Molecular and morphological characterization of Indian farmers rice varieties (Oryza sativa L.)

Genetic relatedness among Indian farmers’ rice varieties were assessed using 24 distinct rice microsatellite markers. The 41 rice genotypes studied included 14 improved varieties and 27 landraces collected from different parts of India. The number of alleles per microsatellite locus ranged from 2 to 4, averaging 2.79 alleles per locus. Polymorphism information content (PIC) values ranged from 0 to 0.66, with an average of 0.38. The band size for a given microsatellite locus varied between 80 bp and 580 bp. Characterization of the varieties was also done for various morphological parameters including number of grains per panicle, thousand grain weight, length and breadth of whole and milled grains, cooking qualities like grain elongation ratio, grain aroma and alkali spreading value. Cluster analyses were used to group cultivars by constructing dendrograms based on SSR marker analysis and morphological characterization of grains. The dendrogram based on molecular marker analysis grouped the 41 rice cultivars into four diverse groups. Genetic relatedness was observed for most of the varieties in cluster II for grain quality traitsaroma and grain length/breadth. Clustering of these varieties according to their genotypes as well as phenotypes revealed the possible linkage or pleiotropic effects of the genomic regions associated with some grain quality traits. Information generated through cluster analysis based on phenotypic and genotypic data could be efficiently used in breeding rice varieties harboring grain quality traits. Pure-line selection can be made using farmer varieties that are characterized morphologically and phenotypically in the study.