Intraspecific variation of recombination rate in maize
Eva Bauer,Matthieu Falque,Hildrun Walter,Cyril Bauland,Christian Camisan,Laura Campo,Nina Meyer,Nicolas Ranc,Renaud Rincent,Wolfgang Schipprack,Thomas Altmann,Pascal Flament,Albrecht E. Melchinger,Monica A. Menz,Jesús Moreno-González,Milena Ouzunova,Pedro Revilla,Alain Charcosset,Olivier C. Martin,Chris-Carolin Schön +19 more
TLDR
The present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes and should pave the way for precise identification of genes controlling recombinations rates in maize and other organisms.Abstract:
In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation. Here, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotype 23 doubled-haploid populations derived from crosses between these lines with a 50 k-SNP array and construct high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtain the recombination rates along chromosomes specific to each population. We identify significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework reveals a negative association between recombination rate and interference strength. To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms.read more
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Journal ArticleDOI
The molecular biology of meiosis in plants.
TL;DR: An overview of advancements in the understanding of all aspects of plant meiosis, including recombination, chromosome synapsis, cell cycle control, chromosome distribution, and the challenge of polyploidy is provided.
Journal ArticleDOI
Variation in recombination frequency and distribution across eukaryotes: patterns and processes
Jessica Stapley,Philine G. D. Feulner,Philine G. D. Feulner,Susan E. Johnston,Anna W. Santure,Carole M. Smadja +5 more
TL;DR: The patterns of, and processes governing recombination in eukaryotes are explored, and how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures is discussed.
Journal ArticleDOI
A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array
Sandra Unterseer,Eva Bauer,Georg Haberer,Michael Seidel,Carsten Knaak,Milena Ouzunova,Thomas Meitinger,Tim M. Strom,Ruedi Fries,Hubert Pausch,Christofer Bertani,Alessandro Davassi,Klaus F. X. Mayer,Chris-Carolin Schön +13 more
TL;DR: The high density Affymetrix® Axiom® Maize Genotyping Array is optimized for European and American temperate maize and was developed based on a diverse sample panel by applying stringent quality filter criteria to ensure its suitability for a broad range of applications.
Journal ArticleDOI
Modeling Epistasis in Genomic Selection.
Yong Jiang,Jochen C. Reif +1 more
TL;DR: It is concluded that prediction accuracy can be improved by modeling epistasis for selfing species but may not for outcrossing species, and why the RKHS model based on a Gaussian kernel captures epistatic effects among markers.
Journal ArticleDOI
Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize
Frank Technow,Tobias A. Schrag,Wolfgang Schipprack,Eva Bauer,Henner Simianer,Albrecht E. Melchinger +5 more
TL;DR: High consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions are found and support the hypothesis of differential fixation of alleles due to pseudo-overdominance in these regions.
References
More filters
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
TL;DR: It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
Journal ArticleDOI
Fast model-based estimation of ancestry in unrelated individuals
TL;DR: The results show that ADMIXTURE's computational speed opens up the possibility of using a much larger set of markers in model-based ancestry estimation and that its estimates are suitable for use in correcting for population stratification in association studies.
Journal ArticleDOI
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
Robert J. Elshire,Jeffrey C. Glaubitz,Qi-ying Sun,Jesse Poland,Ken Kawamoto,Edward S. Buckler,Edward S. Buckler,Sharon E. Mitchell +7 more
TL;DR: A procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs) is reported, which is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches.
Journal ArticleDOI
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Patrick S. Schnable,Doreen Ware,Robert S. Fulton,Joshua C. Stein,Fusheng Wei,Shiran Pasternak,Chengzhi Liang,Jianwei Zhang,Lucinda Fulton,Tina Graves,Patrick Minx,Amy Denise Reily,Laura Courtney,Scott Kruchowski,Chad Tomlinson,Cindy Strong,Kim D. Delehaunty,Catrina Fronick,Bill Courtney,Susan M. Rock,Eddie Belter,Feiyu Du,Kyung Kim,Rachel Abbott,Marc Cotton,Andrew Levy,Pamela Marchetto,Kerri Ochoa,Stephanie M. Jackson,Barbara Gillam,Weizu Chen,Le Yan,Jamey Higginbotham,Marco Cardenas,Jason Waligorski,Elizabeth Applebaum,Lindsey Phelps,Jason Falcone,Krishna L. Kanchi,T. K. Thane,Adam Scimone,Nay Thane,Jessica Henke,Thomas J. Wang,Jessica Ruppert,Neha Shah,Kelsi Rotter,Jennifer S. Hodges,Elizabeth Ingenthron,Matt Cordes,Sara Kohlberg,Jennifer Sgro,Brandon Delgado,Kelly Mead,Asif T. Chinwalla,Shawn Leonard,Kevin Crouse,Kristi Collura,Dave Kudrna,Jennifer Currie,Ruifeng He,Angelina Angelova,Shanmugam Rajasekar,Teri Mueller,Rene Lomeli,Gabriel Scara,Ara Ko,Krista Delaney,Marina Wissotski,Georgina Lopez,David Campos,Michele Braidotti,Elizabeth Ashley,Wolfgang Golser,Hyeran Kim,Seunghee Lee,Jinke Lin,Zeljko Dujmic,Woojin Kim,Jayson Talag,Andrea Zuccolo,Chuanzhu Fan,Aswathy Sebastian,Melissa Kramer,Lori Spiegel,Lidia Nascimento,Theresa Zutavern,Beth Miller,Claude Ambroise,Stephanie Muller,William Spooner,Apurva Narechania,Liya Ren,Sharon Wei,Sunita Kumari,Ben Faga,Michael J. Levy,Linda McMahan,Peter Van Buren,Matthew W. Vaughn,Kai Ying,Cheng Ting Yeh,Scott J. Emrich,Scott J. Emrich,Yi Jia,Ananth Kalyanaraman,Ananth Kalyanaraman,An-Ping Hsia,W. Brad Barbazuk,Regina S. Baucom,Thomas P. Brutnell,Nicholas C. Carpita,Cristian Chaparro,Jer Ming Chia,Jean-Marc Deragon,James C. Estill,Yan Fu,Jeffrey A. Jeddeloh,Yujun Han,Hye-Ran Lee,Pinghua Li,Damon Lisch,Sanzhen Liu,Zhijie Liu,Dawn H. Nagel,Maureen C. McCann,Phillip SanMiguel,Alan M. Myers,Dan Nettleton,John D. Nguyen,Bryan W. Penning,Lalit Ponnala,Kevin L. Schneider,David C. Schwartz,Anupma Sharma,Carol Soderlund,Nathan M. Springer,Qi Sun,Hao Wang,Michael S. Waterman,Richard P. Westerman,Thomas K. Wolfgruber,Lixing Yang,Yeisoo Yu,Lifang Zhang,Shiguo Zhou,Qihui Zhu,Jeffrey L. Bennetzen,R. Kelly Dawe,Jiming Jiang,Ning Jiang,Gernot G. Presting,Susan R. Wessler,Srinivas Aluru,Srinivas Aluru,Robert A. Martienssen,Sandra W. Clifton,W. Richard McCombie,Rod A. Wing,Richard K. Wilson +159 more
TL;DR: The sequence of the maize genome reveals it to be the most complex genome known to date and the correlation of methylation-poor regions with Mu transposon insertions and recombination and how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state is reported.
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