Mirosław Tyrka1, Monika Mokrzycka2, Beata Bakera3, Dorota Tyrka1, Magdalena Szeliga1, Stefan Stojałowski4, Przemysław Matysik5, Michał Rokicki6, Monika Rakoczy-Trojanowska7, Paweł Krajewski8. 1. Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland. 2. Institute of Plant Genetics, Polish Academy of Science, Strzeszyńska 34, 60-479, Poznań, Poland. 3. Warsaw University of Life Sciences, Nowoursynowska 166, 02-787, Warszawa, Poland. 4. West Pomeranian University of Technology Szczecin, Słowackiego 17, 71-434, Szczecin, Poland. 5. Plant Breeding Strzelce Group IHAR Ltd., Kasztanowa 5, 63-004, Tulce, Poland. 6. Poznań Plant Breeding Ltd., Główna 20, 99-307, Strzelce, Poland. 7. Warsaw University of Life Sciences, Nowoursynowska 166, 02-787, Warszawa, Poland. monika_rakoczy_trojanowska@sggw.edu.pl. 8. Institute of Plant Genetics, Polish Academy of Science, Strzeszyńska 34, 60-479, Poznań, Poland. pkra@igr.poznan.pl.
Abstract
BACKGROUND: The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach. RESULTS: More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs. CONCLUSIONS: Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.
BACKGROUND: The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach. RESULTS: More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs. CONCLUSIONS: Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.
Entities:
Keywords:
Breeding; Genetic variation; Population structure; Single nucleotide polymorphisms; Triticum aestivum L
Authors: Colin R Cavanagh; Shiaoman Chao; Shichen Wang; Bevan Emma Huang; Stuart Stephen; Seifollah Kiani; Kerrie Forrest; Cyrille Saintenac; Gina L Brown-Guedira; Alina Akhunova; Deven See; Guihua Bai; Michael Pumphrey; Luxmi Tomar; Debbie Wong; Stephan Kong; Matthew Reynolds; Marta Lopez da Silva; Harold Bockelman; Luther Talbert; James A Anderson; Susanne Dreisigacker; Stephen Baenziger; Arron Carter; Viktor Korzun; Peter Laurent Morrell; Jorge Dubcovsky; Matthew K Morell; Mark E Sorrells; Matthew J Hayden; Eduard Akhunov Journal: Proc Natl Acad Sci U S A Date: 2013-04-29 Impact factor: 11.205
Authors: Carl Friedrich Horst Longin; Manje Gowda; Jonathan Mühleisen; Erhard Ebmeyer; Ebrahim Kazman; Ralf Schachschneider; Johannes Schacht; Martin Kirchhoff; Yusheng Zhao; Jochen Christoph Reif Journal: Theor Appl Genet Date: 2013-08-04 Impact factor: 5.699
Authors: Katherine W Jordan; Shichen Wang; Yanni Lun; Laura-Jayne Gardiner; Ron MacLachlan; Pierre Hucl; Krysta Wiebe; Debbie Wong; Kerrie L Forrest; Andrew G Sharpe; Christine Hd Sidebottom; Neil Hall; Christopher Toomajian; Timothy Close; Jorge Dubcovsky; Alina Akhunova; Luther Talbert; Urmil K Bansal; Harbans S Bariana; Matthew J Hayden; Curtis Pozniak; Jeffrey A Jeddeloh; Anthony Hall; Eduard Akhunov Journal: Genome Biol Date: 2015-02-26 Impact factor: 13.583
Authors: Deepmala Sehgal; Prashant Vikram; Carolina Paola Sansaloni; Cynthia Ortiz; Carolina Saint Pierre; Thomas Payne; Marc Ellis; Ahmed Amri; César Daniel Petroli; Peter Wenzl; Sukhwinder Singh Journal: PLoS One Date: 2015-07-15 Impact factor: 3.240
Authors: Rachel Brenchley; Manuel Spannagl; Matthias Pfeifer; Gary L A Barker; Rosalinda D'Amore; Alexandra M Allen; Neil McKenzie; Melissa Kramer; Arnaud Kerhornou; Dan Bolser; Suzanne Kay; Darren Waite; Martin Trick; Ian Bancroft; Yong Gu; Naxin Huo; Ming-Cheng Luo; Sunish Sehgal; Bikram Gill; Sharyar Kianian; Olin Anderson; Paul Kersey; Jan Dvorak; W Richard McCombie; Anthony Hall; Klaus F X Mayer; Keith J Edwards; Michael W Bevan; Neil Hall Journal: Nature Date: 2012-11-29 Impact factor: 49.962
Authors: Shichen Wang; Debbie Wong; Kerrie Forrest; Alexandra Allen; Shiaoman Chao; Bevan E Huang; Marco Maccaferri; Silvio Salvi; Sara G Milner; Luigi Cattivelli; Anna M Mastrangelo; Alex Whan; Stuart Stephen; Gary Barker; Ralf Wieseke; Joerg Plieske; Morten Lillemo; Diane Mather; Rudi Appels; Rudy Dolferus; Gina Brown-Guedira; Abraham Korol; Alina R Akhunova; Catherine Feuillet; Jerome Salse; Michele Morgante; Curtis Pozniak; Ming-Cheng Luo; Jan Dvorak; Matthew Morell; Jorge Dubcovsky; Martin Ganal; Roberto Tuberosa; Cindy Lawley; Ivan Mikoulitch; Colin Cavanagh; Keith J Edwards; Matthew Hayden; Eduard Akhunov Journal: Plant Biotechnol J Date: 2014-03-20 Impact factor: 9.803