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SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas

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Abstract

Background

The exploration of genetic diversity is the key source of germplasm conservation and potential to broaden its genetic base. The globally growing demand for chickpea suggests superior/climate-resilient varieties, which in turn necessitates the germplasm characterization to unravel underlying genetic variation.

Methodology and results

A chickpea core collection comprising of diverse 192 accessions which include cultivated Cicer arietinum, and wild C. reticulatum, C. echinospermum, and C. microphyllum species were investigated to analyze their genetic diversity and relationship, by assaying 33 unlinked simple sequence repeat (SSR) markers. The results amplified a total of 323 alleles (Na), ranging from 2 to 8 with an average of 4.25 alleles per locus. Expected heterozygosity (He) differed from 0.46 to 0.86 with an average of 0.68. Polymorphic information content (PIC) ranged from 0.73 to 0.98 with an average of 0.89. Analysis of molecular variance (AMOVA) showed that most of the variation was among individuals (87%). Cluster analysis resulted in the formation of four distinct clusters. Cluster I represented all cultivated and clusters II, III, and IV comprised a heterogeneous group of cultivated and wild chickpea accessions.

Conclusion

We report considerable diversity and greater resolving power of SSR markers for assessing variability and interrelationship among the chickpea accessions. The chickpea core is expected to be an efficient resource for breeders for broadening the chickpea genetic base and could be useful for selective breeding of desirable traits and in the identification of target genes for genomics-assisted breeding.

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Data availability

The data analyzed and generated during the current study are available within the article [and/or] its supplementary materials.

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Acknowledgements

The authors are thankful to ICRISAT (Hyderabad), IIPR (Kanpur), NBPGR (New Delhi) for providing the germplasm for the present study.

Funding

This study was not funded by any external funding agency.

Author information

Authors and Affiliations

  1. Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India

    Asma Hamid Mir, Mohd Ashraf Bhat, Humara Fayaz, Mohd Anwar Khan, Parvaze A. Sofi & Reyazul Rouf Mir

  2. Department of Botany, Cytogenetics and Reproductive Biology Laboratory, University of Kashmir, Srinagar, Kashmir, India

    Humara Fayaz & Aijaz A. Wani

  3. Dryland Agriculture Research Station (DARS), SKUAST-Kashmir, Budgam, Kashmir, India

    Sher A. Dar

  4. Division of Animal Genetics and Breeding, SKUAST-Kashmir, FVSc & AH, Shuhama, Srinagar, Kashmir, India

    Showkat Maqbool

  5. Rafi Amhad Kidwai (RAK) College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKV), Sehore, Madhya Pradesh, India

    Mohammad Yasin

  6. ICAR-Central Institute of Temperate Horticulture (CITH), Srinagar, Kashmir, India

    Javid Iqbal Mir

  7. School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China

    Ahmed H. El-Sappah

  8. Center of Excellence in Genomics & Systems Biology (CEGSB), Iinternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India

    Mahendar Thudi & Rajeev Kumar Varshney

  9. Department of Agricultural Biotechnology and Biotechnology, Rajendra Prasad Central Agricultural University, Pusa, Samasthipur, Bihar, India

    Mahendar Thudi

  10. State Agricultural Biotechnology Centre, Crop & Food Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia

    Rajeev Kumar Varshney

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  1. Asma Hamid Mir
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Correspondence to Reyazul Rouf Mir.

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Mir, A.H., Bhat, M.A., Fayaz, H. et al. SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas. Mol Biol Rep 49, 11469–11479 (2022). https://doi.org/10.1007/s11033-022-07858-4

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