Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers

Abstract

The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.

Grain Fe and Zn contents linked SSR markers based genetic diversity in rice

“…Yadav et al [49] reported higher genetic diversity and PIC values in some Indian rice germplasm using trait linked SSR markers. In this study, nearly 70% (17) markers had greater than 0.4085 gene diversity and PIC values, strongly indicating that majority of the markers used in current research are moderate to highly informative for evaluating genetic diversity [50]. These results are further supported by higher inbreeding coefficient values (range; 0.7052-1.0000) ( Table 1).…”

Genetic Architecture and Anthocyanin Profiling of Aromatic Rice From Manipur Reveals Divergence of Chakhao Landraces

“…SSRs are highly useful in assessing diversity among closely related rice cultivars (Singh et al, 2013;Yadav et al, 2013) as they provide better resolvability, are multi-allelic, provide genomewide coverage, are highly reproducible, are easy to score, and are cost-effective (Akagi et al, 1997;Singh and Singh, 2015). There are several studies that used SSR markers for finding the genetic structure of the rice germplasm, as one of the most widely used molecular markers for genetic diversity studies (Nachimuthu et al, 2015;Singh et al, 2016;Aljumaili et al, 2018;Islam et al, 2018a,b;Pathaichindachote et al, 2019;Suvi et al, 2019;Verma et al, 2019). Further, SSR markers are also proven to be efficient in delineating major genetic groups of rice, namely, indica, temperate japonica, tropical japonica, aus, and aromatic (Roy et al, 2015(Roy et al, , 2016Wang et al, 2014).…”

Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

“…(2017) studied genetic diversity in 120 Aus rice genotypes of Bangladesh and observed a PIC value of 0.8217. Other studies conducted using SSR markers reveled a polymorphism information content of 0.697 ( Rashid et al., 2018 ), 0.6533 ( Shakil et al., 2015 ), 0.36 ( Syed et al., 2019 ) and 0.51 ( Verma et al., 2019 ). All these results enumerated from a variety of researches employing RAPD and SSR markers revealed that Bangladesh has a high genetic diversity among rice germplasms.…”