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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #346915

Research Project: SoyBase and the Legume Clade Database

Location: Corn Insects and Crop Genetics Research

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

Author
item Blair, Matthew - Tennessee State University
item Cortes, Andres - Corpoica
item Farmer, Andrew - National Center For Genome Research
item Huang, Wei - Iowa State University
item Penmetsa, Varma - University Of California, Davis
item Cannon, Steven

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/8/2017
Publication Date: 3/9/2018
Citation: Blair, M.W., Cortes, A.J., Farmer, A.D., Huang, W., Penmetsa, V., Cannon, S.B. 2018. Uneven recombination and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.). PLoS One. 13(3):e0189597. https://doi.org/10.1371/journal.pone.0189597.
DOI: https://doi.org/10.1371/journal.pone.0189597

Interpretive Summary: Genetic maps are important for many stages in plant breeding and research. They are useful, for example, in associating a trait of interest (protein content, disease resistance, etc.) with nearby markers. Generally, genetic maps are unique to a species, but it is possible to design markers (which comprise maps) to be useful in multiple species. This paper describes a set of such cross-species genetic markers that are usable in many legume species, and applies them to produce a map in common bean. The results in bean show how near a marker needs to be on a chromosome to a trait of interest, in order to effectively predict that trait. Also, the cross-species markers enable researchers to determine if marker-trait associations in one species are also valid in another species. Both results (regarding marker proximity and cross-species applications) can help breeders more effectively select for traits of interest, and produce better crops for farmers and consumers.

Technical Abstract: Linkage disequilibrium (LD) and recombination (R) analyses are the basis for plant breeding. LD and R vary by breeding system, by generation of inbreeding or outcrossing and by region of the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome and n=11 chromosomes that now has many marker types developed for it. The goal of this study was to describe LD and R in the common bean genome using a 768-feature, single nucleotide polymorphism (SNP) array from trans-legume orthologous genes (TOG) along with a high-generation Recombinant Inbred Line (RIL) 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 and linked to the physical map by sequence data of the TOGs compared to each chromosome sequence of common bean. The genetic map length was smaller than for previous maps reflecting the precision of allele calling and mapping with SNP technology as well as a bias towards gene-rich regions being mapped. TOG markers gave 702 singleton hits to predicted genes and they 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. Recombination was found to be highly repressed around centromeres but frequent at the ends of most chromosomal arms. These results have important implications for association and genetic mapping in common bean.