quantitative trait locus ,Musa acuminata ssp. malaccensis ,Fusarium wilt ,Fusarium oxysporum f. sp. cubense ,tropical race 4 ,subtropical race 4 ,marker-assisted selection ,resistance gene expression ,receptor-like kinase ,RNAseq - Abstract
Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. Cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. Malaccensis segregating populations, segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on chromosome 3 of ‘DH-Pahang’ reference assembly v4. Within this region, there was a cluster of pattern recognition receptors, namely leucine-rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell-wall-associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins, positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant progenies but not in the susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent ‘Ma850’ and a susceptible line ‘Ma848’, to show that the STR4 resistance co-segregated with marker ‘28820’ at this locus. Finally, an informative SNP marker 29730 allowed the locus-specific resistance to be assessed in a collection of diploid and polyploid banana plants. Of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4-resistant, such as ‘Pahang’, ‘SH-3362’, ‘SH-3217’, ‘Ma-ITC0250’, and ‘DH-Pahang/CIRAD 930’. Additional screening in the International Institute for Tropical Agriculture’s collection suggests that the dominant allele is common among the elite ‘Matooke’ NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine mapping and candidate gene identification will allow characterization of molecular mechanisms underlying the TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world.
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- 2023
- Full Text
- View/download PDF
6. Author Correction: Molecular organization of recombinant human-Arabidopsis chromosomes in hybrid cell lines
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Yikun Liu, Yeng Mun Liaw, Chee How Teo, Petr Cápal, Naoki Wada, Kiichi Fukui, Jaroslav Doležel, and Nobuko Ohmido
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Multidisciplinary - Published
- 2023
7. The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase
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Guotai Yu, Oadi Matny, Spyridon Gourdoupis, Naganand Rayapuram, Fatimah R. Aljedaani, Yan L. Wang, Thorsten Nürnberger, Ryan Johnson, Emma E. Crean, Isabel M.-L. Saur, Catherine Gardener, Yajuan Yue, Ngonidzashe Kangara, Burkhard Steuernagel, Sadiye Hayta, Mark Smedley, Wendy Harwood, Mehran Patpour, Shuangye Wu, Jesse Poland, Jonathan D. G. Jones, T. Lynne Reuber, Moshe Ronen, Amir Sharon, Matthew N. Rouse, Steven Xu, Kateřina Holušová, Jan Bartoš, István Molnár, Miroslava Karafiátová, Heribert Hirt, Ikram Blilou, Łukasz Jaremko, Jaroslav Doležel, Brian J. Steffenson, and Brande B. H. Wulff
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Genetics - Abstract
To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool1. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum2,3. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.
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- 2023
8. An unusual tandem kinase fusion protein confers leaf rust resistance in wheat
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Yajun Wang, Michael Abrouk, Spyridon Gourdoupis, Dal-Hoe Koo, Miroslava Karafiátová, István Molnár, Kateřina Holušová, Jaroslav Doležel, Naveenkumar Athiyannan, Emile Cavalet-Giorsa, Łukasz Jaremko, Jesse Poland, and Simon G. Krattinger
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Genetics - Abstract
The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. Here we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata2. We established that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Aegilopstriuncialis3, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.
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- 2023
9. A chromosome arm from Thinopyrum intermedium × Thinopyrum ponticum hybrid confers increased tillering and yield potential in wheat
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Edina Türkösi, Éva Szakács, László Ivanizs, András Farkas, Eszter Gaál, Mahmoud Said, Éva Darkó, Mónika Cséplő, Péter Mikó, Jaroslav Doležel, Márta Molnár-Láng, István Molnár, and Klaudia Kruppa
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Tiller number is a key component of plant architecture with direct effect on grain yield of wheat. Interspecific hybridization using wild relative species are promising approach for increasing wheat genetic diversity, including yield potential. Agropyron glael, a perennial hybrid of Thinopyrum intermedium and Th. ponticum has five subgenomes (J, Jst, Jvs, Jr, and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. This work reports on development of a wheat-A. glael translocation line WT153397. Sequential in situ hybridizations with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA)7 DNA repeats, as well as an analysis using molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6Jvs centric fusion in the translocation line. Field trials in low-input and high-input breeding nurseries over three growing seasons demonstrated high compensating ability of the Agropyron chromosome arm for the missing 6DL as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents. Moreover, the introgressed 6Jvs chromosome arm significantly increased the number of productive tillers, which manifested in the significantly higher grain yield potential relative to the parental wheat cultivars. The translocated chromosome could be flow-sorted in high purity providing an opportunity to employ chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 represents an important genetic stock for functional genetic studies of tiller formation and useful breeding material to increase wheat yield potential.
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- 2023
10. The giant diploid faba genome unlocks variation in a global protein crop
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Murukarthick Jayakodi, Agnieszka A. Golicz, Jonathan Kreplak, Lavinia I. Fechete, Deepti Angra, Petr Bednář, Elesandro Bornhofen, Hailin Zhang, Raphaël Boussageon, Sukhjiwan Kaur, Kwok Cheung, Jana Čížková, Heidrun Gundlach, Asis Hallab, Baptiste Imbert, Gabriel Keeble-Gagnère, Andrea Koblížková, Lucie Kobrlová, Petra Krejčí, Troels W. Mouritzen, Pavel Neumann, Marcin Nadzieja, Linda Kærgaard Nielsen, Petr Novák, Jihad Orabi, Sudharsan Padmarasu, Tom Robertson-Shersby-Harvie, Laura Ávila Robledillo, Andrea Schiemann, Jaakko Tanskanen, Petri Törönen, Ahmed O. Warsame, Alexander H. J. Wittenberg, Axel Himmelbach, Grégoire Aubert, Pierre-Emmanuel Courty, Jaroslav Doležel, Liisa U. Holm, Luc L. Janss, Hamid Khazaei, Jiří Macas, Martin Mascher, Petr Smýkal, Rod J. Snowdon, Nils Stein, Frederick L. Stoddard, Jens Stougaard, Nadim Tayeh, Ana M. Torres, Björn Usadel, Ingo Schubert, Donal Martin O’Sullivan, Alan H. Schulman, Stig Uggerhøj Andersen, Institute of Biotechnology, Computational genomics, Organismal and Evolutionary Biology Research Programme, Genetics, Bioinformatics, Department of Agricultural Sciences, Viikki Plant Science Centre (ViPS), Helsinki Institute of Sustainability Science (HELSUS), Crop Science Research Group, Legume science, and Plant Production Sciences
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Multidisciplinary ,1184 Genetics, developmental biology, physiology ,ddc:500 ,11831 Plant biology ,metabolism ,Genome-Wide Association Study ,Plant Proteins ,genetics ,Plant Breeding ,Vicia faba ,DNA Copy Number Variations ,Diploidy ,4111 Agronomy - Abstract
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
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- 2023
11. Both male and female meiosis contribute to non‐Mendelian inheritance of parental chromosomes in interspecific plant hybrids (Lolium x Festuca)
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Majka, Joanna, Glombik, Marek, Doležalová, Alžběta, Kneřová, Jana, Mendes Ferreira, Marco Tulio, Zwierzykowski, Zbigniew, Duchoslav, Martin, Studer, Bruno, Doležel, Jaroslav, Bartoš, Jan, and Kopecký, David
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centromere ,chromosomeelimination ,genome dominance ,interspecifichybrid ,kinetochore ,NDC80 ,NNF1 ,pollenmeiosis - Abstract
Some interspecific plant hybrids show unequal transmission of chromosomes from parental genomes to the successive generations. It has been suggested that this is due to a differential behavior of parental chromosomes during meiosis. However, underlying mechanism is unknown. We analyzed chromosome composition of the F2 generation of Festuca × Lolium hybrids and reciprocal backcrosses to elucidate effects of male and female meiosis on the shift in parental genome composition. We studied male meiosis, including the attachment of chromosomes to the karyokinetic spindle and gene expression profiling of the kinetochore genes. We found that Lolium and Festuca homoeologues were transmitted differently to the F2 generation. Female meiosis led to the replacement of Festuca chromosomes by their Lolium counterparts. In male meiosis, Festuca univalents were attached less frequently to microtubules than Lolium univalents, lagged in divisions and formed micronuclei, which were subsequently eliminated. Genome sequence analysis revealed a number of non-synonymous mutations between copies of the kinetochore genes from Festuca and Lolium genomes. Furthermore, we found that outer kinetochore proteins NDC80 and NNF1 were exclusively expressed from the Lolium allele. We hypothesize that silencing of Festuca alleles results in improper attachment of Festuca chromosomes to karyokinetic spindle and subsequently their gradual elimination., New Phytologist, 238 (2), ISSN:0028-646X, ISSN:1469-8137
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- 2023
- Full Text
- View/download PDF
12. Helical coiling of metaphase chromatids
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Ivona Kubalová, Amanda Souza Câmara, Petr Cápal, Tomáš Beseda, Jean-Marie Rouillard, Gina Marie Krause, Kateřina Holušová, Helena Toegelová, Axel Himmelbach, Nils Stein, Andreas Houben, Jaroslav Doležel, Martin Mascher, Hana Šimková, and Veit Schubert
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epigenetics ,chromatin ,gene regulation ,Genetics - Abstract
Chromatids of mitotic chromosomes were suggested to coil into a helix in early cytological studies and this assumption was recently supported by chromosome conformation capture (3C) sequencing. Still, direct differential visualization of a condensed chromatin fibre confirming the helical model was lacking. Here, we combined Hi-C analysis of purified metaphase chromosomes, biopolymer modelling and spatial structured illumination microscopy of large fluorescently labeled chromosome segments to reveal the chromonema - a helically-wound, 400 nm thick chromatin thread forming barley mitotic chromatids. Chromatin from adjacent turns of the helix intermingles due to the stochastic positioning of chromatin loops inside the chromonema. Helical turn size varies along chromosome length, correlating with chromatin density. Constraints on the observable dimensions of sister chromatid exchanges further supports the helical chromonema model.
