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1,369 results on '"Doležel, Jaroslav"'

1. Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Author

Li, Yinghui, Wei, Zhen-Zhen, Sela, Hanan, Govta, Liubov, Klymiuk, Valentyna, Roychowdhury, Rajib, Chawla, Harmeet Singh, Ens, Jennifer, Wiebe, Krystalee, Bocharova, Valeria, Ben-David, Roi, Pawar, Prerna B, Zhang, Yuqi, Jaiwar, Samidha, Molnár, István, Doležel, Jaroslav, Coaker, Gitta, Pozniak, Curtis J, and Fahima, Tzion

Subjects
Plant Biology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Triticum, Genes, Plant, Chromosome Mapping, Cloning, Molecular, Multigene Family, Plant biology
Abstract

Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

Published
2024

2. A single NLR gene confers resistance to leaf and stripe rust in wheat

Author

Sharma, Davinder, Avni, Raz, Gutierrez-Gonzalez, Juan, Kumar, Rakesh, Sela, Hanan, Prusty, Manas Ranjan, Shatil-Cohen, Arava, Molnár, István, Holušová, Kateřina, Said, Mahmoud, Doležel, Jaroslav, Millet, Eitan, Khazan-Kost, Sofia, Landau, Udi, Bethke, Gerit, Sharon, Or, Ezrati, Smadar, Ronen, Moshe, Maatuk, Oxana, Eilam, Tamar, Manisterski, Jacob, Ben-Yehuda, Pnina, Anikster, Yehoshua, Matny, Oadi, Steffenson, Brian J., Mascher, Martin, Brabham, Helen J., Moscou, Matthew J., Liang, Yong, Yu, Guotai, Wulff, Brande B. H., Muehlbauer, Gary, Minz-Dub, Anna, and Sharon, Amir

Published
2024
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12. Chromosome evolution and the genetic basis of agronomically important traits in greater yam

Author

Bredeson, Jessen V, Lyons, Jessica B, Oniyinde, Ibukun O, Okereke, Nneka R, Kolade, Olufisayo, Nnabue, Ikenna, Nwadili, Christian O, Hřibová, Eva, Parker, Matthew, Nwogha, Jeremiah, Shu, Shengqiang, Carlson, Joseph, Kariba, Robert, Muthemba, Samuel, Knop, Katarzyna, Barton, Geoffrey J, Sherwood, Anna V, Lopez-Montes, Antonio, Asiedu, Robert, Jamnadass, Ramni, Muchugi, Alice, Goodstein, David, Egesi, Chiedozie N, Featherston, Jonathan, Asfaw, Asrat, Simpson, Gordon G, Doležel, Jaroslav, Hendre, Prasad S, Van Deynze, Allen, Kumar, Pullikanti Lava, Obidiegwu, Jude E, Bhattacharjee, Ranjana, and Rokhsar, Daniel S

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Horticultural Production, Human Genome, Chromosomes, Dioscorea, Humans, Plant Breeding, Plant Tubers, Quantitative Trait Loci
Abstract

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Published
2022

13. The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase

Author

Yu, Guotai, Matny, Oadi, Gourdoupis, Spyridon, Rayapuram, Naganand, Aljedaani, Fatimah R., Wang, Yan L., Nürnberger, Thorsten, Johnson, Ryan, Crean, Emma E., Saur, Isabel M.-L., Gardener, Catherine, Yue, Yajuan, Kangara, Ngonidzashe, Steuernagel, Burkhard, Hayta, Sadiye, Smedley, Mark, Harwood, Wendy, Patpour, Mehran, Wu, Shuangye, Poland, Jesse, Jones, Jonathan D. G., Reuber, T. Lynne, Ronen, Moshe, Sharon, Amir, Rouse, Matthew N., Xu, Steven, Holušová, Kateřina, Bartoš, Jan, Molnár, István, Karafiátová, Miroslava, Hirt, Heribert, Blilou, Ikram, Jaremko, Łukasz, Doležel, Jaroslav, Steffenson, Brian J., and Wulff, Brande B. H.

