Choice of microsatellite markers for isolation of fertility restorers of wild abortive (WA) type cytoplasmic male sterility in rice

Abstract

Simple sequence length polymorphism was examined in a set of eight effective restorers, four partial restorers, two weak maintainers and four complete maintainers of WA type CMS system in rice using a set of thirty-two microsatellite primer pairs in order to assess the nature and extent of genetic variation among them at molecular level. Altogether 248 allelic variants were detected with an average of 7.75 alleles per primer pairs. Polymorphic information content ranged from 0.508 for RM 6737 to 0.882 for RM 1 with an average value of 0.740 per primer pair. Amongst the primer pairs used, RM 1, RM 206, RM 591 RM 3873 and RM 8146 had remarkably higher number of allelic variants with greater gene diversity and genotype discrimination ability. Using similarity coefficient in numerical taxonomic approach of classification, the entries were differentiated and classified into different groups. Analysis based on molecular profiles allowed discrimination of effective fertility restorers from rest of the entries including partial fertility restorers, weak sterility maintainers and complete sterility maintainers. Principal coordinate analysis based two dimensional plotting of genetic profiles completely supported the results obtained from hierarchical classification of entries and effective fertility restorers were distinctly discriminated from the remaining entries. Four microsatellite primer pairs namely, RM 171, RM 315, RM 3873 and RM 6100, which allowed unambiguous discrimination of the eight effective fertility restorers from rest of the entries. These microsatellite primer pairs, may be further utilized in identification of effective fertility restorers of WA based CMS system in rice.

Seedling stage salt stress response specific characterization of genetic polymorphism and validation of SSR markers in rice

“…Contrarily, the loci with GA and CA di-nucleotide motifs of simple sequence repeats detected relatively lesser number of alleles. This is not in conformity with the earlier report in which perfect di-nucleotide repeat unit GA has been documented to exhibit high level of allelic variation among the rice genotypes (Sajib et al 2012;Kumar et al 2018). The discrepancy may be attributed to a different set of experimental materials and different primer pairs used in the present study.…”

“…Similarly, the number of unique alleles per primer ranged from zero in the case of RM 1287, RM 10745 and RM 10764 to eleven in the case of RM 10825 (Table 2). Precise analysis of the amplification pattern further revealed that the marker revealing greater number of allelic variants per locus, in general, recorded more number of unique alleles in accordance with the earlier reports (Bajracharya et al 2006;Brondani et al 2006;Joshi and Behera 2006;Lapitan et al 2007;Ebana et al 2008;Herrera et al 2008;Borba et al 2009;Pervaiz et al 2010;Rabbani et al 2010;Singh et al 2011;Kumari et al 2016a;Kumar et al 2018). Abundance of unique alleles indicated that the experimental materials subjected to molecular profiling represent a rich source of genetic diversity for their purposeful and effective utilization in rice breeding program with the basic objective to bring genetic improvement in respect of salt tolerance.…”

“…Ample genetic diversity at the molecular level was, therefore, revealed by the range of similarity coefficients (0.0-0.7) obtained for pair-wise combinations of the entries, providing greater confidence for the classification of entries and assessment of genetic relationships. Similar inference has been derived in the studies conducted on the molecular markers including SSR marker based divergence analysis in rice by earlier researchers (Aliyu et al 2011;Kanawapee et al 2011;Dhar et al 2012;Sudharani et al 2013;Shakil et al 2013;Kumar et al 2018;Priyadarshini et al 2018).…”

“…Simple sequence repeat loci with di-nucleotide and trinucleotide repeat motifs, in general, detected greater number of alleles than the repeat loci with tetra-nucleotide and complex repeat motifs. Therefore, the results provided the evidence to strengthen the view point that the primers targeting di-nucleotide repeat sequence motifs are found to be more polymorphic than those amplifying tri-nucleotide, tetra-nucleotide and complex repeat motifs (Lapitan et al 2007;Pervaiz et al 2009;Kumar et al 2018). While establishing the relation between di-nucleotide repeat motifs having a particular type of nucleotide composition and the number of alleles generated by primer pairs (Table 3), it was observed that the simple sequence repeat loci with CT, GT, AC, AT and AG di-nucleotide repeat motifs detected greater number of alleles.…”

“…While most of the entries were placed far away from the centroid of the clusters and only few entries were placed more or less around the centroid, it is evident that entries were distinctly divided into three multi-genotypic groups and susceptible varieties were unambiguously discriminated from moderately and highly tolerant varieties. Therefore, the inferences derived from the similarity coefficients based hierarchical classification were completely supported by the principal coordinate analysis (Islam et al 2015;Kumar et al 2018;Priyadarshini et al 2018). Using both the approaches, susceptible rice varieties were discriminated from tolerant rice varieties without intermixing of varieties.…”