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- 2023
13. Chromosome-centric approaches in crop genomics: Focus on Mendel's pea plant
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Petr Cápal and Jaroslav Doležel
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Genetics ,food and beverages ,Plant Science - Published
- 2022
14. Analysis of BRCT5 domain-containing proteins reveals a new component of DNA damage repair in Arabidopsis
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Jovanka Vladejić, Fen Yang, Eva Dvořák Tomaštíková, Jaroslav Doležel, Jan J. Palecek, and Ales Pecinka
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Plant Science - Abstract
The integrity of plant genetic information is constantly challenged by various internal and external factors. Therefore, plants use a sophisticated molecular network to identify, signal and repair damaged DNA. Here, we report on the identification and analysis of four uncharacterized Arabidopsis BRCT5 DOMAIN CONTAINING PROTEINs (BCPs). Proteins with the BRCT5 domain are frequently involved in the maintenance of genome stability across eukaryotes. The screening for sensitivity to induced DNA damage identified BCP1 as the most interesting candidate. We show that BCP1 loss of function mutants are hypersensitive to various types of DNA damage and accumulate an increased number of dead cells in root apical meristems upon DNA damage. Analysis of publicly available sog1 transcriptomic and SOG1 genome-wide DNA binding data revealed that BCP1 is inducible by gamma radiation and is a direct target of this key DNA damage signaling transcription factor. Importantly, bcp1 plants showed a reduced frequency of somatic homologous recombination in response to both endogenous and induced DNA damage. Altogether, we identified a novel plant-specific DNA repair factor that acts downstream of SOG1 in homology-based repair.
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- 2022
15. An autoactive
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Philippa, Borrill, Rohit, Mago, Tianyuan, Xu, Brett, Ford, Simon J, Williams, Adinda, Derkx, William D, Bovill, Jessica, Hyles, Dhara, Bhatt, Xiaodi, Xia, Colleen, MacMillan, Rosemary, White, Wolfram, Buss, István, Molnár, Sean, Walkowiak, Odd-Arne, Olsen, Jaroslav, Doležel, Curtis J, Pozniak, and Wolfgang, Spielmeyer
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Plant Breeding ,Binding Sites ,Nucleotides ,Dwarfism ,Triticum ,Plant Proteins - Abstract
Semidwarfing genes have greatly increased wheat yields globally, yet the widely used gibberellin (GA)-insensitive genes
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- 2022
16. A single amino acid change can alter the specificity of the multi-allelic wheat stem rust resistance locus SR9
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Jianping Zhang, Jayaveeramuthu Nirmala, Shisheng Chen, Matthias Jost, Burkhard Steuernagel, Miroslava Karafiátová, Timothy Hewitt, Hongna Li, Erena Edae, Keshav Sharma, Sami Hoxha, Dhara Bhatt, Rea Antoniou-Kourounioti, Peter Dodds, Brande Wulff, Jaroslav Doležel, Michael Ayliffe, Colin Hiebert, Robert McIntosh, Jorge Dubcovsky, Peng Zhang, Matthew Rouse, and Evans Lagudah
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Most resistance genes thus far isolated from wheat have a very limited number of functional alleles, with the exception of the powdery mildew PM3 resistance locus. Here we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9, representing the largest multi-allelic rust resistance locus in common wheat. The seven previously reported resistance alleles (Sr9a, Sr9b, Sr9d, Sr9e, Sr9f, Sr9g, and Sr9h) at the locus were characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation were used to confirm Sr9b, two haplotypes of Sr9e (Sr9e_h1, Sr9e_h2), Sr9g, and Sr9h. Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing a previously unreported motif at their N termini and an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differed from SR9B by a single amino acid. SR9B and SR9G resistance proteins were also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences.
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- 2022
17. Barley MLA3 recognizes the host-specificity determinant PWL2 from rice blast (M. oryzae)
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Helen J. Brabham, Diana Gómez De La Cruz, Vincent Were, Motoki Shimizu, Hiromasa Saitoh, Inmaculada Hernández-Pinzón, Phon Green, Jennifer Lorang, Koki Fujisaki, Kazuhiro Sato, István Molnár, Hana Šimková, Jaroslav Doležel, James Russell, Jodie Taylor, Matthew Smoker, Yogesh Kumar Gupta, Tom Wolpert, Nicholas J. Talbot, Ryohei Terauchi, and Matthew J. Moscou
- Abstract
Plant nucleotide-binding leucine-rich repeat immune receptors (NLRs) directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley NLRMlahas undergone functional diversification andMlaalleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminisf. sp.hordei; Bgh). Here, we show thatMla3also confers resistance to rice blast (Magnaporthe oryzae) in a dosage dependent manner. Using a forward genetic screen, we discovered that the recognized effector fromM. oryzaeisPWL2, a host range determinant factor that preventsM. oryzaefrom infecting weeping lovegrass (Eragrostis curvula).Mla3has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.
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- 2022
18. Long-read genome sequencing accelerated the cloning ofPm69by resolving the complexity of a rapidly evolving resistance gene cluster in wheat
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Yinghui Li, Zhen-Zhen Wei, Hanan Sela, Liubov Govta, Valentyna Klymiuk, Rajib Roychowdhury, Harmeet Singh Chawla, Jennifer Ens, Krystalee Wiebe, Valeria Bocharova, Roi Ben-David, Prerna B. Pawar, Samidha Jaiwar, István Molnár, Jaroslav Doležel, Curtis J. Pozniak, and Tzion Fahima
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Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks in the cloning of the powdery mildew (Pm) resistance gene (R-gene)Pm69derived from tetraploid wild emmer wheat (WEW). A conventional positional cloning approach encountered suppressed recombination due to structural variations, while chromosome sorting yielded an insufficient purity level. APm69physical map, constructed by assembling ONT long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster. A single candidate NLR was identified within this cluster by anchoring RNASeq reads of susceptible mutants to ONT contigs and was validated by the virus-induced gene silencing (VIGS) approach.Pm69, comprising Rx_N with RanGAP interaction sites, NB-ARC, and LRR domains, is probably a newly evolved NLR discovered only in one location across the WEW distribution range in the Fertile Crescent.Pm69was successfully introgressed into durum and bread wheat, and a diagnostic molecular marker could be used to accelerate its deployment and pyramiding with other resistance genes.
