Identification of Genomic Region Associated to Drought Tolerance Traits during Vegetative Growth Stage of Rice Using Genotyping By Sequencing Approach.

Identification of genomic region associated to drought tolerance traits during vegetative growth stage of rice using genotyping by sequencing approach

Uttam Bhattarai¹ and Prasanta K. Subudhi¹

¹School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA

Abstract

Drought is a major abiotic stress which limits rice productivity under rainfed environment. The quantitative trait loci (QTLs) for drought tolerance traits identified in the previous studies have large confidence intervals due to low saturation of markers. Further, drought studies largely focused on the above ground agronomic traits and little emphasis was given to root traits. Therefore, this study aims to identify QTLs for root and shoot traits at the vegetative stage with narrow confidence interval using a genotyping by sequencing (GBS) based highly saturated SNP linkage map. One hundred eighty-one recombinant inbred lines developed from a cross between Cocodrie and N-22 was used to evaluate eight root and shoot traits under drought stress. Plants were grown in 75cm long plastic pots to allow maximum root growth and drought was imposed during the vegetative growth stage. A total of 4748 GBS-based SNPs were used for construction of a linkage map that covered 365Mb of the rice genome. Thirty-three additive QTLs and fifty-four pairs of epistatic QTLs were identified for root length, shoot length, fresh root weight, fresh shoot weight, number of tillers, dry root weight, dry shoot weight, and root-shoot ratio. QTLs for shoot length (qSL1.38), dry root mass (qDRM1.38), and dry shoot mass (qDSM1.38) were congruent. qSL1.37 and qSL1.38 were found to be consistently expressed in both stressed and non-stressed environments. Annotation and functional classification of genes showed that protein kinase, actin orthologue, heat shock protein, and WRKY protein family play major roles in controlling drought tolerance in rice. This study identified some of the QTLs within low confidence interval and predicted some candidate genes involved in drought tolerance in rice.