Published
2023
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19. Direct evidence for crossover and chromatid interference in meiosis of two plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei)

Author

Ferreira, Marco Tulio Mendes, Glombik, Marek, Perničková, Kateřina, Duchoslav, Martin, Scholten, Olga, Karafiátová, Miroslava, Techio, Vania Helena, Doležel, Jaroslav, Lukaszewski, Adam J, and Kopecký, David

Subjects
Biological Sciences, Genetics, Biotechnology, Chromatids, Crossing Over, Genetic, Festuca, Lolium, Meiosis, Onions, Centromere, chromatid interference, crossover interference, homoeologous chromosome, hybrid, meiosis, recombination, Plant Biology, Crop and Pasture Production, Plant Biology & Botany, Crop and pasture production, Biochemistry and cell biology, Plant biology
Abstract

Crossing over, in addition to its strictly genetic role, also performs a critical mechanical function, by bonding homologues in meiosis. Hence, it is responsible for an orderly reduction of the chromosome number. As such, it is strictly controlled in frequency and distribution. The well-known crossover control is positive crossover interference which reduces the probability of a crossover in the vicinity of an already formed crossover. A poorly studied aspect of the control is chromatid interference. Such analyses are possible in very few organisms as they require observation of all four products of a single meiosis. Here, we provide direct evidence of chromatid interference. Using in situ probing in two interspecific plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei) during anaphase I, we demonstrate that the involvement of four chromatids in double crossovers is significantly more frequent than expected (64% versus 25%). We also provide a physical measure of the crossover interference distance, covering ~30-40% of the relative chromosome arm length, and show that the centromere acts as a barrier for crossover interference. The two arms of a chromosome appear to act as independent units in the process of crossing over. Chromatid interference has to be seriously addressed in genetic mapping approaches and further studies.

Published
2021

20. The giant diploid faba genome unlocks variation in a global protein crop

Author

Jayakodi, Murukarthick, Golicz, Agnieszka A., Kreplak, Jonathan, Fechete, Lavinia I., Angra, Deepti, Bednář, Petr, Bornhofen, Elesandro, Zhang, Hailin, Boussageon, Raphaël, Kaur, Sukhjiwan, Cheung, Kwok, Čížková, Jana, Gundlach, Heidrun, Hallab, Asis, Imbert, Baptiste, Keeble-Gagnère, Gabriel, Koblížková, Andrea, Kobrlová, Lucie, Krejčí, Petra, Mouritzen, Troels W., Neumann, Pavel, Nadzieja, Marcin, Nielsen, Linda Kærgaard, Novák, Petr, Orabi, Jihad, Padmarasu, Sudharsan, Robertson-Shersby-Harvie, Tom, Robledillo, Laura Ávila, Schiemann, Andrea, Tanskanen, Jaakko, Törönen, Petri, Warsame, Ahmed O., Wittenberg, Alexander H. J., Himmelbach, Axel, Aubert, Grégoire, Courty, Pierre-Emmanuel, Doležel, Jaroslav, Holm, Liisa U., Janss, Luc L., Khazaei, Hamid, Macas, Jiří, Mascher, Martin, Smýkal, Petr, Snowdon, Rod J., Stein, Nils, Stoddard, Frederick L., Stougaard, Jens, Tayeh, Nadim, Torres, Ana M., Usadel, Björn, Schubert, Ingo, O’Sullivan, Donal Martin, Schulman, Alan H., and Andersen, Stig Uggerhøj

Published
2023
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23. The genome of cowpea (Vigna unguiculata [L.] Walp.)