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- 2022
19. Flow karyotyping of wheat-Aegilops additions facilitate dissecting the genomes of Ae. biuncialis and Ae. geniculata into individual chromosomes
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Mahmoud Said, Petr Cápal, András Farkas, Eszter Gaál, László Ivanizs, Bernd Friebe, Jaroslav Doležel, and István Molnár
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Plant Science - Abstract
Breeding of wheat adapted to new climatic conditions and resistant to diseases and pests is hindered by a limited gene pool due to domestication and thousands of years of human selection. Annual goatgrasses (Aegilops spp.) with M and U genomes are potential sources of the missing genes and alleles. Development of alien introgression lines of wheat may be facilitated by the knowledge of DNA sequences of Aegilops chromosomes. As the Aegilops genomes are complex, sequencing relevant Aegilops chromosomes purified by flow cytometric sorting offers an attractive route forward. The present study extends the potential of chromosome genomics to allotetraploid Ae. biuncialis and Ae. geniculata by dissecting their M and U genomes into individual chromosomes. Hybridization of FITC-conjugated GAA oligonucleotide probe to chromosomes suspensions of the two species allowed the application of bivariate flow karyotyping and sorting some individual chromosomes. Bivariate flow karyotype FITC vs. DAPI of Ae. biuncialis consisted of nine chromosome-populations, but their chromosome content determined by microscopic analysis of flow sorted chromosomes indicated that only 7Mb and 1Ub could be sorted at high purity. In the case of Ae. geniculata, fourteen chromosome-populations were discriminated, allowing the separation of nine individual chromosomes (1Mg, 3Mg, 5Mg, 6Mg, 7Mg, 1Ug, 3Ug, 6Ug, and 7Ug) out of the 14. To sort the remaining chromosomes, a partial set of wheat-Ae. biuncialis and a whole set of wheat-Ae. geniculata chromosome addition lines were also flow karyotyped, revealing clear separation of the GAA-rich Aegilops chromosomes from the GAA-poor A- and D-genome chromosomes of wheat. All of the alien chromosomes represented by individual addition lines could be isolated at purities ranging from 74.5% to 96.6% and from 87.8% to 97.7%, respectively. Differences in flow karyotypes between Ae. biuncialis and Ae. geniculata were analyzed and discussed. Chromosome-specific genomic resources will facilitate gene cloning and the development of molecular tools to support alien introgression breeding of wheat.
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- 2022
20. Author Correction: Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins
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Javier Sánchez-Martín, Victoria Widrig, Gerhard Herren, Thomas Wicker, Helen Zbinden, Julien Gronnier, Laurin Spörri, Coraline R. Praz, Matthias Heuberger, Markus C. Kolodziej, Jonatan Isaksson, Burkhard Steuernagel, Miroslava Karafiátová, Jaroslav Doležel, Cyril Zipfel, and Beat Keller
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Plant Science - Published
- 2023
21. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
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Eva Hřibová, Angélique D'Hont, Patrick Wincker, Franc-Christophe Baurens, Arnaud Lemainque, Benjamin Noel, Corinne Cruaud, Jean-Marc Aury, Caroline Belser, Guillaume Martin, Jaroslav Doležel, Nabila Yahiaoui, Benjamin Istace, Karine Labadie, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), France GenomiqueANR-10-INBS-09-08, Center de cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), Agropolis Fondation1504-006, ERDF project 'Plants as a tool for sustainable global development'CZ.02.1.01/0.0/0.0/16_019/0000827, Genoscope, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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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0106 biological sciences ,QH301-705.5 ,[SDV]Life Sciences [q-bio] ,Medicine (miscellaneous) ,Computational biology ,Genome informatics ,Musa acuminata ,01 natural sciences ,Genome ,Chromosomes, Plant ,Article ,General Biochemistry, Genetics and Molecular Biology ,F30 - Génétique et amélioration des plantes ,génomique ,Nanopores ,03 medical and health sciences ,Gapless playback ,Centromere ,Biology (General) ,Gene ,030304 developmental biology ,0303 health sciences ,Génome ,biology ,Contig ,phytogénétique ,food and beverages ,Biotechnologie végétale ,Musa ,Genomics ,Télomères ,Telomere ,biology.organism_classification ,Nanopore Sequencing ,Plant biotechnology ,Nanopore sequencing ,General Agricultural and Biological Sciences ,Genome, Plant ,010606 plant biology & botany - Abstract
Long-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes., Belser, Baurens et al. report a chromosome-scale assembly of a banana genome (Musa acuminata) with five out of eleven chromosomes entirely reconstructed in a single contig from telomere to telomere. This work sheds light on the content of complex regions like centromeres or clusters of paralogous genes in the banana genome.
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- 2021
22. The giant diploid faba genome unlocks variation in a global protein crop
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Murukarthick Jayakodi, Agnieszka A. Golicz, Jonathan Kreplak, Lavinia I. Fechete, Deepti Angra, Petr Bednář, Elesandro Bornhofen, Hailin Zhang, Raphaël Boussageon, Sukhjiwan Kaur, Kwok Cheung, Jana Čížková, Heidrun Gundlach, Asis Hallab, Baptiste Imbert, Gabriel Keeble-Gagnère, Andrea Koblížková, Lucie Kobrlová, Petra Krejčí, Troels W. Mouritzen, Pavel Neumann, Marcin Nadzieja, Linda Kærgaard Nielsen, Petr Novák, Jihad Orabi, Sudharsan Padmarasu, Tom Robertson-Shersby-Harvie, Laura Ávila Robledillo, Andrea Schiemann, Jaakko Tanskanen, Petri Törönen, Ahmed O. Warsame, Alexander H.J. Wittenberg, Axel Himmelbach, Grégoire Aubert, Pierre-Emmanuel Courty, Jaroslav Doležel, Liisa U. Holm, Luc L. Janss, Hamid Khazaei, Jiří Macas, Martin Mascher, Petr Smýkal, Rod J. Snowdon, Nils Stein, Frederick L. Stoddard, Nadim Tayeh, Ana M. Torres, Björn Usadel, Ingo Schubert, Donal Martin O’Sullivan, Alan H. Schulman, and Stig Uggerhøj Andersen
- Abstract
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emission and loss of biodiversity. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value. Faba bean (Vicia faba L.) has a high yield potential and is well-suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has grown to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, though with significant copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association (GWA) analysis to dissect the genetic basis of hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate improvement of sustainable protein production across Mediterranean, subtropical, and northern temperate agro-ecological zones.
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- 2022
23. Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale
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Jakob Petereit, Cassandria Tay Fernandez, Jacob I. Marsh, Philipp E. Bayer, William J. W. Thomas, Aybeniz Javad Aliyeva, Miroslava Karafiátová, Jaroslav Doležel, Jacqueline Batley, and David Edwards
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Inorganic Chemistry ,Organic Chemistry ,rye ,isolated chromosome arm sequencing ,presence-absence variation ,General Medicine ,Physical and Theoretical Chemistry ,Molecular Biology ,Spectroscopy ,Catalysis ,Computer Science Applications - Abstract
Rye (Secale cereale) is a climate-resilient cereal grown extensively as grain or forage crop in Northern and Eastern Europe. In addition to being an important crop, it has been used to improve wheat through introgression of genomic regions for improved yield and disease resistance. Understanding the genomic diversity of rye will assist both the improvement of this crop and facilitate the introgression of more valuable traits into wheat. Here, we isolated and sequenced the short arm of rye chromosome 7 (7RS) from Triticale 380SD using flow cytometry and compared it to the public Lo7 rye whole genome reference assembly. We identify 2747 Lo7 genes present on the isolated chromosome arm and two clusters containing seven and sixty-five genes that are present on Triticale 380SD 7RS, but absent from Lo7 7RS. We identified 29 genes that are not assigned to chromosomal locations in the Lo7 assembly but are present on Triticale 380SD 7RS, suggesting a chromosome arm location for these genes. Our study supports the Lo7 reference assembly and provides a repertoire of genes on Triticale 7RS.
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- 2022
- Full Text
- View/download PDF
24. Flow karyotyping of wheat
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Mahmoud, Said, Petr, Cápal, András, Farkas, Eszter, Gaál, László, Ivanizs, Bernd, Friebe, Jaroslav, Doležel, and István, Molnár
- Abstract
Breeding of wheat adapted to new climatic conditions and resistant to diseases and pests is hindered by a limited gene pool due to domestication and thousands of years of human selection. Annual goatgrasses (
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- 2022
25. Isolation and Sequencing of Chromosome Arm 7RS of Rye
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Jakob, Petereit, Cassandria, Tay Fernandez, Jacob I, Marsh, Philipp E, Bayer, William J W, Thomas, Aybeniz Javad, Aliyeva, Miroslava, Karafiátová, Jaroslav, Doležel, Jacqueline, Batley, and David, Edwards
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Secale ,Triticale ,Edible Grain ,Chromosomes, Plant ,Triticum ,Disease Resistance - Abstract
Rye (
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- 2022
26. The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase
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Guotai Yu, Oadi Matny, Spyridon Gourdoupis, Ryan Johnson, Fatimah R. Aljedaani, Ikram Blilou, Catherine H. Gardener, Yajuan Yue, Ngoni Kangara, Burkhard Steuernagel, Sadiye Hayta, Mark Smedley, Wendy Harwood, Mehran Patpour, Shuangye Wu, Jesse A. Poland, Jonathan Jones, Lynne Reuber, Moshe Ronen, Amir Sharon, Matthew Rouse, Steven Xu, Kateřina Holušová, Jan Bartos, István Molnár, Miroslava Karafiátová, Łukasz Jaremko, Jaroslav Doležel, Brian Steffenson, and Brande B. H. Wulff
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kinase ,resistance gene ,stem rust ,wheat - Abstract
To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum. Sr43 encodes a protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.
