Molecular characterization in relation to seed vigour related traits in rice
Loading...
Date
2021
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
DRPCAU, PUSA
Abstract
Seed vigour is important for crop establishment in rice. The present study was undertaken to characterize the rice genotypes using seed vigour influencing physio-biochemical traits, as well as, molecular profiling based on microsatellite markers to investigate molecular level genetic divergence and population structure pattern among a set of rice genotypes and to evaluate the marker trait association, if any, between marker phenotype and seed vigour related traits under consideration. Significant genotypic differences were observed for all physio-biochemical traits recorded in a set of locally adapted rice genotypes. On the basis of mean performance, six genotypes, namely, Rajendra Neelam, RAU1421-12-1-7-4-3, Vaidehi, Rajshree, RAU1415-35-76-9-5-3-4 and Rajendra Suwasini appeared to be superior entries based on the score of physio-biochemical traits. The correlation studies revealed, significant positive correlation of seed vigour with catalase, chlorophyll, carotenoid and amylose content. A significant positive correlation of higher order was observed among chlorophyll and carotenoid and between starch and amylopectin, although, correlation of starch with amylose was relatively weak. Significant positive correlation was also found between total anthocyanin, total flavonoids and total phenolics content. Catalase activity was positively correlated with superoxide dismutase activity. Negatively significant correlation was observed only between peroxidase activity and total flavonoid content, albeit of lower magnitude. First
five principal component axes accounted for 82.6% of total variance between the sixteen recorded physio-biochemical traits. Starch, amylose, amylopectin, anthocyanin, phenolics and catalase appeared to be important classification variables, from this investigation. Average taxonomic distance based two-dimensional ordination identified three genotypes, namely, Rajendra Neelam, Sudha and RAU1451-66-1-1-5-1 to be relatively more diverse from rest of the genotypes based on physio-biochemical traits. Simple sequence repeats-based polymorphism survey in 18 genotypes of rice using 38 microsatellite markers detected a total of 275 allelic variants with an average of 7.2 alleles per primer. Polymorphism information content of 38 SSR primer pairs ranged from 0.593 to 0.877 with an average value of 0.766 and polymorphism per cent reflecting the proportion of unique alleles ranged from 0% to 57.14% with an average value of 34.40%. Out of 38 primer pairs, RM85, RM205, RM328, RM337, RM6275, RM7003, RM7364 and RM14978 appeared to be relatively more polymorphic and informative primers. Analysis of genetic divergence revealed ample molecular level genetic variation and allowed differentiation and classification of rice genotypes into four groups. Structure analysis revealed that the targeted genomic regions of eighteen rice genotypes are basically the admixtures of different combinations of three ancestral components. Single marker analysis detected the association of the traits, namely, amylose, total protein, total anthocyanin, total flavonoids, total phenolics, starch, carotenoids, total chlorophyll, chlorophyll a, chlorophyll b, seed vigour index I, superoxide dismutase, catalase and peroxidase with the molecular markers. Association of the trait, catalase with marker RM5310 located on chromosome 1, amylose with marker RM440 on chromosome 5, total anthocyanin with marker RM547 on chromosome 8 and total flavonoid with marker RM286 and RM547 on chromosome 11 and 8, respectively were also reported in earlier study and was validated in this investigation. The marker-trait association can be further validated and effectively utilized in marker-assisted selection program for improvement in marker-associated trait of interest.