Aromatic Rice (Oryza sativa L.) Landraces of Indo-Gangetic Plains of India Harbor Rich Genetic Diversity as Revealed by Phenotypic Traits and Microsatellite Markers

Abstract

Rice (Oryza sativa L.) grains are vital for food security of half of the global population. India has rich diversity for aromatic rice landraces. In order to assess the genetic diversity and population structure in these specialty rices, we characterized 92 germplasm accessions of aromatic rice landraces of Indo-Gangetic Plain region including 10 popular landraces of other states of India using 23 phenotypic traits and 48 microsatellite markers. Landrace accessions displayed huge variability for plant height (PH), culm length (CL), flag-leaf length, auricle colour, leaf-blade pubescence and colour, panicle bearing tillers, panicle length (PL), peduncle length (PdL), panicle exsertion, grain length (GL), grain breadth (GB), hull colour and thousand grain weight (TGW). First five principal components contributed 81.24% phenotypic variation. High positive associations were found between PH and CL (r = 0.83), PdL and PL (0.66), GL and TGW (0.78), and GB and TGW (0.59). Molecular analysis with 48 genome-wide HvSSR markers revealed 11.0 alleles per locus, which evidently showed that a high level of DNA polymorphism exists between landrace accessions. The structure analysis revealed four subpopulations with numerous accessions sharing alleles with other groups. Gene diversity assay revealed high levels of gene diversity (HE = 0.83), Shannon's Information index (I = 1.99) and gene flow (Nm = 1.51) between accessions of aromatic rice landraces. Wright′s F-statistics revealed moderate genetic differentiation (FST = 0.14) among subpopulations and high degree of inbreeding (FIS=0.92) within subpopulations. This was also supported by high polymorphism information content (PIC = 0.806) and analysis of molecular variance (AMOVA), which revealed 79% variance among genotypes. The unique and rare alleles could be used for DNA fingerprinting and differentiation of genotypes. A high number of multiple alleles were observed in number of landrace accessions, which showed the presence of heterogeneity and heterozygotes in the landrace materials. The results of present study are useful for utilization of the landraces in genetic enhancement programmes specially designed for rice quality improvement and consumer's preference.