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- 2022
27. An unusual tandem kinase fusion protein confers leaf rust resistance in wheat
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Yajun Wang, Michael Abrouk, Spyridon Gourdoupis, Dal-Hoe Koo, Miroslava Karafiátová, István Molnár, Jaroslav Doležel, Naveenkumar Athiyannan, Emile Cavalet-Giorsa, Łukasz Jaremko, Jesse Poland, and Simon G. Krattinger
- Abstract
The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with novel disease resistance genes. Here, we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata. We establish that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Ae. triuncialis, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease resistance genes for breeding.
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- 2022
28. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals
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Qilin Tian, Chuanrang Zhu, Rachel E. Melton, Graham Moore, Xuehui Huang, Azahara C. Martín, Guy Polturak, Hengyun Lu, Jiashun Miao, Jaroslav Doležel, Thomas Louveau, Anne Osbourn, Danling Fan, Yan Zhao, Tim Langdon, Rebecca Casson, Zheyong Xue, Michael J. Stephenson, Yan Li, Ying Lu, Tao Huang, Zhenhua Liu, Miroslava Karafiátová, Bin Han, Qi Feng, Aymeric Leveau, Neil Hall, Jiaying Chen, Jan Vrána, Charlotte Owen, Lionel Hill, Brande B. H. Wulff, Eva Wegel, Lei Zhang, Ryan Joynson, Burkhard Steuernagel, James Reed, Congcong Zhou, Qiang Zhao, Wen-Jun Li, Yiqi Lu, Anastasia Orme, Jing Wang, and María-Dolores Rey
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Agricultural genetics ,0106 biological sciences ,0301 basic medicine ,Genome evolution ,Avena ,Science ,General Physics and Astronomy ,RNA-Seq ,Biology ,Synteny ,01 natural sciences ,Genome ,Article ,Evolutionary genetics ,General Biochemistry, Genetics and Molecular Biology ,Homology (biology) ,Evolution, Molecular ,03 medical and health sciences ,Tobacco ,Gene cluster ,Gene ,In Situ Hybridization, Fluorescence ,Disease Resistance ,Repetitive Sequences, Nucleic Acid ,Whole genome sequencing ,Genetics ,Multidisciplinary ,Whole Genome Sequencing ,Comparative genomics ,High-Throughput Nucleotide Sequencing ,food and beverages ,General Chemistry ,Saponins ,Telomere ,030104 developmental biology ,Multigene Family ,Secondary metabolism ,Edible Grain ,Metabolic Networks and Pathways ,010606 plant biology & botany - Abstract
Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat—the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a ‘self-poisoning’ scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity., The genomic organization and origin of the avenacin biosynthetic gene cluster remain unknown. Here, the authors assemble the genome of diploid oat Avena strigosa, reveal the structure and organization of the consecutive genes, characterize the last two missing pathway steps, and investigate the origin of the pathway in cereals.
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- 2021
29. Transfer of the ph1b Deletion Chromosome 5B From Chinese Spring Wheat Into a Winter Wheat Line and Induction of Chromosome Rearrangements in Wheat-Aegilops biuncialis Hybrids
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Edina Türkösi, László Ivanizs, András Farkas, Eszter Gaál, Klaudia Kruppa, Péter Kovács, Éva Szakács, Kitti Szőke-Pázsi, Mahmoud Said, Petr Cápal, Simon Griffiths, Jaroslav Doležel, and István Molnár
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Plant Science - Abstract
Effective utilization of genetic diversity in wild relatives to improve wheat requires recombination between wheat and alien chromosomes. However, this is suppressed by thePairing homoeologous gene, Ph1, on the long arm of wheat chromosome 5B. A deletion mutant of thePh1locus (ph1b) has been used widely to induce homoeologous recombination in wheat × alien hybrids. However, the originalph1bmutation, developed in Chinese Spring (CS) background has poor agronomic performance. Hence, alien introgression lines are first backcrossed with adapted wheat genotypes and after this step, alien chromosome segments are introduced into breeding lines. In this work, theph1bmutation was transferred from two CSph1bmutants into winter wheat line Mv9kr1. Homozygous genotypes Mv9kr1ph1b/ph1bexhibited improved plant and spike morphology compared to Chinese Spring. Flow cytometric chromosome analysis confirmed reduced DNA content of the mutant 5B chromosome in both wheat genotype relative to the wild type chromosome. Theph1bmutation in the Mv9kr1 genotype allowed wheat-alien chromosome pairing in meiosis of Mv9kr1ph1b_K × Aegilops biuncialisF1hybrids, predominantly with the Mb-genome chromosomes ofAegilopsrelative to those of the Ubgenome. High frequency of wheat-Aegilopschromosome interactions resulted in rearranged chromosomes identified in the new Mv9kr1ph1b × Ae. Biuncialisamphiploids, making these lines valuable sources for alien introgressions. The new Mv9kr1ph1bmutant genotype is a unique resource to support alien introgression breeding of hexaploid wheat.
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- 2022
- Full Text
- View/download PDF
30. An autoactive NB-LRR gene causes Rht13 dwarfism in wheat
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Philippa Borrill, Rohit Mago, Tianyuan Xu, Brett Ford, Simon J Williams, Adinda Derkx, William D Bovill, Jessica Hyles, Dhara Bhatt, Xiaodi Xia, Colleen MacMillan, Rosemary White, Wolfram Buss, István Molnár, Sean Walkowiak, Odd-Arne Olsen, Jaroslav Doležel, Curtis J Pozniak, and Wolfgang Spielmeyer
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Multidisciplinary - Abstract
Semidwarfing genes have greatly increased wheat yields globally, yet the widely used gibberellin (GA)-insensitive genes Rht-B1b and Rht-D1b have disadvantages for seedling emergence. Use of the GA-sensitive semidwarfing gene Rht13 avoids this pleiotropic effect. Here, we show that Rht13 encodes a nucleotide-binding site/leucine-rich repeat ( NB-LRR ) gene. A point mutation in the semidwarf Rht-B13b allele autoactivates the NB-LRR gene and causes a height reduction comparable with Rht-B1b and Rht-D1b in diverse genetic backgrounds. The autoactive Rht-B13b allele leads to transcriptional up-regulation of pathogenesis-related genes including class III peroxidases associated with cell wall remodeling. Rht13 represents a new class of reduced height ( Rht ) gene, unlike other Rht genes, which encode components of the GA signaling or metabolic pathways. This discovery opens avenues to use autoactive NB-LRR genes as semidwarfing genes in a range of crop species, and to apply Rht13 in wheat breeding programs using a perfect genetic marker.
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- 2022
31. Long‐range assembly of sequences helps to unravel the genome structure and small variation of the wheat– Haynaldia villosa translocated chromosome 6VS.6AL
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Chen Peidu, Qiang Wang, Liu Jiaqian, Liping Xing, Jan Bartoš, Cao Shuqi, Aizhong Cao, Chunhong Yin, Jan Vrána, Jaroslav Doležel, Zengshuai Lv, Miroslava Karafiátová, Zhenpu Huang, Ruiqi Zhang, and Lu Yuan
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0106 biological sciences ,0301 basic medicine ,genome annotation ,InDel markers ,Gene prediction ,Genomics ,Chromosomal translocation ,Plant Science ,Computational biology ,Biology ,Poaceae ,physical bin map ,01 natural sciences ,Chromosomes, Plant ,Translocation, Genetic ,03 medical and health sciences ,Centromere ,Indel ,Gene ,Triticum ,Research Articles ,Chromosome ,Genome project ,Chicago long‐range linkage assembly ,Plant Breeding ,030104 developmental biology ,wheat–Haynaldia villosa translocation line T6VS·6AL ,Agronomy and Crop Science ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Summary Genomics studies in wild species of wheat have been limited due to the lack of references; however, new technologies and bioinformatics tools have much potential to promote genomic research. The wheat–Haynaldia villosa translocation line T6VS·6AL has been widely used as a backbone parent of wheat breeding in China. Therefore, revealing the genome structure of translocation chromosome 6VS·6AL will clarify how this chromosome formed and will help to determine how it affects agronomic traits. In this study, chromosome flow sorting, NGS sequencing and Chicago long‐range linkage assembly were innovatively used to produce the assembled sequences of 6VS·6AL, and gene prediction and genome structure characterization at the molecular level were effectively performed. The analysis discovered that the short arm of 6VS·6AL was actually composed of a large distal segment of 6VS, a small proximal segment of 6AS and the centromere of 6A, while the collinear region in 6VS corresponding to 230–260 Mb of 6AS‐Ta was deleted when the recombination between 6VS and 6AS occurred. In addition to the molecular mechanism of the increased grain weight and enhanced spike length produced by the translocation chromosome, it may be correlated with missing GW2‐V and an evolved NRT‐V cluster. Moreover, a fine physical bin map of 6VS was constructed by the high‐throughput developed 6VS‐specific InDel markers and a series of newly identified small fragment translocation lines involving 6VS. This study will provide essential information for mining of new alien genes carried by the 6VS·6AL translocation chromosome.
