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Genetic diversity and genome-wide association analysis of cooking time in dry bean (Phaseolus vulgaris L.)

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Fivefold diversity for cooking time found in a panel of 206 Phaseolus vulgaris accessions. Fastest accession cooks nearly 20 min faster than average.   SNPs associated with cooking time on Pv02, 03, and 06.

Abstract

Dry beans (Phaseolus vulgaris L.) are a nutrient dense food and a dietary staple in parts of Africa and Latin America. One of the major factors that limits greater utilization of beans is their long cooking times compared to other foods. Cooking time is an important trait with implications for gender equity, nutritional value of diets, and energy utilization. Very little is known about the genetic diversity and genomic regions involved in determining cooking time. The objective of this research was to assess cooking time on a panel of 206 P. vulgaris accessions, use genome- wide association analysis (GWAS) to identify genomic regions influencing this trait, and to test the ability to predict cooking time by raw seed characteristics. In this study 5.5-fold variation for cooking time was found and five bean accessions were identified which cook in less than 27 min across 2 years, where the average cooking time was 37 min. One accession, ADP0367 cooked nearly 20 min faster than average. Four of these five accessions showed close phylogenetic relationship based on a NJ tree developed with ~5000 SNP markers, suggesting a potentially similar underlying genetic mechanism. GWAS revealed regions on chromosomes Pv02, Pv03, and Pv06 associated with cooking time. Vis/NIR scanning of raw seed explained 68 % of the phenotypic variation for cooking time, suggesting with additional experimentation, it may be possible to use this spectroscopy method to non-destructively identify fast cooking lines as part of a breeding program.

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Acknowledgments

This work was supported in part by funding from the Norman Borlaug Commemorative Research Initiative (US Agency for International Development), by the US Department of Agriculture, Agricultural Research Service. The contents of this publication do not necessarily reflect the views or policies of the US Department of Agriculture, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government. We also thank Yasmin Salat, Dennis Katuuramu, and Scott Shaw for assistance with cooking.

Conflict of interest

The authors declare no conflict of interest.

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Authors and Affiliations

  1. Sugarbeet and Bean Research Unit, USDA-ARS, 1066 Bogue St., Room 494, East Lansing, MI, 48824, USA

    Karen A. Cichy

  2. Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA

    Karen A. Cichy, Jason A. Wiesinger & Fernando A. Mendoza

  3. Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI, 48824, USA

    Fernando A. Mendoza

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  1. Karen A. Cichy
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  2. Jason A. Wiesinger
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Correspondence to Karen A. Cichy.

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Communicated by G. J. Bryan.

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Cichy, K.A., Wiesinger, J.A. & Mendoza, F.A. Genetic diversity and genome-wide association analysis of cooking time in dry bean (Phaseolus vulgaris L.). Theor Appl Genet 128, 1555–1567 (2015). https://doi.org/10.1007/s00122-015-2531-z

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