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Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (Juglans regia L.)

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Abstract

In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection.

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Data availability

The data is publicly available at NCBI [Juglans regia (ID 17683)—Genome—NCBI (nih.gov)].

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Acknowledgements

First and corresponding authors thank Department of Biotechnology, Ministry of Science and Technology India for providing funding (Grant No: BT/PR31931/AGIII/103/1128/2019). We also thank Halima E. Awale, Michigam State University, East Lansing USA for helping us in language editing.

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Authors and Affiliations

  1. Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 192303, India

    H. Itoo, Rafiq Ahmad Shah, Sheikh Khursheed, Zahoor A. Bhat, M. A. Mir & G. H. Rather

  2. Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K, 190 025, India

    S. Qurat & Afnan Jeelani

  3. Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K, 190 025, India

    Sajad Majeed Zargar

  4. Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025, Srinagar, J&K, India

    M. D. Shah & Bilal A. Padder

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  1. H. Itoo
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Contributions

HI and BAP conceived and designed the experiments. RAS, SQ, and AJ performed the experiments. BAP and RAS analyzed the data. HI, BAP, MDS, and RAS contributed reagents/materials/analysis tools. BAP and RAS wrote the paper. HI, BAP, RAS. SK, SMZ, MAM, and ZAB are advisee members to AJ and SQ.

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Correspondence to Bilal A. Padder.

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Itoo, H., Shah, R.A., Qurat, S. et al. Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (Juglans regia L.). 3 Biotech 13, 136 (2023). https://doi.org/10.1007/s13205-023-03563-6

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