Author

Lonardi, Stefano, Muñoz‐Amatriaín, María, Liang, Qihua, Shu, Shengqiang, Wanamaker, Steve I, Lo, Sassoum, Tanskanen, Jaakko, Schulman, Alan H, Zhu, Tingting, Luo, Ming‐Cheng, Alhakami, Hind, Ounit, Rachid, Hasan, Abid Md, Verdier, Jerome, Roberts, Philip A, Santos, Jansen RP, Ndeve, Arsenio, Doležel, Jaroslav, Vrána, Jan, Hokin, Samuel A, Farmer, Andrew D, Cannon, Steven B, and Close, Timothy J

Subjects
Genetics, Biotechnology, Chromosome Mapping, Chromosomes, Plant, DNA, Plant, Genes, Plant, Genome Size, Genome, Plant, Phaseolus, Retroelements, Sequence Analysis, DNA, Synteny, Vigna, chromosomal inversion, cowpea, domestication, genome annotation, genome evolution, genome size, next-generation sequencing, legumes, Phaseolus vulgaris, repetitive elements, Vigna unguiculata, Phaseolus vulgaris, Vigna unguiculata, Biochemistry and Cell Biology, Plant Biology, Plant Biology & Botany
Abstract

Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.

Published
2019

24. Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long-Read Technologies.

Author

Tulpová, Zuzana, Toegelová, Helena, Lapitan, Nora LV, Peairs, Frank B, Macas, Jiří, Novák, Petr, Lukaszewski, Adam J, Kopecký, David, Mazáčová, Mira, Vrána, Jan, Holušová, Kateřina, Leroy, Philippe, Doležel, Jaroslav, and Šimková, Hana

Subjects
Chromosomes, Plant, Animals, Aphids, Triticum, DNA, Plant, Genetic Markers, Chromosome Mapping, Sequence Analysis, DNA, Plant Diseases, Genes, Plant, Disease Resistance, Biotechnology, HIV/AIDS, Genetics, Plant Biology, Crop and Pasture Production
Abstract

Russian wheat aphid (RWA) ( Kurdjumov) is a serious invasive pest of small-grain cereals and many grass species. An efficient strategy to defy aphid attacks is to identify sources of natural resistance and transfer resistance genes into susceptible crop cultivars. Revealing the genes helps understand plant defense mechanisms and engineer plants with durable resistance to the pest. To date, more than 15 RWA resistance genes have been identified in wheat ( L.) but none of them has been cloned. Previously, we genetically mapped the RWA resistance gene into an interval of 0.83 cM on the short arm of chromosome 7D and spanned it with five bacterial artificial chromosome (BAC) clones. Here, we used a targeted strategy combining traditional approaches toward gene cloning (genetic mapping and sequencing of BAC clones) with novel technologies, including optical mapping and long-read nanopore sequencing. The latter, with reads spanning the entire length of a BAC insert, enabled us to assemble the whole region, a task that was not achievable with short reads. Long-read optical mapping validated the DNA sequence in the interval and revealed a difference in the locus organization between resistant and susceptible genotypes. The complete and accurate sequence of the region facilitated the identification of new markers and precise annotation of the interval, revealing six high-confidence genes. Identification of as the most likely candidate opens an avenue for its validation through functional genomics approaches.

Published
2019

25. Instability of Alien Chromosome Introgressions in Wheat Associated with Improper Positioning in the Nucleus.

Author

Perničková, Kateřina, Koláčková, Veronika, Lukaszewski, Adam J, Fan, Chaolan, Vrána, Jan, Duchoslav, Martin, Jenkins, Glyn, Phillips, Dylan, Šamajová, Olga, Sedlářová, Michaela, Šamaj, Jozef, Doležel, Jaroslav, and Kopecký, David

Subjects
Chromosomes, Plant, Cell Nucleolus, Centromere, Telomere, Triticum, Chromosomal Instability, In Situ Hybridization, Fluorescence, Mitosis, 3D-FISH, chromatin, genome stability, hybrid, introgression, nucleus, rye, wheat, Chromosomes, Plant, In Situ Hybridization, Fluorescence, Other Chemical Sciences, Genetics, Other Biological Sciences, Chemical Physics
Abstract