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- 2021
32. Chromosome analysis and sorting
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Petr Cápal, Debora Giorgi, Jaroslav Doležel, Sergio Lucretti, and István Molnár
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0301 basic medicine ,Histology ,Reviews ,Review Article ,Computational biology ,Biology ,liquid chromosome suspension ,Genome ,Chromosomes, Plant ,repetitive DNA labelling ,DNA sequencing ,Pathology and Forensic Medicine ,03 medical and health sciences ,DNA amplification ,0302 clinical medicine ,marker development ,gene mapping and cloning ,Gene ,Mitosis ,Metaphase ,Cell Cycle ,cell cycle synchronization ,Sorting ,mitotic metaphase chromosomes ,Chromosome ,Cell Biology ,Plants ,Flow Cytometry ,DNA isolation ,DNA extraction ,genome sequencing ,030104 developmental biology ,Special issue: Best Practices in Plant Cytometry ,030220 oncology & carcinogenesis - Abstract
Flow cytometric analysis and sorting of plant mitotic chromosomes has been mastered by only a few laboratories worldwide. Yet, it has been contributing significantly to progress in plant genetics, including the production of genome assemblies and the cloning of important genes. The dissection of complex genomes by flow sorting into the individual chromosomes that represent small parts of the genome reduces DNA sample complexity and streamlines projects relying on molecular and genomic techniques. Whereas flow cytometric analysis, that is, chromosome classification according to fluorescence and light scatter properties, is an integral part of any chromosome sorting project, it has rarely been used on its own due to lower resolution and sensitivity as compared to other cytogenetic methods. To perform chromosome analysis and sorting, commercially available electrostatic droplet sorters are suitable. However, in order to resolve and purify chromosomes of interest the instrument must offer high resolution of optical signals as well as stability during long runs. The challenge is thus not the instrumentation, but the adequate sample preparation. The sample must be a suspension of intact mitotic metaphase chromosomes and the protocol, which includes the induction of cell cycle synchrony, accumulation of dividing cells at metaphase, and release of undamaged chromosomes, is time consuming and laborious and needs to be performed very carefully. Moreover, in addition to fluorescent staining chromosomal DNA, the protocol may include specific labelling of DNA repeats to facilitate discrimination of particular chromosomes. This review introduces the applications of chromosome sorting in plants, and discusses in detail sample preparation, chromosome analysis and sorting to achieve the highest purity in flow‐sorted fractions, and their suitability for downstream applications., Flow cytometric analysis allows high throughput classification of mitotic chromosomes according to DNA amount and quantity of some DNA repeats. Flow sorting then simplifies genome sequencing and gene cloning by dissecting genomes into the individual chromosomes and greatly reducing DNA sample complexity. Purified chromosome fractions facilitate the analysis of three‐dimensional organization of DNA in condensed chromosomes and characterization of their proteome. This review introduces the applications of chromosome sorting in plants, and discusses in detail sample preparation, chromosome analysis and sorting to achieve the highest purity in flow‐sorted fractions, and their suitability for downstream applications.
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- 2021
33. Identification of a Major QTL-Controlling Resistance to the Subtropical Race 4 of Fusarium oxysporum f. sp. cubense in Musa acuminata ssp. malaccensis
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Andrew Chen, Jiaman Sun, Guillaume Martin, Lesley-Ann Gray, Eva Hřibová, Pavla Christelová, Nabila Yahiaoui, Steve Rounsley, Rebecca Lyons, Jacqueline Batley, Ning Chen, Sharon Hamill, Subash K. Rai, Lachlan Coin, Brigitte Uwimana, Angelique D’Hont, Jaroslav Doležel, David Edwards, Rony Swennen, Elizabeth A. B. Aitken, Martin, Guillaume, Gray, Lesley A, Hribova, Eva, Christelova, Pavla, Yahiaoui, Nabila, Rounsley, Steve, Lyon, Rebecca, Batley, Jacqueline, Chen, Ning, Hamill, Sharon, Rai, Subash, Coin, Lachlan, Uwimana, Brigitte, D’Hont, Angelique, Dolezel, Jaroslav, Edwards, David, Swennen, Rony, and Aitken, Elizabeth AB
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Microbiology (medical) ,Infectious Diseases ,General Immunology and Microbiology ,Immunology and Allergy ,Molecular Biology - Abstract
Vascular wilt caused by the ascomycete fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) is a major constraint of banana production around the world. The virulent race, namely Tropical Race 4, can infect all Cavendish-type banana plants and is now widespread across the globe, causing devastating losses to global banana production. In this study, we characterized Foc Subtropical Race 4 (STR4) resistance in a wild banana relative which, through estimated genome size and ancestry analysis, was confirmed to be Musa acuminata ssp. malaccensis. Using a self-derived F2 population segregating for STR4 resistance, quantitative trait loci sequencing (QTL-seq) was performed on bulks consisting of resistant and susceptible individuals. Changes in SNP index between the bulks revealed a major QTL located on the distal end of the long arm of chromosome 3. Multiple resistance genes are present in this region. Identification of chromosome regions conferring resistance to Foc can facilitate marker assisted selection in breeding programs and paves the way towards identifying genes underpinning resistance. ispartof: Pathogens vol:12 issue:2 ispartof: location:Switzerland status: Published online
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- 2023
34. Impact of parasitic lifestyle and different types of centromere organization on chromosome and genome evolution in the plant genusCuscuta
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Jana Čížková, Petr Novák, Tae-Soo Jang, Jaroslav Doležel, Ludmila Oliveira, Pavel Neumann, Katarzyna Stelmach, Sonja Klemme, Andrea Koblížková, and Jiří Macas
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Whole genome sequencing ,Genome evolution ,biology ,Physiology ,Centromere ,Chromosome ,Cuscuta ,Plant Science ,biology.organism_classification ,Genome ,Evolution, Molecular ,Evolutionary biology ,Holocentric ,Repeated sequence ,Life Style ,Genome size ,Genome, Plant ,Phylogeny - Abstract
SummaryThe parasitic genus Cuscuta (Convolvulaceae) is exceptional among plants with respect to centromere organization, including both monocentric and holocentric chromosomes, and substantial variation in genome size and chromosome number. We investigated 12 species representing the diversity of the genus in a phylogenetic context to reveal the molecular and evolutionary processes leading to diversification of their genomes.We measured genome sizes and investigated karyotypes and centromere organization using molecular cytogenetic techniques. We also performed low-pass whole genome sequencing and comparative analysis of repetitive DNA composition.A remarkable 102-fold variation in genome sizes (342–34,734 Mbp/1C) was detected for monocentric Cuscuta species, while genomes of holocentric species were of moderate sizes (533–1,545 Mbp/1C). The genome size variation was primarily driven by the differential accumulation of repetitive sequences. The transition to holocentric chromosomes in the subgenus Cuscuta was associated with loss of histone H2A phosphorylation and elimination of centromeric retrotransposons. In addition, the basic chromosome number (x) decreased from 15 to 7, presumably due to chromosome fusions.We demonstrated that the transition to holocentricity in Cuscuta was accompanied by significant changes in epigenetic marks, chromosome number and the repetitive DNA sequence composition.
