title: Recombination in diverse maize is stable, predictable, and associated with genetic load.
abstract: Among the fundamental evolutionary forces, recombination arguably has the largest impact on the practical work of plant breeders. Varying over 1,000-fold across the maize genome, the local meiotic recombination rate limits the resolving power of quantitative trait mapping and the precision of favorable allele introgression. The consequences of low recombination also theoretically extend to the species-wide scale by decreasing the power of selection relative to genetic drift, and thereby hindering the purging of deleterious mutations. In this study, we used genotyping-by-sequencing (GBS) to identify 136,000 recombination breakpoints at high resolution within US and Chinese maize nested association mapping populations. We find that the pattern of cross-overs is highly predictable on the broad scale, following the distribution of gene density and CpG methylation. Several large inversions also suppress recombination in distinct regions of several families. We also identify recombination hotspots ranging in size from 1 kb to 30 kb. We find these hotspots to be historically stable and, compared with similar regions with low recombination, to have strongly differentiated patterns of DNA methylation and GC content. We also provide evidence for the historical action of GC-biased gene conversion in recombination hotspots. Finally, using genomic evolutionary rate profiling (GERP) to identify putative deleterious polymorphisms, we find evidence for reduced genetic load in hotspot regions, a phenomenon that may have considerable practical importance for breeding programs worldwide.
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; er432@cornell.edu pjb39@cornell.edu.
authors.forename: Eli
authors.initials: E
authors.lastname: Rodgers-Melnick
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and er432@cornell.edu pjb39@cornell.edu.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bradbury
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Elshire
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Glaubitz
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
authors.forename: Charlotte B
authors.initials: CB
authors.lastname: Acharya
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
authors.forename: Sharon E
authors.initials: SE
authors.lastname: Mitchell
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Chunhui
authors.initials: C
authors.lastname: Li
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Yongxiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
mesh_terms: D000483:Alleles; D001499:Bayes Theorem; D018899:CpG Islands; D003434:Crossing Over, Genetic; D019175:DNA Methylation; D005785:Gene Conversion; D017353:Gene Deletion; D040741:Genetic Load; D005838:Genotype; D006720:Homozygote; D009154:Mutation; D010641:Phenotype; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D003313:Zea mays / Q000235:genetics*
keywords: deleterious mutations; genetic load; maize; methylation; recombination