Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.)

PLoS One. 2018 Mar 9;13(3):e0189597. doi: 10.1371/journal.pone.0189597. eCollection 2018.

Abstract

Recombination (R) rate and linkage disequilibrium (LD) analyses are the basis for plant breeding. These vary by breeding system, by generation of inbreeding or outcrossing and by region in the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome (514 Mb) and n = 11 chromosomes. The goal of this study was to describe R and LD in the common bean genome using a 768-marker array of single nucleotide polymorphisms (SNP) based on Trans-legume Orthologous Group (TOG) genes along with an advanced-generation Recombinant Inbred Line reference mapping population (BAT93 x Jalo EEP558) and an internationally available diversity panel. A whole genome genetic map was created that covered all eleven linkage groups (LG). The LGs were linked to the physical map by sequence data of the TOGs compared to each chromosome sequence of common bean. The genetic map length in total was smaller than for previous maps reflecting the precision of allele calling and mapping with SNP technology as well as the use of gene-based markers. A total of 91.4% of TOG markers had singleton hits with annotated Pv genes and all mapped outside of regions of resistance gene clusters. LD levels were found to be stronger within the Mesoamerican genepool and decay more rapidly within the Andean genepool. The recombination rate across the genome was 2.13 cM / Mb but R was found to be highly repressed around centromeres and frequent outside peri-centromeric regions. These results have important implications for association and genetic mapping or crop improvement in common bean.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping
  • Chromosomes, Plant
  • DNA, Plant / genetics*
  • Genetic Markers
  • Genome, Plant*
  • Linkage Disequilibrium
  • Multigene Family
  • Phaseolus / genetics*
  • Plant Breeding
  • Polymorphism, Single Nucleotide*
  • Recombination, Genetic*

Substances

  • DNA, Plant
  • Genetic Markers

Grants and funding

This research was supported by the Generation Challenge Program / Bill and Melinda Gates Foundation through the Tropical Legume I grant to MWB as PI for common beans and to DC as PI for comparative legume genomics. Evans Allen funds from Tennessee State University are recognized for senior author’s writing time.