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- 2020
35. Dynamics of endoreduplication in developing barley seeds
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Yueqi Zhang, Barbara Tokarz, Jan Vrána, Anna Nowicka, Jaroslav Doležel, Dorota Weigt, Martin Kovacik, and Ales Pecinka
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0106 biological sciences ,0301 basic medicine ,Programmed cell death ,Pollination ,Physiology ,Cell Cycle ,food and beverages ,Hordeum ,Embryo ,Plant Science ,Endoreduplication ,Cell cycle ,Biology ,01 natural sciences ,Endosperm ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,Seeds ,Hordeum vulgare ,Viability assay ,010606 plant biology & botany - Abstract
Seeds are complex biological systems comprising three genetically distinct tissues: embryo, endosperm, and maternal tissues (including seed coats and pericarp) nested inside one another. Cereal grains represent a special type of seeds, with the largest part formed by the endosperm, a specialized triploid tissue ensuring embryo protection and nourishment. We investigated dynamic changes in DNA content in three of the major seed tissues from the time of pollination up to the dry seed. We show that the cell cycle is under strict developmental control in different seed compartments. After an initial wave of active cell division, cells switch to endocycle and most endoreduplication events are observed in the endosperm and seed maternal tissues. Using different barley cultivars, we show that there is natural variation in the kinetics of this process. During the terminal stages of seed development, specific and selective loss of endoreduplicated nuclei occurs in the endosperm. This is accompanied by reduced stability of the nuclear genome, progressive loss of cell viability, and finally programmed cell death. In summary, our study shows that endopolyploidization and cell death are linked phenomena that frame barley grain development.
- Published
- 2020
36. Identification of New QTLs for Dietary Fiber Content in Aegilops biuncialis
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László Ivanizs, Ilaria Marcotuli, Marianna Rakszegi, Balázs Kalapos, Kitti Szőke-Pázsi, András Farkas, Edina Türkösi, Eszter Gaál, Klaudia Kruppa, Péter Kovács, Éva Darkó, Éva Szakács, Mahmoud Said, Petr Cápal, Jaroslav Doležel, Agata Gadaleta, and István Molnár
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Inorganic Chemistry ,Organic Chemistry ,food and beverages ,General Medicine ,Physical and Theoretical Chemistry ,Molecular Biology ,Spectroscopy ,Catalysis ,Aegilops biuncialis ,dietary fiber ,β-glucan ,DArTseq analysis ,genome-wide association study (GWAS) ,Computer Science Applications - Abstract
Grain dietary fiber content is an important health-promoting trait of bread wheat. A dominant dietary fiber component of wheat is the cell wall polysaccharide arabinoxylan and the goatgrass Aegilops biuncialis has high β-glucan content, which makes it an attractive gene source to develop wheat lines with modified fiber composition. In order to support introgression breeding, this work examined genetic variability in grain β-glucan, pentosan, and protein content in a collection of Ae. biuncialis. A large variation in grain protein and edible fiber content was revealed, reflecting the origin of Ae. biuncialis accessions from different eco-geographical habitats. Association analysis using DArTseq-derived SNPs identified 34 QTLs associated with β-glucan, pentosan, water-extractable pentosan, and protein content. Mapping the markers to draft chromosome assemblies of diploid progenitors of Ae. biuncialis underlined the role of genes on chromosomes 1Mb, 4Mb, and 5Mb in the formation of grain β-glucan content, while other QTLs on chromosome groups 3, 6, and 1 identified genes responsible for total- and water-extractable pentosan content. Functional annotation of the associated marker sequences identified fourteen genes, nine of which were identified in other monocots. The QTLs and genes identified in the present work are attractive targets for chromosome-mediated gene transfer to improve the health-promoting properties of wheat-derived foods.
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- 2022
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37. Genomic sequencing of Thinopyrum elongatum chromosome arm 7EL, carrying fusarium head blight resistance, and characterization of its impact on the transcriptome of the introgressed line CS-7EL
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David, Konkin, Ya-Chih, Hsueh, Morgan, Kirzinger, Marie, Kubaláková, Aparna, Haldar, Margaret, Balcerzak, Fangpu, Han, George, Fedak, Jaroslav, Doležel, Andrew, Sharpe, and Thérèse, Ouellet
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disease resistance ,non-coding RNA ,Triticum aestivum ,food and beverages ,Genomics ,Thinopyrum elongatum ,Poaceae ,Chromosomes, Plant ,Fusarium graminearum ,Fusarium ,alien introgression ,Genetics ,RNA-seq ,transcriptome ,Plant Diseases ,Biotechnology - Abstract
Background The tall wheatgrass species Thinopyrum elongatum carries a strong fusarium head blight (FHB) resistance locus located on the long arm of chromosome 7 (7EL) as well as resistance to leaf and stem rusts, all diseases with a significant impact on wheat production. Towards understanding the contribution of Th. elongatum 7EL to improvement of disease resistance in wheat, the genomic sequence of the 7EL fragment present in the wheat Chinese Spring (CS) telosomic addition line CS-7EL was determined and the contribution and impact of 7EL on the rachis transcriptome during FHB infection was compared between CS and CS-7EL. Results We assembled the Th. elongatum 7EL chromosome arm using a reference-guided approach. Combining this assembly with the available reference sequence for CS hexaploid wheat provided a reliable reference for interrogating the transcriptomic differences in response to infection conferred by the 7EL fragment. Comparison of the transcriptomes of rachis tissues from CS and CS-7EL showed expression of Th. elongatum transcripts as well as modulation of wheat transcript expression profiles in the CS-7EL line. Expression profiles at 4 days after infection with Fusarium graminearum, the causal agent of FHB, showed an increased in expression of genes associated with an effective defense response, in particular glucan endo-1,3-beta-glucosidases and chitinases, in the FHB-resistant line CS-7EL while there was a larger increase in differential expression for genes associated with the level of fungal infection in the FHB-susceptible line CS. One hundred and seven 7EL transcripts were expressed in the smallest 7EL region defined to carry FHB resistance. Conclusion 7EL contributed to CS-7EL transcriptome by direct expression and through alteration of wheat transcript profiles. FHB resistance in CS-7EL was associated with transcriptome changes suggesting a more effective defense response. A list of candidate genes for the FHB resistance locus on 7EL has been established.
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- 2022
38. Identification of New QTLs for Dietary Fiber Content in
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László, Ivanizs, Ilaria, Marcotuli, Marianna, Rakszegi, Balázs, Kalapos, Kitti, Szőke-Pázsi, András, Farkas, Edina, Türkösi, Eszter, Gaál, Klaudia, Kruppa, Péter, Kovács, Éva, Darkó, Éva, Szakács, Mahmoud, Said, Petr, Cápal, Jaroslav, Doležel, Agata, Gadaleta, and István, Molnár
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Dietary Fiber ,Plant Breeding ,beta-Glucans ,Aegilops ,Quantitative Trait Loci ,Water ,Genes, Plant ,Triticum - Abstract
Grain dietary fiber content is an important health-promoting trait of bread wheat. A dominant dietary fiber component of wheat is the cell wall polysaccharide arabinoxylan and the goatgrass
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- 2022
39. Transfer of the
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Edina, Türkösi, László, Ivanizs, András, Farkas, Eszter, Gaál, Klaudia, Kruppa, Péter, Kovács, Éva, Szakács, Kitti, Szőke-Pázsi, Mahmoud, Said, Petr, Cápal, Simon, Griffiths, Jaroslav, Doležel, and István, Molnár
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Effective utilization of genetic diversity in wild relatives to improve wheat requires recombination between wheat and alien chromosomes. However, this is suppressed by the
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- 2022
40. Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi‐omics approach
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Zuzana Tulpová, Aleš Kovařík, Helena Toegelová, Pavla Navrátilová, Veronika Kapustová, Eva Hřibová, Jan Vrána, Jiří Macas, Jaroslav Doležel, and Hana Šimková
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Polyploidy ,RNA, Ribosomal ,Genetics ,Bread ,Plant Science ,DNA, Ribosomal ,Agronomy and Crop Science ,Triticum - Abstract
Three out of four RNA components of ribosomes are encoded by 45S ribosomal DNA (rDNA) loci, which are organized as long head-to-tail tandem arrays of nearly identical units, spanning several megabases of sequence. Due to this structure, the rDNA loci are the major sources of gaps in genome assemblies, and gene copy number, sequence composition, and expression status of particular arrays remain elusive, especially in complex genomes harboring multiple loci. Here we conducted a multi-omics study to decipher the 45S rDNA loci in hexaploid bread wheat. Coupling chromosomal genomics with optical mapping, we reconstructed individual rDNA arrays, enabling locus-specific analyses of transcription activity and methylation status from RNA- and bisulfite-sequencing data. We estimated a total of 6,650 rDNA units in the bread wheat genome, with approximately 2,321, 3,910, 253, and 50 gene copies located in short arms of chromosomes 1B, 6B, 5D, and 1A, respectively. Only 1B and 6B loci contributed substantially to rRNA transcription at a roughly 2:1 ratio. The ratio varied among five tissues analyzed (embryo, coleoptile, root tip, primary leaf, mature leaf), being the highest (2.64:1) in mature leaf and lowest (1.72:1) in coleoptile. Cytosine methylation was considerably higher in CHG context in the silenced 5D locus as compared with the active 1B and 6B loci. In conclusion, a fine genomic organization and tissue-specific expression of rDNA loci were deciphered, for the first time, in a complex polyploid species. The results are discussed in the context of wheat evolution and transcription regulation.
