Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers

Abstract

Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-á-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer's varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI's Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm.

Application of principal component analysis for rice f5 families characterization and evaluation

“…It was therefore inferred that the essential features of the data set had been represented in the first four principal components, explaining 76.43 percent of total variability. These results were in accordance with the reports of Yadav et al [6] where four principal components were formed to describe the maximum variance of the data set. (-0.288) were negatively loaded.…”

Review of methods for the detection and quantification of adulteration of rice: Basmati as a case study

“…As of now, more than 50,000 microsatellite markers are on hand in the rice. Microsatellite DNA markers have been extensively used in mapping and tagging genes, study of diversity, phylogeny and population genetics, disease diagnosis, and forensic Nakamura and Ohtsubo (2010) investigations (Coburn et al 2002;Srividhya et al 2010;Yadav et al 2013;Choudhury et al 2013;Vemireddy et al 2007). In addition, microsatellite markers have the potential to be used for unequivocal detection and quantification of adulteration in Basmati rice (Bligh 2000;Archak et al 2007;Vemireddy et al 2007).…”

Phylogenetic Relationship among the Wild Rice (Oryza Nivara) and Intraspecies of Rice Genotypes Belonging to Chhattisgarh Revealed by Chloroplast Dna Regions psbA-trnH

“…Rice is first crops by which complete genome was sequenced and it has been ideal model plant for study due to its relatively small genome size of 430 Mb compared to other plants [12]. Indian cultivars, landraces, wild and weedy relatives are the main source of rice diversity and are the rich source of worthy genes that plant breeders can exploit for crop improvement [5]. Collection and characterization of existing germplasm is not only important for utilizing the appropriate attribute, but also essential for protecting the intellectual property rights by correct identification of a genotypes, worldwide.…”