Alien introgressions introduce beneficial alleles into existing crops and hence, are widely used in plant breeding. Generally, introgressed alien chromosomes show reduced meiotic pairing relative to the host genome, and may be eliminated over generations. Reduced pairing appears to result from a failure of some telomeres of alien chromosomes to incorporate into the leptotene bouquet at the onset of meiosis, thereby preventing chiasmate pairing. In this study, we analysed somatic nuclei of rye introgressions in wheat using 3D-FISH and found that while introgressed rye chromosomes or chromosome arms occupied discrete positions in the Rabl's orientation similar to chromosomes of the wheat host, their telomeres frequently occupied positions away from the nuclear periphery. The frequencies of such abnormal telomere positioning were similar to the frequencies of out-of-bouquet telomere positioning at leptotene, and of pairing failure at metaphase I. This study indicates that improper positioning of alien chromosomes that leads to reduced pairing is not a strictly meiotic event but rather a consequence of a more systemic problem. Improper positioning in the nuclei probably impacts the ability of introgressed chromosomes to migrate into the telomere bouquet at the onset of meiosis, preventing synapsis and chiasma establishment, and leading to their gradual elimination over generations.

Published
2019

27. Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution

Author

Blavet, Nicolas, Yang, Hua, Su, Handong, Solanský, Pavel, Douglas, Ryan N., Karafiátová, Miroslava, Šimková, Lucie, Zhang, Jing, Liu, Yalin, Hou, Jie, Shi, Xiaowen, Chen, Chen, El-Walid, Mohamed, McCaw, Morgan E., Albert, Patrice S., Gao, Zhi, Zhao, Changzeng, Ben-Zvi, Gil, Glick, Lior, Kol, Guy, Shi, Jinghua, Vrána, Jan, Šimková, Hana, Lamb, Jonathan C., Newton, Kathleen, Dawe, R. Kelly, Doležel, Jaroslav, Ji, Tieming, Baruch, Kobi, Cheng, Jianlin, Han, Fangpu, Birchler, James A., and Bartoš, Jan

Published
2021

29. Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

Author

Yu, Guotai, Matny, Oadi, Champouret, Nicolas, Steuernagel, Burkhard, Moscou, Matthew J., Hernández-Pinzón, Inmaculada, Green, Phon, Hayta, Sadiye, Smedley, Mark, Harwood, Wendy, Kangara, Ngonidzashe, Yue, Yajuan, Gardener, Catherine, Banfield, Mark J., Olivera, Pablo D., Welchin, Cole, Simmons, Jamie, Millet, Eitan, Minz-Dub, Anna, Ronen, Moshe, Avni, Raz, Sharon, Amir, Patpour, Mehran, Justesen, Annemarie F., Jayakodi, Murukarthick, Himmelbach, Axel, Stein, Nils, Wu, Shuangye, Poland, Jesse, Ens, Jennifer, Pozniak, Curtis, Karafiátová, Miroslava, Molnár, István, Doležel, Jaroslav, Ward, Eric R., Reuber, T. Lynne, Jones, Jonathan D. G., Mascher, Martin, Steffenson, Brian J., and Wulff, Brande B. H.

Published
2022
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32. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Author

Beier, Sebastian, Himmelbach, Axel, Colmsee, Christian, Zhang, Xiao-Qi, Barrero, Roberto A, Zhang, Qisen, Li, Lin, Bayer, Micha, Bolser, Daniel, Taudien, Stefan, Groth, Marco, Felder, Marius, Hastie, Alex, Šimková, Hana, Staňková, Helena, Vrána, Jan, Chan, Saki, Muñoz-Amatriaín, María, Ounit, Rachid, Wanamaker, Steve, Schmutzer, Thomas, Aliyeva-Schnorr, Lala, Grasso, Stefano, Tanskanen, Jaakko, Sampath, Dharanya, Heavens, Darren, Cao, Sujie, Chapman, Brett, Dai, Fei, Han, Yong, Li, Hua, Li, Xuan, Lin, Chongyun, McCooke, John K, Tan, Cong, Wang, Songbo, Yin, Shuya, Zhou, Gaofeng, Poland, Jesse A, Bellgard, Matthew I, Houben, Andreas, Doležel, Jaroslav, Ayling, Sarah, Lonardi, Stefano, Langridge, Peter, Muehlbauer, Gary J, Kersey, Paul, Clark, Matthew D, Caccamo, Mario, Schulman, Alan H, Platzer, Matthias, Close, Timothy J, Hansson, Mats, Zhang, Guoping, Braumann, Ilka, Li, Chengdao, Waugh, Robbie, Scholz, Uwe, Stein, Nils, and Mascher, Martin