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- 2022
41. Migration of repetitive DNAs during evolution of the permanent translocation heterozygosity in the oyster plant (Tradescantia section Rhoeo)
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Hieronim Golczyk, Eva Hřibová, Jaroslav Doležel, Ángeles Cuadrado, Frauke Garbsch, Stephan Greiner, Monika Janeczko, Marek Szklarczyk, Maciej Masłyk, and Konrad Kubiński
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Heterochromatin ,Tradescantia ,Genetics ,Animals ,DNA, Ribosomal ,Ostreidae ,Genetics (clinical) ,In Situ Hybridization, Fluorescence ,Translocation, Genetic ,Repetitive Sequences, Nucleic Acid - Abstract
Due to translocation heterozygosity for all chromosomes in the cell complement, the oyster plant (Tradescantia spathacea) forms a complete meiotic ring. It also shows Rabl-arrangement at interphase, featured by polar centromere clustering. We demonstrate that the pericentromeric regions of the oyster plant are homogenized in concert by three subtelomeric sequences: 45S rDNA, (TTTAGGG)n motif, and TSrepI repeat. The Rabl-based clustering of pericentromeric regions may have been an excellent device to combine the subtelomere-pericentromere sequence migration (via inversions) with the pericentromere-pericentromere DNA movement (via whole arm translocations) that altogether led to the concerted homogenization of all the pericentromeric domains by the subtelomeric sequences. We also show that the repetitive sequence landscape of interstitial chromosome regions contains many loci consisting of Arabidopsis-type telomeric sequence or of TSrepI repeat, and it is extensively heterozygous. However, the sequence arrangement on some chromosomal arms suggest segmental inversions that are fully or partially homozygous, a fact that could be explained if the inversions started to create linkages already in a bivalent-forming ancestor. Remarkably, the subterminal TSrepI loci reside exclusively on the longer arms that could be due to sharing sequences between similarly-sized chromosomal arms in the interphase nucleus. Altogether, our study spotlights the supergene system of the oyster plant as an excellent model to link complex chromosome rearrangements, evolution of repetitive sequences, and nuclear architecture.
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- 2022
42. Karyotype Differentiation in Cultivated Chickpea Revealed by Oligopainting Fluorescence in situ Hybridization
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Alžběta Doležalová, Lucia Sládeková, Denisa Šimoníková, Kateřina Holušová, Miroslava Karafiátová, Rajeev K. Varshney, Jaroslav Doležel, and Eva Hřibová
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desi type ,Cicer arietinum L ,oligopainting FISH ,Plant culture ,Plant Science ,chromosome identification ,chromosome translocation ,kabuli type ,SB1-1110 - Abstract
Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of the chickpea genome at the chromosomal level, including the long-range molecular chromosome organization, is limited. Earlier cytogenetic studies in chickpea suffered from a limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes in situ. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea. We demonstrate that even draft genome sequences are adequate to develop oligo-fluorescence in situ hybridization (FISH) barcodes for the identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for the identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both kabuli and desi reference genomes. Thus, oligo-FISH appears as a powerful tool not only for comparative karyotyping but also for the validation of genome assemblies.
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- 2022
43. Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62
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Guotai Yu, Oadi Matny, Nicolas Champouret, Burkhard Steuernagel, Matthew J. Moscou, Inmaculada Hernández-Pinzón, Phon Green, Sadiye Hayta, Mark Smedley, Wendy Harwood, Ngonidzashe Kangara, Yajuan Yue, Catherine Gardener, Mark J. Banfield, Pablo D. Olivera, Cole Welchin, Jamie Simmons, Eitan Millet, Anna Minz-Dub, Moshe Ronen, Raz Avni, Amir Sharon, Mehran Patpour, Annemarie F. Justesen, Murukarthick Jayakodi, Axel Himmelbach, Nils Stein, Shuangye Wu, Jesse Poland, Jennifer Ens, Curtis Pozniak, Miroslava Karafiátová, István Molnár, Jaroslav Doležel, Eric R. Ward, T. Lynne Reuber, Jonathan D. G. Jones, Martin Mascher, Brian J. Steffenson, and Brande B. H. Wulff
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Plant Breeding ,Multidisciplinary ,Molecular engineering in plants ,Agricultural genetics ,Biotic ,Plant evolution ,Aegilops ,Basidiomycota ,General Physics and Astronomy ,food and beverages ,General Chemistry ,Genes, Plant ,General Biochemistry, Genetics and Molecular Biology ,Triticum ,Disease Resistance ,Plant Diseases - Abstract
The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.
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- 2022
44. Cytogenetic insights into Festulolium
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J. Majka, David Kopecký, Jaroslav Doležel, and M. Majka
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0106 biological sciences ,0301 basic medicine ,Abiotic component ,Festuca ,food and beverages ,Introgression ,Plant Science ,Horticulture ,Biology ,biology.organism_classification ,01 natural sciences ,Genome ,Breed ,Lolium ,03 medical and health sciences ,030104 developmental biology ,Agronomy ,Cultivar ,010606 plant biology & botany ,Hybrid - Abstract
Climate change calls for new methods and plant materials to breed crops adapted to new environmental conditions. Sustainable forage and amenity grass production during periods of severe drought and heat waves during summer, and unequal distribution of precipitation over the year will require drought-tolerant genotypes. However, high-yielding ryegrasses (Lolium spp.), which are the most commonly used grass species, suffer during abiotic stresses. Introgression of drought and heat tolerance from closely related fescues (Festuca spp.) offers an opportunity to develop superior hybrid cultivars to mitigate the negative impact of climate change. Intergeneric cross-hybridization and the development of Festulolium (Festuca × Lolium) hybrids was initiated 100 years ago and resulted in registration of almost one hundred cultivars. For a long time, their genome composition was not known and was debated by breeders and geneticists. In the last three decades, molecular cytogenetic and genomic approaches have enabled their detailed characterization. These studies revealed a gradual replacement of Festuca chromosomes by those of Lolium in consecutive generations leading to an almost complete elimination of Festuca chromatin in the introgression forms. On the other hand, amphiploid cultivars seem to be more stable with the optimal proportions of the Lolium to Festuca genomes at about 2:1. In this mini review, we discuss recent advances in the analysis of the genome composition of Festulolium hybrids with a specific focus on genome (in)stability.
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- 2020
45. DNA replication and chromosome positioning throughout the interphase in three-dimensional space of plant nuclei
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Alžběta Němečková, Jan Vrána, Eva Hřibová, Jaroslav Doležel, and Veronika Koláčková
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Cell Nucleus ,DNA Replication ,Replication timing ,Euchromatin ,Physiology ,Heterochromatin ,Centromere ,DNA replication ,Interphase Chromosome ,Plant Science ,Biology ,Evolutionary biology ,DNA Replication Timing ,Chromosome Positioning ,Interphase ,Genome size ,Genome, Plant - Abstract
Despite much recent progress, our understanding of the principles of plant genome organization and its dynamics in three-dimensional space of interphase nuclei remains surprisingly limited. Notably, it is not clear how these processes could be affected by the size of a plant’s nuclear genome. In this study, DNA replication timing and interphase chromosome positioning were analyzed in seven Poaceae species that differ in their genome size. To provide a comprehensive picture, a suite of advanced, complementary methods was used: labeling of newly replicated DNA by ethynyl-2'-deoxyuridine, isolation of nuclei at particular cell cycle phases by flow cytometric sorting, three-dimensional immunofluorescence in situ hybridization, and confocal microscopy. Our results revealed conserved dynamics of DNA replication in all species, and a similar replication timing order for telomeres and centromeres, as well as for euchromatin and heterochromatin regions, irrespective of genome size. Moreover, stable chromosome positioning was observed while transitioning through different stages of interphase. These findings expand upon earlier studies in suggesting that a more complex interplay exists between genome size, organization of repetitive DNA sequences along chromosomes, and higher order chromatin structure and its maintenance in interphase, albeit controlled by currently unknown factors.
