Abstract
Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs. Compared to recombination variation in whole genome, more QTLs were mapped for variations in recombination hot regions. The majority QTLs for recombination hot regions are trans-QTLs and co-localized with genes from the recombination pathway. We also found that recombination variation was positively associated with the presence of genes and DNA transposons, but negatively related to the presence of long terminal repeat retrotransposons. Additionally, 41 recombination hot regions were fine-mapped. The high-resolution genotyping of five randomly selected regions in two F2 populations verified that they indeed have ultra-high recombination frequency, which is even higher than that of the well-known recombination hot regions sh1-bz and a1-sh2. Taken together, our results further our understanding of recombination variation in plants.
Highlights
Recombination refers to the phenomenon of genomic exchange among chromatids, which leads to new alleles and new combinations of existing alleles[1,2,3]
Based on the identified features that are associated with recombination, we identified 41 putative recombination hot regions and 5 of them were verified in two separate F2 populations
To decipher the genetic mechanisms conferring the nonuniformity of recombination events across maize genome, we considered the global recombination event number of all chromosomes (GRE) and the recombination number of each chromosome (GREchr) as phenotypic traits to perform quantitative trait locus (QTL) mapping across 11 recombination inbred line (RIL) (Fig. 1A)
Summary
Recombination refers to the phenomenon of genomic exchange among chromatids, which leads to new alleles and new combinations of existing alleles[1,2,3]. Using recombination crossover number as a quantitative trait, quantitative trait locus (QTL) mapping method was employed to dissect the genetic mechanism underlying recombination variation in maize segregating population, and several recombination QTLs were identified[27]. These studies suggest that the regulation of recombination is very complex in both animals and plants. We conducted QTL mapping for recombination event number using 11 recombination inbred line (RIL) populations that have been genotyped with ~50000 SNPs41 We identified both cis- and trans- QTLs. We found candidate genes for some trans- QTLs. We identified tens of genomic features as the cis- factors that are associated with the variation of recombination frequency. Our results provide a comprehensive genome-wide scan of genetic and genomic factors conferring maize recombination variation, which will further our understanding of recombination and aid breeding in maize
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