Subjects
Hordeum, Chromosome Mapping, Sequence Analysis, Genome, Plant, Genome, Plant
Abstract

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Published
2017

33. A chromosome conformation capture ordered sequence of the barley genome

Author

Mascher, Martin, Gundlach, Heidrun, Himmelbach, Axel, Beier, Sebastian, Twardziok, Sven O, Wicker, Thomas, Radchuk, Volodymyr, Dockter, Christoph, Hedley, Pete E, Russell, Joanne, Bayer, Micha, Ramsay, Luke, Liu, Hui, Haberer, Georg, Zhang, Xiao-Qi, Zhang, Qisen, Barrero, Roberto A, Li, Lin, Taudien, Stefan, Groth, Marco, Felder, Marius, Hastie, Alex, Šimková, Hana, Staňková, Helena, Vrána, Jan, Chan, Saki, Muñoz-Amatriaín, María, Ounit, Rachid, Wanamaker, Steve, Bolser, Daniel, Colmsee, Christian, Schmutzer, Thomas, Aliyeva-Schnorr, Lala, Grasso, Stefano, Tanskanen, Jaakko, Chailyan, Anna, Sampath, Dharanya, Heavens, Darren, Clissold, Leah, Cao, Sujie, Chapman, Brett, Dai, Fei, Han, Yong, Li, Hua, Li, Xuan, Lin, Chongyun, McCooke, John K, Tan, Cong, Wang, Penghao, Wang, Songbo, Yin, Shuya, Zhou, Gaofeng, Poland, Jesse A, Bellgard, Matthew I, Borisjuk, Ljudmilla, Houben, Andreas, Doležel, Jaroslav, Ayling, Sarah, Lonardi, Stefano, Kersey, Paul, Langridge, Peter, Muehlbauer, Gary J, Clark, Matthew D, Caccamo, Mario, Schulman, Alan H, Mayer, Klaus FX, Platzer, Matthias, Close, Timothy J, Scholz, Uwe, Hansson, Mats, Zhang, Guoping, Braumann, Ilka, Spannagl, Manuel, Li, Chengdao, Waugh, Robbie, and Stein, Nils

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Cell Nucleus, Centromere, Chromatin, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Chromosomes, Plant, Genetic Variation, Genome, Plant, Genomics, Haplotypes, Hordeum, Meiosis, Repetitive Sequences, Nucleic Acid, Seeds, General Science & Technology
Abstract

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

Published
2017

34. Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Author

Rabanus-Wallace, M. Timothy, Hackauf, Bernd, Mascher, Martin, Lux, Thomas, Wicker, Thomas, Gundlach, Heidrun, Baez, Mariana, Houben, Andreas, Mayer, Klaus F. X., Guo, Liangliang, Poland, Jesse, Pozniak, Curtis J., Walkowiak, Sean, Melonek, Joanna, Praz, Coraline R., Schreiber, Mona, Budak, Hikmet, Heuberger, Matthias, Steuernagel, Burkhard, Wulff, Brande, Börner, Andreas, Byrns, Brook, Čížková, Jana, Fowler, D. Brian, Fritz, Allan, Himmelbach, Axel, Kaithakottil, Gemy, Keilwagen, Jens, Keller, Beat, Konkin, David, Larsen, Jamie, Li, Qiang, Myśków, Beata, Padmarasu, Sudharsan, Rawat, Nidhi, Sesiz, Uğur, Biyiklioglu-Kaya, Sezgi, Sharpe, Andy, Šimková, Hana, Small, Ian, Swarbreck, David, Toegelová, Helena, Tsvetkova, Natalia, Voylokov, Anatoly V., Vrána, Jan, Bauer, Eva, Bolibok-Bragoszewska, Hanna, Doležel, Jaroslav, Hall, Anthony, Jia, Jizeng, Korzun, Viktor, Laroche, André, Ma, Xue-Feng, Ordon, Frank, Özkan, Hakan, Rakoczy-Trojanowska, Monika, Scholz, Uwe, Schulman, Alan H., Siekmann, Dörthe, Stojałowski, Stefan, Tiwari, Vijay K., Spannagl, Manuel, and Stein, Nils

