Vol.:(0123456789) 1 3 Molecular Biology Reports https://doi.org/10.1007/s11033-023-08324-5 ORIGINAL ARTICLE Trait specifc marker‑based characterization and population structure analysis in rice (Oryza sativa L.) germplasm of Kashmir Himalayas Deepika Pandita 1  · Reetika Mahajan 2  · Sajad Majeed Zargar 2  · Firdous A Nehvi 1  · Bhagyashree Dhekale 3  · Fouzia Shaf 4  · Mehraj‑Ul‑Din Shah 5  · Najeebul Rehman Sof 6  · Amjad M. Husaini 1 Received: 8 February 2022 / Accepted: 2 February 2023 © The Author(s), under exclusive licence to Springer Nature B.V. 2023 Abstract Background Rice is a key food grain contributor to the global food grain basket and is considered the main food crop in India with a large number of varieties released every year. SSR markers have proven to be an excellent tool for studying genetic diversity. As a result, the present study was done to characterize and assess genetic diversity as well as population structural aspects. Methods and results Fifty genotypes of rice were characterized using 40 SSR markers to assess the genetic diversity and genetic relationship. A total of 114 alleles were amplifed with an average of 2.85 alleles per locus. The Polymorphism Information Content (PIC) values varied from 0.30 (RM162) to 0.58 (RM413) with an average of 0.44. Gene diversity was in the range of 0.35 (RM162) to 0.66 (RM413), with an average value of 0.52, while heterozygosity ranged from 0.18 (RM27) to 0.74 (RM55), with an average of 0.39. The population structure revealed a narrow genetic base with only three major subpopulations. Analysis of molecular variance revealed that 74% of the variation was attributed within individuals, 23% was among individuals, and 3% was among populations. Pairwise Fst value of population A & B is 0.024, population B & C is 0.120 and population A & C is 0.115. Dendrogram grouped the genotypes into three clusters with wide variation among the accessions. Conclusion Genotyping combined with phylogeny and population structure analysis proved to be a powerful method for characterizing germplasm in this study. There is signifcant gene fow within populations, as well as the presence of difer- ent combinations of alleles, and that allelic exchange rates within the populations are higher than among the populations. Assessing the genetic diversity among individual genotypes within populations is quite useful in selecting candidate parents for future breeding programs to improve the target traits in rice for the Himalayan region. Keywords Rice · Genetic diversity · SSR · Polymorphism · Himalayas · Population structure Introduction Domestication of rice (Oryza sativa) was done roughly 10,000 years back. Rice is a modal crop with a compara- tively small genome, and is used for understanding the genetic mechanisms of crop improvement. After the com- pletion of rice genome sequencing project, the study of the history and course of rice domestication has hastened remarkably [1]. Rice has two genetically divergent cultivars, japonica and indica, and ecologically distinct wild progeni- tors, Oryza rufipogon and Oryza nivara [2, 3]. The centre of origin and diversity of two cultivated spe- cies O. sativa and Oryza glaberrima were identifed using genetic diversity analysis and geographical distribution. River valleys of Yangtze and Mekon rivers are considered * Amjad M. Husaini amjadhusaini@skuastkashmir.ac.in 1 Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, J&K 190025, India 2 Division of Plant Biotechnology, SKUAST-K, Srinagar, India 3 Division of Agricultural Statistics, SKUAST-K, Srinagar, India 4 Division of Basic Sciences, SKUAST-K, Srinagar, India 5 Division of Plant Pathology, SKUAST-K, Srinagar, India 6 MRCFC, Khudwani, SKUAST-K, Anantnag, India