Recombination frequency variation in maize as revealed by genomewide single‐nucleotide polymorphisms

Abstract

Recombination frequency greatly affects selection efficiency in plant breeding. A high-density single-nucleotide polymorphism (SNP) map integrated with physical map and other molecular maps is very useful for characterizing genetic recombination variation. In this study, recombination frequency in maize was investigated through SNP linkage maps constructed with three recombinant inbred line populations. The integrated map consisted of 1443 molecular markers, including 1155 SNPs, spanning 1346 cM. A 100-fold difference in recombination frequency was observed between different chromosomal regions, ranging from an average of 0.09 cM/Mb for pericentromeric regions to 7.08 cM/Mb for telomeric regions. Recombination suppression in non-centromeric regions identified nine recombinationsuppressed regions, one of which likely contained condensed heterochromatin (knobs). Recombination variation along chromosomes was highly predictable for pericentromeric and telomeric regions, but population-specific with 4.5-fold difference for the same marker interval across the three populations or specific chromosome regions because of the presence of knobs. As recombination variation can be identified and well characterized as shown in this study, the related information will facilitate future genetic studies, gene cloning and marker-assisted plant breeding.

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

“…Recombination events in plants have been mapped using genetic markers. In maize, recombination has been mapped in regions around four target genes (Yao et al, 2002) and over the entire genome using linkage maps (Farkhari et al, 2011). An older study used restriction fragment length polymorphisms (RFLPs) to map recombination in B. nigra (wild Catania x CrGC no.…”

Ultrahigh-Density Linkage Map for Cultivated Cucumber (Cucumis sativus L.) Using a Single-Nucleotide Polymorphism Genotyping Array

“…In this linkage map, we removed those SNPs; however, if better resolution is needed in the future for SDRs, the other option can be used. Recombination rate has been shown to be correlated with sequence parameters [ 59 ] and with the rate of genetic variations [ 60 , 61 ]. Thus, the local rates of recombination reveal regions on the linkage groups where the rate of evolution is of interest.…”

Positional cloning in maize (Zea mays subsp. mays, Poaceae)

“…Dividing the recombination frequency between flanking markers calculated in step 4a by the physical distance between those markers in the maize genome will provide a rough estimate of recombination rate around your mutation. For example, flanking markers that are 20 cM apart and span a physical distance of 28 Mb would indicate that recombination in this region is 0.71 cM/Mb, which is slightly higher than the average in maize of 0.67 cM/Mb ( Farkhari et al, 2011 ). In this situation, a mapping population of 500 chromosomes would generate ∼100 total recombinants, which in turn corresponds to a recombinant every 280 kb, about the size of an average BAC.…”