Published
2021
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35. A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

Author

Li, Guangwei, Wang, Lijian, Yang, Jianping, He, Hang, Jin, Huaibing, Li, Xuming, Ren, Tianheng, Ren, Zhenglong, Li, Feng, Han, Xue, Zhao, Xiaoge, Dong, Lingli, Li, Yiwen, Song, Zhongping, Yan, Zehong, Zheng, Nannan, Shi, Cuilan, Wang, Zhaohui, Yang, Shuling, Xiong, Zijun, Zhang, Menglan, Sun, Guanghua, Zheng, Xu, Gou, Mingyue, Ji, Changmian, Du, Junkai, Zheng, Hongkun, Doležel, Jaroslav, Deng, Xing Wang, Stein, Nils, Yang, Qinghua, Zhang, Kunpu, and Wang, Daowen

Published
2021
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36. DArTseq genotyping facilitates the transfer of "exotic" chromatin from a Secale cereale × S. strictum hybrid into wheat.

Author

Szőke-Pázsi, Kitti, Kruppa, Klaudia, Tulpová, Zuzana, Kalapos, Balázs, Türkösi, Edina, Gaál, Eszter, Darkó, Éva, Said, Mahmoud, Farkas, András, Kovács, Péter, Ivanizs, László, Doležel, Jaroslav, Rabanus-Wallace, M. Timothy, Molnár, István, and Szakács, Éva

Subjects
RYE, IN situ hybridization, GENETIC variation, CHROMOSOMAL rearrangement, GENETIC transformation, WHEAT breeding
Abstract

Cultivated and wild species of the genus rye (Secale) are important but underexploited gene sources for increasing the genetic diversity of bread wheat. Gene transfer is possible via bridge genetic materials derived from intergeneric hybrids. During this process, it is essential to precisely identify the rye chromatin in the wheat genetic background. In the present study, backcross generation BC2F8 from a cross between Triticum aestivum (Mv9kr1) and S. cereanum ('Kriszta,' a cultivar from the artificial hybrid of S. cereale and S. strictum) was screened using in-situ hybridization (GISH and FISH) and analyzed by DArTseq genotyping in order to select potentially agronomically useful genotypes for prebreeding purposes. Of the 329,267 high-quality short sequence reads generated, 27,822 SilicoDArT and 8,842 SNP markers specific to S. cereanum 1R-7R chromosomes were identified. Heatmaps of the marker densities along the 'Lo7' rye reference pseudomolecules revealed subtle differences between the FISH- and DArTseq-based results. This study demonstrates that the "exotic" rye chromatin of S. cereanum introgressed into wheat can be reliably identified by high-throughput DArTseq genotyping. The Mv9kr1-'Kriszta' addition and translocation lines presented here may serve as valuable prebreeding genetic materials for the development of stress-tolerant or disease-resistant wheat varieties. [ABSTRACT FROM AUTHOR]

Published
2024
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38. Cytonuclear interplay in auto‐ and allopolyploids: a multifaceted perspective from the Festuca‐Lolium complex

Author

Shahbazi, Mehrdad, primary, Majka, Joanna, additional, Kubíková, Denisa, additional, Zwierzykowski, Zbigniew, additional, Glombik, Marek, additional, Wendel, Jonathan F., additional, Sharbrough, Joel, additional, Hartmann, Stephan, additional, Szecówka, Marek, additional, Doležel, Jaroslav, additional, Bartoš, Jan, additional, Kopecký, David, additional, and Kneřová, Jana, additional

Published
2024
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41. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

Author

Staňková, Helena, Hastie, Alex, Chan, Saki, Vrána, Jan, Tulpová, Zuzana, Kubaláková, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav, and Šimková, Hana

Subjects
chromosomes, flow sorting, optical mapping, physical map, sequencing, wheat, Biotechnology, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Chromosomes, Plant, Genome, Plant, Sequence Analysis, DNA, Tandem Repeat Sequences, Triticum
Abstract

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.

