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

<div><p>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 (<i>Phaseolus vulgaris</i> 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.</p></div

Relationship between D′and r² for the SNP markers.

<p>Relationship between D′and r² for the SNP markers.</p

SNP marker amplicon similarity hits in the common bean genome from physical chromosome position (y-axis) to genetic position to (x-axis) with all chromosomes placed end-to-end and oriented per sequence information.

<p>SNP marker amplicon similarity hits in the common bean genome from physical chromosome position (y-axis) to genetic position to (x-axis) with all chromosomes placed end-to-end and oriented per sequence information.</p

Correlation between linkage map distance (cM) and physical distance (Mb) for the SNP markers across each of the eleven chromosomes of common bean (Pv) showing (a) Absolute values and (b) polynomial fitted lines.

<p>Filled dots in (b) mark the centromeres according to Schmutz <i>et al</i>. (2014).</p

Relationship for each chromosome (labelled as Pv) between linkage map position (on the cM axis) and physical map position (on the Mb axis) for 11 chromosomes of common bean based on the SNP marker mapping described in this text and the BAT93 x JaloEEP558 recombinant inbred line population.

<p>Relationship for each chromosome (labelled as Pv) between linkage map position (on the cM axis) and physical map position (on the Mb axis) for 11 chromosomes of common bean based on the SNP marker mapping described in this text and the BAT93 x JaloEEP558 recombinant inbred line population.</p

Genome-wide linkage disequilibrium as measured by r² (upper triangles) and its p-value (lower triangles) (a) across genepools, (b) within the Andean genepool, and (c) within the Mesoamerican genepool.

<p>Linkage groups are shown in the margins.</p

Intra-chromosal decay of linkage disequilibrium (r²) as a funcion of genetic distance (cM) (a) across genepools, (b) within the Andean genepool, and (c) within the Mesoamerican genepool.

<p>Exponential tendency lines are shown when significant.</p

Physical and genetic mapping and map distance in base pairs (bp) or centiMorgans for each linkage group on the G19833 reference genome v 2.1 or in the BAT93 x Jalo EEP558 population, respectively, using SNP markers from the trans-legume orthologous genes (TOG) combined with other types of markers, including restriction fragment length polymorphism (RFLP) markers of the Bng and D series, simple sequence repeat (SSR) markers and isozyme, protein or phenotypic markers.

<p>Physical and genetic mapping and map distance in base pairs (bp) or centiMorgans for each linkage group on the G19833 reference genome v 2.1 or in the BAT93 x Jalo EEP558 population, respectively, using SNP markers from the trans-legume orthologous genes (TOG) combined with other types of markers, including restriction fragment length polymorphism (RFLP) markers of the Bng and D series, simple sequence repeat (SSR) markers and isozyme, protein or phenotypic markers.</p

Phylogeny of <i>Cajanus</i> species depicted as a 50% majority rule consensus tree.

<p>Tree topology was inferred with maximum parsimony via heuristic searches among 1000 trees. Numbers above branches indicate bootstrap support (>50%). The vertical bar indicates the putative projentitor species (two <i>C. Cajanifolius</i> accessions). Tree length  = 2145, consistency index (CI)  = 0.638, and retention index (RI)  = 0.837. The Bootstrap support for the sister relationship between wild-Australia and Wild-India clades (in the absence of the two <i>C. cajan</i> accessions) is 100% (data not shown).</p

Summary results of AMOVA analyses within and among populations of 95 accessions of the domesticated and wild groups.

<p>d.f.: Degrees of freedom; SS, sum of squared observations; MS, mean of squared observations; Est. var., estimated variance % Var., percentage of total variance; Fct, proportion of the total genetic variance between groups; FSc, proportion of the total genetic variance among populations within a group; Fst, proportion of the total genetic variance within populations.</p