Genetic structure and diversity analysis of traditional rice (Oryza sativa L.) varieties of north Kerala

Abstract

The study entitled “Genetic structure and diversity analysis of traditional rice (Oryza sativa L.) varieties of North Kerala” was carried out at the department of Genetics and Plant Breeding, College of Agriculture, Padannakkad. The main objective of the study was to assess genetic diversity and population genetic structure of traditional rice varieties (TRVs) of North Kerala based on Distinctiveness, Uniformity and Stability (DUS) characterization and SSR marker-based molecular analysis. The material for the study comprised of 50 TRVs collected from different districts of North Kerala. The experiment was laid out in augmented design at IF-II, Karuvacheri (12°14′45′′N; 75° 8′6′′E). Morpho-metric characterization of TRVs for 24 vegetative, 22 reproductive and three seed traits were carried out during September-February 2021 following the DUS descriptor of rice. Quantitative traits (QTs) recorded included five DUS traits and four additional traits (plant height, number of tillers plant-1, number of productive tillers plant-1 and number of spikelets panicle-1). Among 49 DUS traits, seven were monomorphic, 10 were dimorphic and 32 were polymorphic. As per analysis of variance (ANOVA) for QTs, TRVs showed highly significant mean squares for four quantitative traits such as plant height, number of spikelets panicle-1, 1000 grain weight and grain length. Variation due to ‘checks’ were also significant for the said traits. Hence, actual trait mean values were adjusted by calculating the block effect. TRVs showed a mean height of 112.87 cm, 5.61 tillers plant- 1, 5.24 productive tillers-1 and 113.64 spikelets panicle-1 and 23.54 g weight for 1000 grains. Among nine QTs, higher variance was observed for spikelets panicle-1 and plant height. The Phenotypic Coefficient of variation (PCV) and Genotypic Coefficient of Variation (GCV) was higher for number of tillers plant-1, number of productive tillers plant-1, number of panicles plant-1, number of spikelets panicle-1 and 1000 grain weight. High broad-sense heritability coupled with high genetic advance was observed for plant height, number of tillers plant-1, number of spikelets panicle-1, 1000 grain weight and grain length indicating additive gene effects and efficiency of selection-based breeding methods. K-means clustering analysis grouped 50 TRVs into two clusters. The total variability among 50 TRVs were extracted through principal component (PC) analysis 153 and three significant PCs (accounting 72.57% of total variability) were obtained. Further, total variability was visualized in the form of PC1 vs PC2 biplot. In order to decipher molecular diversity among TRVs, laboratory experiment was carried out at NAHEP-CAAST lab, College of Agriculture, Padannakkad. Genomic DNA was isolated from 21 days old seedlings following modified CTAB method. The 50 TRVs were genotyped with 30 SSR markers (shortlisted by IRRI based on genome-wide coverage and higher PIC value) following standard PCR, electrophoresis and visualization techniques. Among SSRs, 18 were monomorphic and 12 were polymorphic. Among polymorphic SSRs, RM 413 and OSR 13 detected 3 alleles/locus and showed highest PIC value (0.559 and 0.594, respectively) and Nei’s genetic diversity (0.55 and 0.59, respectively). STRUCTURE analysis revealed three sub-populations and admixture among 50 TRVs. Population admixture and preferential gene flow among TRVs were further confirmed by Analysis of molecular variance (AMOVA) as estimate of ‘among population’ variance was lower. Among three sub-populations, maximum diversity was observed among TRVs of first sub-population as indicated by higher estimates of the Shannon index and unbiased expected heterozygosity. In conclusion, 50 TRVs were diverse with respect to 32 DUS traits and highly variable for 4 QTs. Polymorphic descriptors like leaf colouration, lemma pubescence, panicle exertion etc. are of special significance as they have the potential to act as morphological markers for TRV conservation and registration. The TRVs namely, ‘Chuvannachitteni’ and ‘Mundom’ were most diverse as per biplot analysis and K means clustering. However, SSR- based diversity analysis revealed low level of polymorphism and population structure among TRVs. Genetic diversity as a whole includes both exon and intron variability, conservation and registration of TRVs will be optimized by complementing DUS characterization with more functional markers.