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

Debjani Roy Choudhury, Ramesh Kumar, Avantika Maurya, Dinesh P. Semwal, Ranbir S. Rathi, Raj K. Gautam, Ajaya K. Trivedi, Santosh K. Bishnoi, Sudhir P. Ahlawat, Kuldeep Singh, Nagendra K. Singh and Rakesh Singh ()
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Debjani Roy Choudhury: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
Ramesh Kumar: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
Avantika Maurya: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
Dinesh P. Semwal: Division of Plant Exploration and Germplasm Collection, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
Ranbir S. Rathi: Division of Plant Exploration and Germplasm Collection, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
Raj K. Gautam: Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
Ajaya K. Trivedi: ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O Kakori 226101, India
Santosh K. Bishnoi: ICAR-Indian Institute of Wheat and Barley Research, GaehoonVihar, Karnal 132001, India
Sudhir P. Ahlawat: Division of Plant Exploration and Germplasm Collection, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
Kuldeep Singh: International Crops Research Institute for Semi-Arid Tropics, Patancheru, Hyderabad 502324, India
Nagendra K. Singh: ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
Rakesh Singh: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India

Agriculture, 2023, vol. 13, issue 4, 1-17

Abstract: 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.

Keywords: SNP markers; SSR markers; genetic diversity; geographical isolation; rice landrace (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2023
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