Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array
Shichen Wang,Debbie Wong,Kerrie Forrest,Alexandra M. Allen,Shiaoman Chao,Bevan Emma Huang,Marco Maccaferri,Silvio Salvi,Sara Giulia Milner,Luigi Cattivelli,Anna M. Mastrangelo,Alex Whan,Stuart Stephen,Gary L A Barker,Ralf Wieseke,Joerg Plieske,Morten Lillemo,Diane E. Mather,Rudi Appels,Rudy Dolferus,Gina Brown-Guedira,Abraham B. Korol,Alina Akhunova,Catherine Feuillet,Catherine Feuillet,Jérôme Salse,Michele Morgante,Curtis J. Pozniak,Ming-Cheng Luo,Jan Dvorak,Matthew K. Morell,Jorge Dubcovsky,Jorge Dubcovsky,Martin W. Ganal,Roberto Tuberosa,Cindy Lawley,Ivan Mikoulitch,Colin Cavanagh,Keith J. Edwards,Matthew J. Hayden,Eduard Akhunov +40 more
TLDR
The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.Abstract:
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.read more
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A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
Klaus F. X. Mayer,Jane Rogers,Jaroslav Doležel,Curtis J. Pozniak,Kellye Eversole,Catherine Feuillet,Bikram S. Gill,Bernd Friebe,Adam J. Lukaszewski,Pierre Sourdille,Takashi R. Endo,M. Kubaláková,Jarmila Číhalíková,Zdeňka Dubská,Jan Vrána,Romana Šperková,Hana Šimková,Melanie Febrer,Leah Clissold,Kirsten McLay,Kuldeep Singh,Parveen Chhuneja,Nagendra K. Singh,Jitendra P. Khurana,Eduard Akhunov,Frédéric Choulet,Adriana Alberti,Valérie Barbe,Patrick Wincker,Hiroyuki Kanamori,Fuminori Kobayashi,Takeshi Itoh,Takashi Matsumoto,Hiroaki Sakai,Tsuyoshi Tanaka,Jianzhong Wu,Yasunari Ogihara,Hirokazu Handa,P. Ron Maclachlan,Andrew G. Sharpe,Darrin Klassen,David Edwards,Jacqueline Batley,Odd-Arne Olsen,Simen Rød Sandve,Sigbjørn Lien,Burkhard Steuernagel,Brande B. H. Wulff,Mario Caccamo,Sarah Ayling,Ricardo H. Ramirez-Gonzalez,Bernardo J. Clavijo,Jonathan M. Wright,Matthias Pfeifer,Manuel Spannagl,Mihaela Martis,Martin Mascher,Jarrod Chapman,Jesse Poland,Uwe Scholz,Kerrie Barry,Robbie Waugh,Daniel S. Rokhsar,Gary J. Muehlbauer,Nils Stein,Heidrun Gundlach,Matthias Zytnicki,Véronique Jamilloux,Hadi Quesneville,Thomas Wicker,Primetta Faccioli,Moreno Colaiacovo,Antonio Michele Stanca,Hikmet Budak,Luigi Cattivelli,Natasha Glover,Lise Pingault,Etienne Paux,Sapna Sharma,Rudi Appels,Matthew I. Bellgard,Brett Chapman,Thomas Nussbaumer,Kai Christian Bader,Hélène Rimbert,Shichen Wang,Ron Knox,Andrzej Kilian,Michael Alaux,Françoise Alfama,Loïc Couderc,Nicolas Guilhot,Claire Viseux,Mikaël Loaec,Beat Keller,Sébastien Praud +95 more
TL;DR: Insight 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.
Journal ArticleDOI
Durum wheat genome highlights past domestication signatures and future improvement targets
Marco Maccaferri,Marco Maccaferri,Neil S. Harris,Sven Twardziok,Raj K. Pasam,Heidrun Gundlach,Manuel Spannagl,Danara Ormanbekova,Thomas Lux,Verena M. Prade,Sara Giulia Milner,Axel Himmelbach,Martin Mascher,Paolo Bagnaresi,Primetta Faccioli,Paolo Cozzi,Massimiliano Lauria,Barbara Lazzari,Alessandra Stella,Andrea Manconi,Matteo Gnocchi,Marco Moscatelli,Raz Avni,Jasline Deek,Sezgi Biyiklioglu,Elisabetta Frascaroli,Simona Corneti,Silvio Salvi,Gabriella Sonnante,Francesca Desiderio,Caterina Marè,Cristina Crosatti,E. Mica,Hakan Özkan,Benjamin Kilian,Pasquale De Vita,Daniela Marone,Reem Joukhadar,Elisabetta Mazzucotelli,Domenica Nigro,Agata Gadaleta,Shiaoman Chao,Justin D. Faris,Arthur T. O. Melo,Michael O. Pumphrey,Nicola Pecchioni,Luciano Milanesi,Krystalee Wiebe,Jennifer Ens,Ron MacLachlan,John M. Clarke,Andrew G. Sharpe,Chu Shin Koh,Kevin Y. H. Liang,Gregory J. Taylor,Ron Knox,Hikmet Budak,Anna M. Mastrangelo,Steven S. Xu,Nils Stein,Iago Hale,Assaf Distelfeld,Matthew J. Hayden,Roberto Tuberosa,Sean Walkowiak,Klaus F. X. Mayer,Aldo Ceriotti,Curtis J. Pozniak,Luigi Cattivelli +68 more
TL;DR: The assembly of the genome of durum wheat cultivar Svevo enables genome-wide genetic diversity analyses highlighting modifications imposed by thousands of years of empirical selection and breeding.
Journal ArticleDOI
Past and Future Use of Wild Relatives in Crop Breeding
Hannes Dempewolf,Gregory J. Baute,Justin E. Anderson,Benjamin Kilian,Chelsea Smith,Luigi Guarino +5 more
TL;DR: The role that CWR play in modern crop breeding is documented, including their past and current use, advanced breeding methods and technologies that promise to facilitate the continued use, and what constraints continue to hinder increased use of CWR in breeding.
Journal ArticleDOI
High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool
Mark O. Winfield,Alexandra M. Allen,Amanda J. Burridge,Gary L A Barker,Harriet R. Benbow,Paul A. Wilkinson,Jane A. Coghill,Christy Waterfall,Alessandro Davassi,Geoff Scopes,Ali Pirani,Teresa Webster,Fiona Brew,Claire Bloor,Julie King,Claire West,Simon Griffiths,Ian P. King,Alison R. Bentley,Keith J. Edwards +19 more
TL;DR: The identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources are described.
Journal ArticleDOI
Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments
TL;DR: Through genome-wide association study, loci for grain yield and yield components were identified in chromosomes 5A and 6A in spring wheat (Triticum aestivum) and it was indicated that lines with 1B/1R translocation had higher YLD, grain weight, and taller plants than lines without the translocation.
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