Intraspecific Variation of Recombination Rate in Maize

Meiotic crossovers shuffle intra-chromosomal allelic combinations, which is exploited in plant breeding to combine favourable alleles of genes. Using linkage or association-based approaches, crossovers are also exploited to identify the genetic factors underlying the traits of interest. Crossover numbers and distributions along chromosomes vary from species to species but little is known about their intraspecies variation, though it would help optimizing breeding schemes by taking into account the recombination rates when choosing the genotypes to be used as parents for crosses. Here, we report on the variation of recombination rates between 22 European maize inbred lines belonging to the Dent and Flint genetic groups. We produced 23 doubled-haploid populations derived from crosses between these lines, genotyped them with a 50k-SNP array, and constructed high-density genetic maps. We found significant differences of genome-wide recombination rates among populations (0.57 to 0.74 cM/Mbp when pooling all chromosomes). Recombination rates also showed significant differences between chromosomes (0.60 to 0.88 cM/Mbp when pooling all populations). Using an additive genetic model, we estimated individual genetic values of recombination rate for the 22 parental lines, given the data obtained from the 23 double-haploid populations. Genetic values showed up to two-fold differences between parental lines, but no evidence for general differences between Dent and Flint material. Aligning each genetic map to the B73 sequence, intra-chromosomal recombination landscapes revealed regions with significant differences in local recombination rate between populations. Finally, crossover interference analysis using a two-pathway modelling framework revealed a negative association between recombination rate and interference strength.