Molecular diversity analysis in rice (Oryza sativa L.) using SSR markers

Abstract

Rice is the most important staple food crop among the cereals and feeds more than half of the world's population. Assessment of genetic diversity is of utmost importance in rice breeding from the perspective of selection, conservation and proper utilization. The present study was undertaken with an objective to assess the genetic diversity among 27 rice cultivars with 12 SSR markers. The results revealed a total of 40 alleles were detected across 27 rice cultivars tested. PIC values varied widely among SSR loci tested and it ranged from 0.38 to 0.65, with an average of 0.56 per marker. The 27 rice cultivars were grouped into two major clusters i.e., cluster I and II with similarity coefficient 0.13. Cluster I was sub divided into two minor subgroups IA and IB having 5 and 8 genotypes respectively. These subgroups were further subdivided into minor groups. In similar way, the second main cluster i.e. Cluster II was also sub divided into two minor subgroups that is IIA and IIB having 5 and 9 genotypes respectively. These subgroups were further divided into minor groups. This indicated presence of considerable diversity in the genotypes studied and the most diverse cultivars were IR 98846-2-1-2-3 and IR 14D201.

Assessing the Genetic Diversity of Parents for Developing Hybrids Through Morphological and Molecular Markers in Rice (Oryza sativa L.)

“…Bhattacharjee et al ( 2021 ) also reported marker-based grouping independent of geographical origin. The average PIC (0.55) and the number of alleles (4) were in close accordance with the reports of Tripathi et al ( 2020 ) who reported average alleles of 3.7 and average PIC of 0.56 in molecular diversity analysis of 27 rice cultivars using 12 SSR markers and Salem and Sallam ( 2016 ) who obtained average values of 4.5 and 0.57 for number of alleles per locus and PIC respectively in genetic diversity study of 22 Egyptian and exotic rice genotypes using 23 SSR markers. Whereas Pandita et al ( 2023 ), Akter et al ( 2022 ) and Bajracharya et al ( 2006 ) reported lower mean values than our findings for PIC and number of alleles per locus.…”

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

“…Huo et al (2021) stated that other types of repeat sequences in the flanking region could become a significant constraint in the primer design process. Moreover, the use of SSR primers, designed using the polymorphic dinucleotide SSR motifs was reported as effective in the date palm (Naeem et al 2018), oil palm (Zhou et al 2020b), chilli (Zhong et al 2021), tomato (Castellana et al 2020), rice (Tripathi et al 2020), and wheat (Haque et al 2021). Therefore, only dinucleotide repeats were further evaluated in this study.…”