IDENTIFICATION OF LOCI INVOLVED IN SALT TOLERANCE BY ASSOCIATION ANALYSIS ON japonica RICE
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Date
2018-01
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AAU, Jorhat
Abstract
Soil salinity is one of the environmental constraints that affect crop cultivation worldwide. More than 800 Mha of land throughout the world and about 20% of the irrigated areas suffer from salinization problems (FAO, 2008). Among cereals, rice (Oryza sativa L.) is one of the most salt-sensitive although cultivars can differ in their response to salt stress (Horie et al., 2012; Munns and Tester, 2008). In European coastal rice areas, salty raining and the salt water intrusion phenomenon caused by the rise in the sea levels due to climate changes are provoking a tendency toward salinization in the adjacent paddy fields where rice is grown (Yáñez, 2010.) Moreover, the island apple snail (Pomacea maculata) is becoming one of the major pest problems for rice throughout the world, including the European areas. Till date its only effective control measure is to flood the field with sea water, which even though kill the pest but leads to residual salinization problem. In India too, soil salinity is a problem in the coastal rice growing area. It has been estimated that an approximate area of 6.3 million hectares of land is covered by saline soil in India (Patel et al., 2011). Taking into account the above statements, it is clear that the identification of elite rice varieties tolerant to salt stress is necessary. Salinity tolerance in rice is a very complex trait. Genome-wide association study (GWAS) is proving to be an effective approach for identifying loci controlling complex traits in plants (Ingvarsson and Street, 2011; Korte and Farlow, 2013; Huang and Han, 2014). In the present work, a phenotyping activity for mid-salt stress has been performed on a subset of rice panel of 281 japonica rice accessions. Then, a GWAS was carried out in order to identify possible loci involved in salt tolerance in japonica rice. The measurement of phenotypic data highlighted variability among the genotypes in response to the treatment. This suggests that the panel might be a good resource for the discovery of traits related to salt stress response. The genome-wide association study identified significant associations between SNPs and the analyzed salt stress-related traits. A preliminary functional analysis of the identified loci by the GWAS has revealed many possible candidate genes involved in salt tolerance in japonica rice.