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Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation

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Abstract

Microsatellite or single sequence repeat (SSR) markers have been commonly used in genetic research in many crop species, including common bean (Phaseolus vulgaris L.). A limited number of existing SSR markers have been designed from high-throughput sequencing of the genome, warranting the exploitation of new SSR markers from genomic regions. In this paper, we sequenced total DNA from the genotype Hong Yundou with a 454-FLX pyrosequencer and found numerous SSR loci. Based on these, a large number of SSR markers were developed and 90 genomic-SSR markers with clear bands were tested for mapping and diversity detection. The new SSR markers proved to be highly polymorphic for molecular polymorphism, with an average polymorphism information content value of 0.44 in 131 Chinese genotypes and breeding lines, effective for distinguishing Andean and Mesoamerican genotypes. In addition, we integrated 85 primers of the 90 polymorphism markers into the bean map using an F2 segregating population derived from Hong Yundou crossed with Jingdou. The distribution of SSR markers among 11 chromosomes was not random and tended to cluster on the linkage map, with 14 new markers mapped on chromosome Pv01, whereas only four loci were located on chromosome Pv04. Overall, these new markers have potential for genetic mapping, genetic diversity studies and map-based cloning in common bean.

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Acknowledgments

This work was supported by China Agriculture Research System (CARS-09) and the Crop Germplasm Conservation and Utilization System (NB2012-2130135-25-09).

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Authors and Affiliations

  1. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Mingli Chen, Jing Wu, Lanfeng Wang, Jizeng Jia & Shumin Wang

  2. Qingdao Academy of Agricultural Sciences, Shandong, 266100, China

    Xiaoyan Zhang

  3. Department of Plant Breeding, Cornell University, 242 Emerson Hall, Ithaca, NY, 14853, USA

    Matthew W. Blair

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  1. Mingli Chen
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  2. Jing Wu
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  3. Lanfeng Wang
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  4. Xiaoyan Zhang
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  6. Jizeng Jia
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  7. Shumin Wang
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Corresponding author

Correspondence to Shumin Wang.

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Accession code 454 Genome sequences and all short-read data are under BioProject ID PRJNA200997.

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Chen, M., Wu, J., Wang, L. et al. Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation. Mol Breeding 33, 489–496 (2014). https://doi.org/10.1007/s11032-013-9949-2

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