SSR and SNP Marker-Based Investigation of Indian Rice Landraces in Relation to Their Genetic Diversity, Population Structure, and Geographical Isolation

Choudhury, D R and Kumar, R and Maurya, A and Semwal, D P and Rathi, R S and Gautam, R K and Trivedi, A K and Bishnoi, S K and Ahlawat, S P and Singh, K and Singh, N K and Singh, R (2023) SSR and SNP Marker-Based Investigation of Indian Rice Landraces in Relation to Their Genetic Diversity, Population Structure, and Geographical Isolation. Agriculture (TSI), 13 (4). pp. 1-17. ISSN 2077-0472

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India is blessed with an abundance of diverse rice landraces in its traditional cultivated areas. Two marker systems (simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)) were used to study a set of 298 rice landrace accessions collected from six different regions of India (Andaman and Nicobar Islands, Chhattisgarh, Jharkhand, Uttar Pradesh, Uttarakhand, and West Bengal). Thirty hyper-variable simple sequence repeats (HvSSRs) and 32,782 single nucleotide polymorphisms (SNPs) were used in inferring genetic structure and geographical isolation. Rice landraces from Uttar Pradesh were the most diverse, with a gene diversity value of 0.42 and 0.49 with SSR and SNP markers, respectively. Neighbor-joining trees classified the rice landraces into two major groups with SSR and SNP markers, and complete geographical isolation was observed with SSR markers. Fast STRUCTURE analysis revealed four populations for SSR markers and three populations for SNP markers. The population structure with SSR markers showed that few individuals from Uttarakhand and Andaman and Nicobar Islands were grouped in small clusters. Population structure analysis with SNP markers showed not very distinct region-wise clustering among the rice landraces. Discriminant analysis of principal components (DAPC) and minimum spanning network (MSN) using SSR markers showed region-wise grouping of landraces with some intermixing, but DAPC and MSN with SNP markers showed very clear region-wise clustering. Genetic differentiation of rice landraces between the regions was significant with both SSR (Fst 0.094–0.487) and SNP markers (Fst 0.047–0.285). A Mantel test revealed a positive correlation between the genetic and geographic distance of rice landraces. The present study concludes that rice landraces investigated in this study were very diverse, and unlinked SSR markers show better geographical isolation than a large set of SNP markers.

Item Type: Article
Divisions: Genebank
Uncontrolled Keywords: SNP markers, SSR markers, genetic diversity, geographical isolation, rice landrace
Subjects: Others > Rice
Others > Genetics and Genomics
Depositing User: Mr Nagaraju T
Date Deposited: 22 Feb 2024 11:19
Last Modified: 22 Feb 2024 11:19
Official URL:
Funders: Indian Council of Agricultural Research, ICAR-Network project on Functional Genomics and Genetic Modification in Crops
Acknowledgement: We are thankful to the Director, ICAR-NBPGR, New Delhi, for providing facilities to carry out this work.
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