www.IndianJournals.com Members Copy, Not for Commercial Sale Downloaded From IP - 14.139.229.194 on dated 24-Jun-2015 Indian J. Genet., 75(2): 157-166 (2015) DOI: 10.5958/0975-6906.2015.00025.5 Abstract 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. Key words: Association analysis, haplotype diversity, single nucleotide polymorphism, SNAC1 gene, wild rice Introduction Drought is the most serious abiotic stress that limits crop production under rainfed conditions. Rice (Oryza sativa L.) is generally grown in flooded conditions and it is susceptible to drought stress due to its shallow root distribution and limited capacity to absorb water from deep soil (Kondo et al. 2003). The global warming that has occurred in recent years has caused serious drought damage in rice-growing areas that rely on rainwater and lacking source for irrigation. So, the enhancement of drought tolerance in rice is becoming an important way to stabilize rice production in areas with rainfed agriculture. Some drought stress related parameters in crop species have been investigated as criteria for improving water deficit tolerance through breeding programmes. Assessment of drought tolerance in rice can be easily evaluated using physiological parameters like canopy temperature, chlorophyll content, leaf rolling and relative water content (RWC). First response to drought stress is the reduction of transpiration which increases canopy temperature due to less transpiration cooling (Rizhsky et al. 2004) and it can be measured using infrared (IR) thermometry (Carrity and Toole 1995). Drought stress produces reactive oxygen species (ROS) which lead to lipid per-oxidation and consequently, results in chlorophyll destruction (Fotovat et al. 2007). Leaf rolling occurs due to the inability of leaves to sustain the transpiration demand of the plant (Blum 1988) and can successfully used to assess drought tolerance (Chang et al. 1974). Plants showing leaf rolling at early stage of stress appear to have poor drought tolerance (Abd Allah 2009). Stress intensity also affects leaf RWC and tolerant genotypes have higher rate of RWC than susceptible genotypes (Alizade 2002; Ganji Arjenaki 2012). Drought tolerance is a complex quantitative trait, and in rice, tremendous efforts have been made to dissect drought tolerance through QTL mapping (Yu et al. 2006). The loci controlling drought tolerance are widely distributed across the rice genome but only few major QTLs are mapped for a specific population and environment. Drought tolerance leads to induction *Corresponding author’s e-mail: nksingh@nrcpb.org Published by the Indian Society of Genetics & Plant Breeding, F2, First Floor, NASC Complex, PB#11312, IARI, New Delhi 110 012 Online management by indianjournals.com Haplotype diversity and association analysis of SNAC1 gene in wild rice germplasm Bikram Pratap Singh # , Balwant Singh, Vinod Kumar, Pankaj Kumar Singh, Pawan K. Jayaswal, Shefali Mishra and Nagendra K. Singh* National Research Center on Plant Biotechnology, Pusa Campus, New Delhi 110 012 # Banasthali Vidyapith, Rajasthan 304 022 (Received:January 2015; Revised: April 2015; Accepted: April 2015)