title: Genome-wide recombination dynamics are associated with phenotypic variation in maize.
abstract: Meiotic recombination is a major driver of genetic diversity, species evolution, and agricultural improvement. Thus, an understanding of the genetic recombination landscape across the maize (Zea mays) genome will provide insight and tools for further study of maize evolution and improvement. Here, we used c. 50 000 single nucleotide polymorphisms to precisely map recombination events in 12 artificial maize segregating populations. We observed substantial variation in the recombination frequency and distribution along the ten maize chromosomes among the 12 populations and identified 143 recombination hot regions. Recombination breakpoints were partitioned into intragenic and intergenic events. Interestingly, an increase in the number of genes containing recombination events was accompanied by a decrease in the number of recombination events per gene. This kept the overall number of intragenic recombination events nearly invariable in a given population, suggesting that the recombination variation observed among populations was largely attributed to intergenic recombination. However, significant associations between intragenic recombination events and variation in gene expression and agronomic traits were observed, suggesting potential roles for intragenic recombination in plant phenotypic diversity. Our results provide a comprehensive view of the maize recombination landscape, and show an association between recombination, gene expression and phenotypic variation, which may enhance crop genetic improvement.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Qingchun
authors.initials: Q
authors.lastname: Pan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.|Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.affiliation: National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Tong
authors.affiliation: National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
authors.forename: Shutu
authors.initials: S
authors.lastname: Xu
authors.affiliation: National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Li
authors.affiliation: National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
authors.forename: Weiya
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.|Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Muehlbauer
authors.affiliation: National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
authors.forename: Jiansheng
authors.initials: J
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Jianbing
authors.initials: J
authors.lastname: Yan
mesh_terms: D002874:Chromosome Mapping; D018506:Gene Expression Regulation, Plant; D056426:Genetic Loci; D018745:Genome, Plant; D005838:Genotype; D010641:Phenotype; D011995:Recombination, Genetic; D003313:Zea mays / Q000033:anatomy & histology* / Q000235:genetics*
keywords: intergenic recombination; intragenic recombination; maize (Zea mays); phenotypic variation; recombination