Indian Society of Genetics & Plant Breeding

Haplotype diversity and association analysis of SNAC1 gene in wild rice germplasm

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Effect of SNAC1 gene variants on drought tolerance was
investigated in wild rice accessions. A total of 46 INDELs
and 44 SNPs were identified including 17 SNPs in the coding
region of the gene across the 164 Indian wild rice accessions
and four cultivated rice genotypes. Based on the sequence
variation, 25 haplotypes were identified including four
specific to drought tolerant accessions. Translation of
different allele sequences showed existence of five different
SNAC1 protein variants. Evolutionary study on the basis of
nucleotide sequence variation in the SNAC1 gene with
different neutrality test suggested purifying selection in
the wild rice accessions. Association analysis revealed that
four SNPs were showing significant association with
drought tolerance. The significantly associated SNPs and
their associated haplotypes can further be used for the
development of drought tolerant rice cultivars.

Keywords: Association analysis, haplotype diversity, single nucleotide polymorphism, SNAC1 gene, wild rice


Year: 2015
Volume: 75
Issue: 2
Article DOI: 10.5958/0975-6906.2015.00025.5
Print ISSN: 0019-5200
Online ISSN: 0975-6906


Balwant Singh, Vinod Kumar, Pankaj Kumar Singh, Pa info_circle

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