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Development of genome-wide SSR markers in horsegram and their use for genetic diversity and cross-transferability analysis

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Abstract

Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] commonly known as kulthi or Madras gram is an important drought tolerant legume crop used as food and fodder in India and across the globe. Horsegram is tolerant to many biotic and abiotic stresses and considered a potential future food legume. Despite being a multiutility crop, insufficient genomic information is available in this species, which is otherwise required for genetic improvement. Hence, in the present work we used next-generation sequencing (NGS) technology for genome-wide development and characterization of novel simple sequence repeat (SSR) markers in horsegram. In all, 2458 SSR primer pairs were designed from NGS data and 117 SSRs were characterized in 48 diverse lines of horsegram. Cross-transferability of these markers was also checked in nine related legume species. The polymorphic SSRs revealed high diversity measures such as mean values of expected heterozygosity (He; 0.54), observed heterozygosity (Ho; 0.64), and polymorphism information content (PIC; 0.46). Analysis of molecular variance (AMOVA) revealed high degree of genetic variance within the populations. Dendrogram based on Jaccard’s similarity coefficient and principal component analysis (PCA) revealed two groups in the analyzed accessions. This observation was further confirmed by Bayesian genetic STRUCTURE analysis. The SSR markers developed herein can be used in diverse genetic analysis including association map** in this crop and also in related legume crops with limited marker resources. Hence, this new SSR dataset can be useful for molecular breeding research in this underutilized pulse crop. In addition, genetic diversity estimates of analyzed germplasm can be important for devising future breeding programmes in horsegram.

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Acknowledgements

Authors gratefully acknowledge the Department of Biotechnology (DBT), Department of Science and Technology (DST), Government of India and Japanese Society for Promotion of Science (JSPS) for providing financial support to conduct this work.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, 176062, India

    Rahul Kaldate, Rakesh Kumar Chahota & Tilak Raj Sharma

  2. Division of Crop Improvement, ICAR-Indian Grassland & Fodder Research Institute, Jhansi, 284128, India

    Maneet Rana

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

    Vikas Sharma

  4. Kazusa DNA Research Institute, Kisarazu, Chiba, Japan

    Hideki Hirakawa & Sachiko N. Isobe

  5. Department of Agriculture, DAV University Jalandhar, Punjab, India

    Rahul Kumar

  6. Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India

    Gagandeep Singh

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

    Tilak Raj Sharma

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  1. Rahul Kaldate
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  2. Maneet Rana
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  3. Vikas Sharma
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  4. Hideki Hirakawa
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  7. Rakesh Kumar Chahota
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Correspondence to Tilak Raj Sharma.

Electronic supplementary material

Supplementary Table 1

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Supplementary Table 2

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Supplementary Table 3

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Supplementary Fig. 1

Polymorphism shown in amplification profiles of 48 horsegram genotypes generated by newly developed markers a) MUGSSR-530 b) MUGSSR-32 c) MUGSSR-546 and d) Cross-transferability of MUGSSR-542 in nine releated species namely- M. gharwalensis, Cicer arietinum, Vigna unguiculata, Lens culinaris, Vigna mungo, Pisum sativum, Trifolium pratense, Vigna umbelleta and Phaseolu vulgaris (DOC 79 kb)

Supplementary Fig. 2

Percentage of species-wise cross-transferability observed in nine selected related species (DOC 50 kb)

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Kaldate, R., Rana, M., Sharma, V. et al. Development of genome-wide SSR markers in horsegram and their use for genetic diversity and cross-transferability analysis. Mol Breeding 37, 103 (2017). https://doi.org/10.1007/s11032-017-0701-1

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