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Development and Characterization of SSR Markers to Study Genetic Diversity and Population Structure of Horsegram Germplasm (Macrotyloma uniflorum)

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Abstract

Development of genomic resources in any crop is the pre-requisite for the construction of linkage map and implementation of molecular breeding strategies to develop superior cultivars. Large number of molecular markers are required to enrich the scanty information available in horsegram (Macrotyloma uniflorum).We employed the next-generation Illumina sequencing platform to develop a large number of microsatellite markers in this species. Of the total 23,305 potential SSRs motifs, 5755 primers were designed. Of these, 1425, 1310, 856, 1276, and 888 were of di-, tri-, tetra-, penta-, and hexa-nucleotide repeats respectively. Thirty polymorphic SSR primers and 24 morphological traits were used in 360 horsegram accessions to detect the genetic diversity and population structure. Thirty primers amplified 170 polymorphic alleles with an average of 5.6 alleles per primer having size 80 to 380 bp. The polymorphism information content (PIC) ranged from 0.15 to 0.76 with an average of 0.50, suggesting that SSR markers used in the study were polymorphic and suitable for characterization of horsegram germplasm. Dendrogram-based on Jaccard’s similarity coefficient and neighbor-joining tree grouped the horsegram accessions into two major clusters. Similarly, STRUCTURE analysis assigned genotypes into two gene pools namely Himalayan origin and Southern India. Diversity analysis based on 24 agro-morphological traits also suggested the presence of high level of diversity among the accessions.

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Acknowledgements

This work was funded by the Department of Science and Technology, Govt of India, and Japan Society for the Promotion of Science, Japan in the form of Collaborative Research Project.

Author Contribution Statement

RKC and TRS designed the experiments and wrote the manuscript. JCR provided the material. DS and MR performed the experiment. SI and HK designed the primers from Illumina sequence data. VS and AN analyzed data.

Key Message

This is the first attempt to develop the genomic SSR markers in this crop and it is also a maiden attempt to assess the genetic diversity using molecular and morphological markers in lesser known but important legume. The study revealed the presence of two gene pools Indian horsegram germplasm.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology, CSK Himachal Pradesh Agriculture University, Palampur, 176061, India

    R. K. Chahota, Divya Shikha, Maneet Rana, Akshay Nag & T. R. Sharma

  2. Department of Botany, Punjabi University, Patiala, Punjab, 147002, India

    Vikas Sharma

  3. ICAR-Indian Institute of Agricultural Biotechnology, C/O ICAR-IINRG PDU Campus, Namkum, Ranchi, 834010, India

    T. R. Sharma

  4. Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi, India

    J. C. Rana

  5. Laboratory of Plant Genome Research, Kazusa DNA Research Laboratory, Chiba, Japan

    Hideki Hirakawa & Sachiko Isobe

Authors
  1. R. K. Chahota
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  2. Divya Shikha
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  3. Maneet Rana
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  4. Vikas Sharma
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  5. Akshay Nag
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  6. T. R. Sharma
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  7. J. C. Rana
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  8. Hideki Hirakawa
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  9. Sachiko Isobe
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Corresponding authors

Correspondence to R. K. Chahota or Sachiko Isobe.

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The authors declare that they have no conflict of interest.

Ethical Standards

The authors declare that the experiments comply with the current laws of the countries in which the experiments were performed

Electronic supplementary material

Supplementary Fig 1

Distribution of horsegram germplasm in India (DOC 355 kb)

Supplementary Fig 2

Population structure of 360 horsegram accessions showing two genetic stocks (DOC 39 kb)

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Chahota, R.K., Shikha, D., Rana, M. et al. Development and Characterization of SSR Markers to Study Genetic Diversity and Population Structure of Horsegram Germplasm (Macrotyloma uniflorum). Plant Mol Biol Rep 35, 550–561 (2017). https://doi.org/10.1007/s11105-017-1045-z

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  • DOI: https://doi.org/10.1007/s11105-017-1045-z

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