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Development of transcriptome-wide SSR markers for genetic diversity and structure analysis in Macrotyloma uniflorum (Lam.) Verdc.

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Abstract

Horsegram is an important drought resistant pulse crop from Fabaceae and can be easily grown in dry lands with no irrigation facilities. However, it remained neglected since long and has been considered as orphan legume which requires immediate attention for its improvement and for the development of new promising varieties in future. In the present study, 7352 simple sequence repeat (SSR) markers were developed from the transcriptome data and 150 SSR were randomly synthesized for validation and diversity analysis in a panel of 58 horsegram genotypes. The synthesized primers included all types of repeats spanning direpeats to hexarepeats. Of the validated SSR markers, 33 markers were polymorphic and produced 40 loci which were used to analyze the genetic diversity and structure of horsegram. In total, 130 alleles were produced in a range of 2–9 alleles with maximum alleles produced by primer HTSSR 155. Expected heterozygosity (He) ranged from 0.03 to 1.00 and observed heterozygosity (Ho) ranged from 0.13 to 0.81. Polymorphism information content value ranged from 0.065 to 0.78. Dendrogram based on UPGMA and principal component analysis showed four groups of the 58 genotypes of horsegram. Structure analysis showed three genetic stocks for the analyzed germplasm. Thus, the developed SSRs can be useful in future population genetics analysis, molecular breeding studies and mapping works in horsegram germplasm as well as in related legume species.

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Acknowledgments

Dr. Rahul Kumar acknowledges the financial grant received from DST-SERB, New Delhi in the form of young scientist research project. NBPGR, New Delhi is also duly acknowledged for providing the germplasm of Horsegram. Dr. Rahul Kumar is also thankful to Dr. Poonam Suri, Chancellor, DAV University and President, DAVCMC New Delhi for providing logistics support at DAV University, Jalandhar to conduct and complete the current research work.

Funding

This study was funded by DST-SERB, Government of India (YSS/2015/00521).

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Authors and Affiliations

  1. DAV University, Jalandhar, Punjab, India

    Rahul Kumar, Sumeet Parkash Kaundal & Ashutosh Sharma

  2. Sant Baba Bhag Singh University, Khiala, Jalandhar, Punjab, India

    Vikas Sharma

  3. Central University of Himachal Pradesh, Dharamshala (H.P), India

    Gagandeep Singh

  4. CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P), India

    Ram Kumar Sharma

  5. CSKHP Agriculture University, Palampur (H.P), India

    Rakesh Kumar Chahota

  6. ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India

    Tilak Raj Sharma

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  1. Rahul Kumar
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  4. Ashutosh Sharma
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Correspondence to Rahul Kumar or Vikas Sharma.

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Kumar, R., Kaundal, S.P., Sharma, V. et al. Development of transcriptome-wide SSR markers for genetic diversity and structure analysis in Macrotyloma uniflorum (Lam.) Verdc.. Physiol Mol Biol Plants 26, 2255–2266 (2020). https://doi.org/10.1007/s12298-020-00898-9

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