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Development and polymorphism of Vigna unguiculata ssp. unguiculata microsatellite markers used for phylogenetic analysis in asparagus bean (Vigna unguiculata ssp. sesquipedialis (L.) Verdc.)

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Abstract

Asparagus bean (V. unguiculata ssp. sesquipedialis), a specific form of cowpea (V. unguiculata L. Walp.), is cultivated as a vegetable crop throughout eastern and southern Asia for its tender long pods. Little is known about the genetic relationship between asparagus bean and the broader species, particularly the dominant ssp. unguiculata. We report here the development and transferability of simple sequence repeat (SSR) markers, over 40% of which are EST-derived, from ssp. unguiculata to asparagus bean and the use of a subset of the polymorphic markers to assess the genetic diversity of asparagus bean cultivars from diverse geographic origins across China. A total of 410 EST derived SSR (eSSR) markers and 600 SSR markers derived from cowpea genespace sequences (GSS) were developed, with a cross-subspecies transferability of 100% and 98.5%, respectively. In a recombinant inbred line population of asparagus bean, a 1:1 segregation was observed for most loci. Principal coordinate analysis (PCA) and phylogenetic clustering based on 62 alleles detected by 14 polymorphic SSR markers distinguished ssp. unguiculata and sesquipedialis into separate groups. Improved asparagus bean cultivars in China generally have a narrow genetic basis compared with landraces varieties. This suggests that asparagus bean breeding programs need to consider utilizing landrace germplasm to enhance genetic variability and ensure long-term gains from selection and reduce genetic vulnerability to pathogen/pest epidemics. Because of their transferability across subspecies, the SSR markers described in this study could be effectively employed in cross-subspecies trait introgression breeding from ssp. unguiculata to sesquipedialis.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

EST:

Expressed sequence tag

GSS:

Gene space sequence

PCA:

Principal coordinate analysis

PIC:

Polymorphism information content

RAPD:

Rapid amplification polymorphism of DNA

RFLP:

Restriction fragment length polymorphism

RIL:

Recombinant inbred line

SFP:

Single feature polymorphisms

SSR:

Simple sequence repeat

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Acknowledgments

This study was partially supported by the National Science Foundation of China (No. 30871711), the Science Foundation of Zhejiang Province (No. Y306224), and the fund from Science and Technology Department of Zhejiang Province, China (No. 2007C24018). The authors would thank Dr. Dave Edwards of University of Queensland, Australia, for his help in bioinformatics.

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Authors and Affiliations

  1. Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 310021, Hangzhou, People’s Republic of China

    Pei Xu, Xiaohua Wu, Baogen Wang, Yonghua Liu, Tingting Hu, Zhongfu Lu & Guojing Li

  2. Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 310021, Hangzhou, People’s Republic of China

    Dehui Qin

  3. Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521-0124, USA

    Jeffery D. Ehlers & Timothy J. Close

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  1. Pei Xu
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  2. Xiaohua Wu
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  3. Baogen Wang
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  4. Yonghua Liu
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  5. Dehui Qin
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  6. Jeffery D. Ehlers
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  7. Timothy J. Close
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  8. Tingting Hu
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  9. Zhongfu Lu
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  10. Guojing Li
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Correspondence to Guojing Li.

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Xu, P., Wu, X., Wang, B. et al. Development and polymorphism of Vigna unguiculata ssp. unguiculata microsatellite markers used for phylogenetic analysis in asparagus bean (Vigna unguiculata ssp. sesquipedialis (L.) Verdc.). Mol Breeding 25, 675–684 (2010). https://doi.org/10.1007/s11032-009-9364-x

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