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SNP marker diversity in common bean (Phaseolus vulgaris L.)

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Abstract

Single nucleotide polymorphism (SNP) markers have become a genetic technology of choice because of their automation and high precision of allele calls. In this study, our goal was to develop 94 SNPs and test them across well-chosen common bean (Phaseolus vulgaris L.) germplasm. We validated and accessed SNP diversity at 84 gene-based and 10 non-genic loci using KASPar technology in a panel of 70 genotypes that have been used as parents of mapping populations and have been previously evaluated for SSRs. SNPs exhibited high levels of genetic diversity, an excess of middle frequency polymorphism, and a within-genepool mismatch distribution as expected for populations affected by sudden demographic expansions after domestication bottlenecks. This set of markers was useful for distinguishing Andean and Mesoamerican genotypes but less useful for distinguishing within each gene pool. In summary, slightly greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool but polymorphism rate between genotypes was consistent with genepool and race identity. Our survey results represent a baseline for the choice of SNP markers for future applications because gene-associated SNPs could themselves be causative SNPs for traits. Finally, we discuss that the ideal genetic marker combination with which to carry out diversity, mapping and association studies in common bean should consider a mix of both SNP and SSR markers.

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Acknowledgments

The authors wish to thank the personnel of the Genetic Resource Unit and Bean Programs for seed multiplication. In particular, we are grateful with L. Díaz and A. Hoyos for providing us with the SSR data and passport information, respectively, and with V.M. Mayor for facilitating DNA of drought tolerance lines. We also acknowledge the KBioscience Center for support in SNP genotyping, are grateful to S. Madriñán for advice and analytical support and to the anonymous reviewers for their valuable comments. This research was supported by the Tropical Legume I project of the Generation Challenge Program.

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Authors and Affiliations

  1. Centro Internacional de Agricultura Tropical (CIAT), Apartado Aéreo 6713, Cali, Colombia

    Andrés J. Cortés, Martha C. Chavarro & Matthew W. Blair

  2. Universidad de los Andes, Carrera 1 N 18A-12, J302, Bogotá, Colombia

    Andrés J. Cortés

  3. International Center for Tropical Agriculture (CIAT), 1380 N.W. 78th Ave, Miami, FL, 33126, USA

    Matthew W. Blair

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  1. Andrés J. Cortés
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Correspondence to Matthew W. Blair.

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Communicated by A. Schulman.

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Supplemental table 1 (DOC 96 kb)

122_2011_1630_MOESM2_ESM.ppt

Supplemental figure 1. Allele frequency for 94 SNP (84 gene-based and 10 non-genic) markers organized according to their polymorphism information content (PIC) (PPT 119 kb)

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Supplemental figure 2. Nucleotide diversity (pairwise differences) for each SNP marker along the 70 common bean accessions. Non-genic and Dreb2 SNPs are indicated. The first 81 SNPs are EST-based (PPT 109 kb)

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Supplemental figure 3. Comparison of pairwise differences between all possible combinations of accessions for SNP and SSR markers. Subfigure a) considers intra and inter-genepool comparisons. Subfigure b) only considers intra-genepool comparisons. The most likelihood equation is presented in each case. SSR markers from Blair et al. (2006a, b) (PPT 637 kb)

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Supplemental figure 4. Principal component analysis (PCoA) for 70 common bean accessions based on 94 SNP markers and considering genepool structure. Subfigure a) shows the Andean genepool; subfigure b) shows the Mesoamerican genepool. Accession names are shown for cases where introgression is recognizable (PDF 232 kb)

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Supplemental figure 5. Structure analysis from K = 2 to K = 3 presented for a) the Andean and b) the Mesoamerican gene pools independently with sub-group abbreviations as D-J (Durango–Jalisco complex), G (race Guatemala) M1, M2 (race Mesoamerica subgroups); NG1, NG2 (race Nueva Granada subgroups) and P (race Peru). Arrows show cases of inter gene pool introgression detailed in the PCoA analysis (PDF 155 kb)

122_2011_1630_MOESM7_ESM.pdf

Supplemental figure 6. Level of polymorphism in hypothetical parental combinations. Red scale and distribution: pairwise differences between any two accessions. Green scale and distribution: level of heterozygosity for each accession. Discontinuous black lines at margins divide Andean (upper-left) and Mesoamerican (lower-right) gene pools. Accessions are organized according to the PCoA analysis (PDF 127 kb)

122_2011_1630_MOESM8_ESM.pdf

Supplemental figure 7. Permutation tests comparing a) the Andean and the Mesoamerican uniqueness and b) the Andean and Mesoamerican intra-genepool diversity. 10000 iterations were considered. The t for unequal sample sizes and variances was used as test statistic. Box-plot diagrams are shown in the insets (PDF 95 kb)

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Cortés, A.J., Chavarro, M.C. & Blair, M.W. SNP marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 123, 827–845 (2011). https://doi.org/10.1007/s00122-011-1630-8

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