Published
2016

44. Chromosomal Genomics of Barley

Author

Šimková, Hana, Kubaláková, Marie, Vrána, Jan, Cápal, Petr, Doležel, Jaroslav, Kole, Chittaranjan, Series Editor, Stein, Nils, editor, and Muehlbauer, Gary J., editor

Published
2018
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47. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals

Author

Li, Yan, Leveau, Aymeric, Zhao, Qiang, Feng, Qi, Lu, Hengyun, Miao, Jiashun, Xue, Zheyong, Martin, Azahara C., Wegel, Eva, Wang, Jing, Orme, Anastasia, Rey, Maria-Dolores, Karafiátová, Miroslava, Vrána, Jan, Steuernagel, Burkhard, Joynson, Ryan, Owen, Charlotte, Reed, James, Louveau, Thomas, Stephenson, Michael J., Zhang, Lei, Huang, Xuehui, Huang, Tao, Fan, Danling, Zhou, Congcong, Tian, Qilin, Li, Wenjun, Lu, Yiqi, Chen, Jiaying, Zhao, Yan, Lu, Ying, Zhu, Chuanrang, Liu, Zhenhua, Polturak, Guy, Casson, Rebecca, Hill, Lionel, Moore, Graham, Melton, Rachel, Hall, Neil, Wulff, Brande B. H., Doležel, Jaroslav, Langdon, Tim, Han, Bin, and Osbourn, Anne

Published
2021
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49. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Author

Consortium, The International Wheat Genome Sequencing, Mayer, Klaus FX, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam J, Sourdille, Pierre, Endo, Takashi R, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, McLay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Sandve, Simen Rød, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Pfeifer, Matthias, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikaël, Keller, Beat, and Praud, Sebastien

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Human Genome, Bread, Chromosomes, Plant, Evolution, Molecular, Gene Order, Genetic Variation, Genome, Plant, Molecular Sequence Annotation, Phylogeny, Plant Proteins, Polyploidy, Sequence Analysis, DNA, Transcriptome, Triticum, International Wheat Genome Sequencing Consortium, General Science & Technology
Abstract

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Published
2014

50. Gametocidal genes: from a discovery to the application in wheat breeding.

Author

Said, Mahmoud, Gaál, Eszter, Farkas, András, Molnár, István, Bartoš, Jan, Doležel, Jaroslav, Cabrera, Adoración, and Endo, Takashi R.

Subjects
WHEAT breeding, INTROGRESSION (Genetics), PLANT germplasm, CHROMOSOME abnormalities, WHEAT genetics, CHROMOSOMAL rearrangement, EVIDENCE gaps
Abstract

Some species of the genus Aegilops, a wild relative of wheat, carry chromosomes that after introducing to wheat exhibit preferential transmission to progeny. Their selective retention is a result of the abortion of gametes lacking them due to induced chromosomal aberrations. These chromosomes are termed Gametocidal (Gc) and, based on their effects, they are categorized into three types: mild, intense or severe, and very strong. Gc elements within the same homoeologous chromosome groups of Aegilops (II, III, or IV) demonstrate similar Gc action. This review explores the intriguing dynamics of Gc chromosomes and encompasses comprehensive insights into their source species, behavioral aspects, mode of action, interactions, suppressions, and practical applications of the Gc system in wheat breeding. By delving into these areas, this work aims to contribute to the development of novel plant genetic resources for wheat breeding. The insights provided herein shed light on the utilization of Gc chromosomes to produce chromosomal rearrangements in wheat and its wild relatives, thereby facilitating the generation of chromosome deletions, translocations, and telosomic lines. The Gc approach has significantly advanced various aspects of wheat genetics, including the introgression of novel genes and alleles, molecular markers and gene mapping, and the exploration of homoeologous relationships within Triticeae species. The mystery lies in why gametes possessing Gc genes maintain their normality while those lacking Gc genes suffer abnormalities, highlighting an unresolved research gap necessitating deeper investigation. [ABSTRACT FROM AUTHOR]

Published
2024
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