Punctuated distribution of recombination hotspots and demarcation of pericentromeric regions in Phaseolus vulgaris L.

Mehul S Bhakta,Valerie A Jones,C Eduardo Vallejos,Paul Hohenlohe

doi:10.1371/journal.pone.0116822

Abstract

High density genetic maps are a reliable tool for genetic dissection of complex plant traits. Mapping resolution is often hampered by the variable crossover and non-crossover events occurring across the genome, with pericentromeric regions (pCENR) showing highly suppressed recombination rates. The efficiency of linkage mapping can further be improved by characterizing and understanding the distribution of recombinational activity along individual chromosomes. In order to evaluate the genome wide recombination rate in common beans (Phaseolus vulgaris L.) we developed a SNP-based linkage map using the genotype-by-sequencing approach with a 188 recombinant inbred line family generated from an inter gene pool cross (Andean x Mesoamerican). We identified 1,112 SNPs that were subsequently used to construct a robust linkage map with 11 groups, comprising 513 recombinationally unique marker loci spanning 943 cM (LOD 3.0). Comparative analysis showed that the linkage map spanned >95% of the physical map, indicating that the map is almost saturated. Evaluation of genome-wide recombination rate indicated that at least 45% of the genome is highly recombinationally suppressed, and allowed us to estimate locations of pCENRs. We observed an average recombination rate of 0.25 cM/Mb in pCENRs as compared to the rest of genome that showed 3.72 cM/Mb. However, several hot spots of recombination were also detected with recombination rates reaching as high as 34 cM/Mb. Hotspots were mostly found towards the end of chromosomes, which also happened to be gene-rich regions. Analyzing relationships between linkage and physical map indicated a punctuated distribution of recombinational hot spots across the genome.

Highlights

Molecular marker-based linkage maps have been used to connect the phenotype to the genotype using classical forward genetics
At one extreme are the pericentromeric regions where recombination is highly suppressed [5], and at the other extreme are the hotspots of recombination, which have been detected in plants using a population genetics approach [6], and a targeted approach [7]
A subset of previously mapped BNG (BeaN Genomic random sequences) markers [14] were mapped in a subgroup of this recombinant inbred (RI) family as RFLPs and most of the remainder were mapped as PCR markers using high resolution melting

Summary

Introduction

Molecular marker-based linkage maps have been used to connect the phenotype to the genotype using classical forward genetics. These maps have been used to position genes in the genome, genetically deconstruct complex traits, and initiate map-based cloning. A dense linkage map doesn’t always guarantee high resolution mapping at the molecular level because the probability of a crossover event is not uniform along chromosomes [4]. Linkage analysis doesn’t provide the resolution for recombination hotspots afforded by pollen-typing [7] or deep sequencing of diverse populations [6], it can still provide useful information for genetic analysis when these maps are aligned to the corresponding sequenced genome

Methods

Results

Discussion

Conclusion