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- 2020
46. Development of oligonucleotide probes for FISH karyotyping in Haynaldia villosa, a wild relative of common wheat
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Haojie Sun, Jia Lei, Xiue Wang, Jaroslav Doležel, Wentao Wan, Jin Xiao, Haiyan Wang, Yuan Chunxia, Jiawen Zhou, and Miroslava Karafiátová
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0106 biological sciences ,0301 basic medicine ,Plant Science ,01 natural sciences ,DNA sequencing ,lcsh:Agriculture ,03 medical and health sciences ,Tandem repeat ,Tandem DNA repeats ,medicine ,Common wheat ,lcsh:Agriculture (General) ,Genetics ,Villosa ,biology ,medicine.diagnostic_test ,Oligonucleotide ,Oligonucleotide probes ,lcsh:S ,Chromosome ,food and beverages ,Karyotype ,Haynaldia villosa ,biology.organism_classification ,lcsh:S1-972 ,Chromosome identification ,030104 developmental biology ,Agronomy and Crop Science ,010606 plant biology & botany ,Fluorescence in situ hybridization - Abstract
Haynaldia villosa is a wild relative of wheat and a valuable gene resource for wheat improvement. Owing to the limited number of probes available for fluorescence in situ hybridization (FISH), the resolution at which the karyotype of H. villosa can be characterized is poor, hampering accurate characterization of small segmental alien introgressions. We designed ten oligonucleotide probes using tandem repeats in DNA sequences derived from the short arm of H. villosa chromosome 6V (6VS). FISH with seven of them resulted in clear signals on H. villosa chromosomes. Using these, we constructed FISH karyotypes for H. villosa using oligo-6VS-1 and oligo-6VS-35 oligonucleotides and characterized the distribution of the two probes in five different H. villosa accessions. The new FISH probes can efficiently characterize H. villosa introgressions into wheat.
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- 2020
47. A flow cytometry-based analysis to establish a cell cycle synchronization protocol for Saccharum spp
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Xiangxiong Gao, Jaroslav Doležel, Zhiqiang Wang, Muqing Zhang, Kai Zeng, Shan Yang, Ling Luo, Zuhu Deng, and Qian Wang
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0106 biological sciences ,0301 basic medicine ,Cell biology ,Time Factors ,Mitotic index ,lcsh:Medicine ,Buffers ,Biology ,01 natural sciences ,Article ,Chromosomes, Plant ,Microtubule polymerization ,Saccharum ,03 medical and health sciences ,Lysis buffer ,Mitotic Index ,Hydroxyurea ,Cell synchronization ,lcsh:Science ,Metaphase ,Nitrobenzenes ,Multidisciplinary ,Cell Cycle ,lcsh:R ,Temperature ,Chromosome ,Organothiophosphorus Compounds ,Genomics ,Flow Cytometry ,biology.organism_classification ,Horticulture ,030104 developmental biology ,lcsh:Q ,Ploidy ,Plant sciences ,Genome, Plant ,010606 plant biology & botany - Abstract
Modern sugarcane is an unusually complex heteroploid crop, and its genome comprises two or three subgenomes. To reduce the complexity of sugarcane genome research, the ploidy level and number of chromosomes can be reduced using flow chromosome sorting. However, a cell cycle synchronization (CCS) protocol for Saccharum spp. is needed that maximizes the accumulation of metaphase chromosomes. For flow cytometry analysis in this study, we optimized the lysis buffer, hydroxyurea(HU) concentration, HU treatment time and recovery time for sugarcane. We determined the mitotic index by microscopic observation and calculation. We found that WPB buffer was superior to other buffers for preparation of sugarcane nuclei suspensions. The optimal HU treatment was 2 mM for 18 h at 25 °C, 28 °C and 30 °C. Higher recovery treatment temperatures were associated with shorter recovery times (3.5 h, 2.5 h and 1.5 h at 25 °C, 28 °C and 30 °C, respectively). The optimal conditions for treatment with the inhibitor of microtubule polymerization, amiprophos-methyl (APM), were 2.5 μM for 3 h at 25 °C, 28 °C and 30 °C. Meanwhile, preliminary screening of CCS protocols for Badila were used for some main species of genus Saccharum at 25 °C, 28 °C and 30 °C, which showed that the average mitotic index decreased from 25 °C to 30 °C. The optimal sugarcane CCS protocol that yielded a mitotic index of >50% in sugarcane root tips was: 2 mM HU for 18 h, 0.1 X Hoagland’s Solution without HU for 3.5 h, and 2.5 μM APM for 3.0 h at 25 °C. The CCS protocol defined in this study should accelerate the development of genomic research and cytobiology research in sugarcane.
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- 2020
48. Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat
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Klaus F. X. Meyer, O. P. Gupta, Priti Sharma, Parveen Chhuneja, Kuldeep Singh, Parampreet Kaur, J. P. Khurana, Jan Vrána, Satinder Kaur, Bharat Yadav, Bikram S. Gill, Hana Šimková, Ajay Kumar Mahato, Inderjit Singh Yadav, N. K. Singh, Jaroslav Doležel, and Suruchi Jindal
- Subjects
0301 basic medicine ,Genetics ,food and beverages ,Sequence assembly ,Chromosome ,General Medicine ,Marker-assisted selection ,Biology ,Genome ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Genetic linkage ,030220 oncology & carcinogenesis ,Genetic variability ,Ploidy ,Molecular Biology ,Gene - Abstract
Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.
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- 2020
49. Mitotic chromosome organization: General rules meet species-specific variability
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Tomáš Beseda, Petr Cápal, Veit Schubert, Ivona Kubalová, Hana Šimková, and Jaroslav Doležel
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lcsh:Biotechnology ,Condensin ,Biophysics ,Review Article ,Biology ,Biochemistry ,Chromosome conformation capture ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,lcsh:TP248.13-248.65 ,Chromosome condensation ,Chromosome scaffold ,Genetics ,Chromatin fiber folding ,Mitosis ,030304 developmental biology ,Chromatin Fiber ,Structural maintenance of chromosomes proteins ,0303 health sciences ,Cohesin ,Chromosome ,Computer Science Applications ,Chromatin ,Evolutionary biology ,030220 oncology & carcinogenesis ,Premature chromosome condensation ,biology.protein ,Chromosome cavities ,Biotechnology - Abstract
Research on the formation of mitotic chromosomes from interphase chromatin domains, ongoing for several decades, made significant progress in recent years. It was stimulated by the development of advanced microscopic techniques and implementation of chromatin conformation capture methods that provide new insights into chromosome ultrastructure. This review aims to summarize and compare several models of chromatin fiber folding to form mitotic chromosomes and discusses them in the light of the novel findings. Functional genomics studies in several organisms confirmed condensins and cohesins as the major players in chromosome condensation. Here we compare available data on the role of these proteins across lower and higher eukaryotes and point to differences indicating evolutionary different pathways to shape mitotic chromosomes. Moreover, we discuss a controversial phenomenon of the mitotic chromosome ultrastructure – chromosome cavities – and using our super-resolution microscopy data, we contribute to its elucidation.
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- 2020
50. Reference genome-assisted identification of stem rust resistance gene Sr62 encoding a tandem kinase
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Guotai Yu, Oadi Matny, Nicolas Champouret, Burkhard Steuernagel, Matthew J. Moscou, Inmaculada Hernández-Pinzón, Phon Green, Sadiye Hayta, Mark Smedley, Wendy Harwood, Ngonidzashe Kangara, Yajuan Yue, Catherine Gardener, Mark J. Banfield, Pablo D. Olivera, Cole Welchin, Jamie Simmons, Eitan Millet, Anna Minz-Dub, Moshe Ronen, Raz Avni, Amir Sharon, Mehran Patpour, Annemarie F. Justesen, Murukarthick Jayakodi, Axel Himmelbach, Nils Stein, Shuangye Wu, Jesse Poland, Jennifer Ens, Curtis Pozniak, Miroslava Karafiátová, István Molnár, Jaroslav Doležel, Eric R. Ward, T Lynne Reuber, Jonathan D. G. Jones, Martin Mascher, Brian J. Steffenson, and Brande B. H. Wulff
- Subjects
food and beverages - Abstract
The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. We developed a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and used positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which was also transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines showed high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.
- Published
- 2021
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