ASSESSMENT OF GENETIC VARIATION AND ALLELE MINING FOR QUALITY TRAITS IN AROMATIC RICE LANDRACES FROM INDO-GANGETIC PLAINS OF INDIA
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Date
2023
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DIVISION OF PLANT GENETIC RESOURCES ICAR - INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI – 110 012
Abstract
Rice crop is vital for food security of half of the global population. India has rich genetic
diversity for both aromatic and non-aromatic rice landraces. We characterized 92 accessions of
aromatic landrace germplasm collected from Indo-Gangetic region including 10 popular
aromatic landraces of other states of India using 26 morphological characters. Landrace
accessions displayed significant variation for plant height, culm length, flag-leaf length, panicle
length, panicle exsertion, panicle bearing tillers, grain size, husk colour, pericarp colour and
1000-grain weight. First four principal components contributed 79% of phenotypic variation.
Very high positive correlations found between plant height and culm length (r = 0.83), peduncle
length and panicle length (0.66), grain length and TGW (0.78), and grain breadth and TGW
(0.59). However, number of panicle bearing tillers showed negative association with grain
length (-0.32), grain breadth (-0.33) and TGW (-0.43). Similarly, culm length also showed
significant negative correlation with grain breadth (-0.48), grain length (-0.43) and TGW (-.046).
Cluster analysis grouped all 92 landrace accessions into four clusters. Molecular analysis using
48 hypervariable microsatellite loci revealed the amplification of 11.0 alleles per locus, which
clearly showed that a high level of DNA polymorphism exists between landrace accessions. The
structure analysis showed the presence of four subpopulations in 96 accessions with numerous
accessions showing allele sharing with other groups. The gene diversity analysis revealed the
presence of high amount of expected heterozygosity (0.83), Shannon's Information index (1.99)
and high gene flow (1.51). This was also supported by high polymorphism information content
(0.806). The landraces revealed the presence of private alleles. 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 studied. The allele mining in BADH2
gene found that the desirable allele (8 bp deletion) was present in homozygous condition in
57.29% accessions, whereas it was in heterozygous state in 15.63% accessions. The C-A SNP
mutation in GS3 gene was detected in Jeera Sail (IC0419046) and Champaran Basmati
(IC0569188). 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 and conservation of diverse constellation of alleles of rice landrace germplasm
Description
T-11072