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Association mapping of days to flowering in common bean (Phaseolus vulgaris L.) revealed by DArT markers

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Abstract

In the current study, 173 common bean genotypes from several geographic regions were studied. Days to flowering (DF) was evaluated in two experimental locations in Izmir, Turkey (Bornova and Menemen) in 2 years (2015 and 2016) and was found to range from 30 to 62.7 days with a mean value of 41.5 days. A total of 22,848 SNPs based on diversity array technology were developed, and after filtering, the remaining 20,766 SNP markers were used for calculating linkage disequilibrium. Chromosomes 1–11 contained 1846, 2342, 2184, 1153, 1351, 1520, 1953, 2080, 2065, 1199, and 1511 SNPs, respectively. A total of 1562 SNPs were identified as scaffold markers. The PIC value was 0.25, ranging from 0.005 to 0.500. Common bean accessions were divided into two main subpopulations, namely POP1 (Mesoamerican) and POP2 (Andean). Mixed linear model using the Q + K model showed that three SNPs had a significant association (p < 0.01) in Bornova in 2015 and seven SNPs had a significant association (p < 0.01) in the same location in 2016. Five significant associations (p < 0.01) were identified in 2015 while six (p < 0.01) were identified in Menemen in 2016. When the data from both locations and both years was combined, six SNPs were significant (p < 0.01). For DF, 11 putative candidate genes were predicted from the sequences representing homology to linked SNPs. We conclude that the markers, which were significantly associated with the DF of the common bean genotypes in the current study, can be used for marker-assisted selection in plant breeding program of common bean.

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Acknowledgements

We would like to especially thank Paul Gepts from the University of California-Davis (USA) for kindly sharing his control group of common bean accessions (the Mesoamerican and Andean gene pools).

Funding

The study was financially supported by The Scientific and Technological Research Council of Turkey (TUBITAK) with project no TUBITAK-114O555.

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Author notes

  1. Duygu Ates and Tansel Kaygisiz Asciogul contributed equally to this work.

Authors and Affiliations

  1. Department of Bioengineering, Ege University, Bornova, 35040, Izmir, Turkey

    Duygu Ates, Seda Nemli, Semih Erdogmus & Muhammed Bahattin Tanyolac

  2. Department of Horticulture, Ege University, Bornova, 35040, Izmir, Turkey

    Tansel Kaygisiz Asciogul & Dursun Esiyok

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  1. Duygu Ates
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Correspondence to Muhammed Bahattin Tanyolac.

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Electronic supplementary material

ESM 1.

Detailed information on the 173 common bean accessions used in the study (DOCX 22 kb)

ESM 2.

Minimum, maximum, and mean DF of the 173 common bean accessions grown in Bornova and Menemen, Izmir, Turkey in 2015 and 2016 (DOCX 12 kb)

ESM 3.

Variance analyses of DF of the 173 common bean accessions grown at two locations in 2015 and 2016 (DOCX 13 kb)

ESM 4.

DArT data obtained in current study (XLSX 17086 kb)

ESM 5.

SNPs distribution by chromosomes in common bean (PNG 57 kb)

ESM 6.

ΔK calculation based on the value of LnP (D) between successive K-values. (PNG 55 kb)

ESM 7.

Considerable differences between the groups (subpopulations) and average distances (expected heterozygosity) between the common bean accessions (DOCX 12 kb)

ESM 8.

Relative kinships of the 173 common bean accessions (PNG 76 kb)

ESM 9.

Analysis of linkage disequilibrium decay in 173 common bean accessions (PNG 6316 kb)

ESM 10.

Quantile-quantile plots for days to flowering (PNG 97 kb)

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Ates, D., Asciogul, T.K., Nemli, S. et al. Association mapping of days to flowering in common bean (Phaseolus vulgaris L.) revealed by DArT markers. Mol Breeding 38, 113 (2018). https://doi.org/10.1007/s11032-018-0868-0

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