Genetic Analysis of Drought Tolerance in Rice (Oryza sativa L.)

Abstract

Drought is a major challenge in rice production system worldwide. We conducted a phenotypic screening of the USA rice genotypes for drought tolerance and assessed genetic diversity using SSR markers. Identification of QTLs for drought tolerance during both vegetative and reproductive stage was done using genotyping by sequencing (GBS) based saturated SNP linkage map. The rice genotypes Jes, Leah, Roy J, Jazzman, and Madison were found to be drought tolerant. Population structure analysis grouped the USA rice genotypes into California, Louisiana, and Arkansas types. Marker-trait association showed that markers RM570 and RM351 were significantly associated with grain yield, spikelet fertility, and harvest index with 7% of the phenotypic variance. RM302 and RM461 were significantly associated with shoot dry weight with 9% of the phenotypic variance. Fourteen additive QTLs were identified for root length, shoot length, fresh root mass, fresh shoot mass, number of tillers, dry root mass, dry shoot mass, and root-shoot ratio. A majority of the drought responsive QTLs were located on chromosome 1. The expression of QTLs varied under stress and irrigated conditions. Shoot length QTLs qSL1.38 and qSL1.11 were congruent to dry shoot mass QTL qDSM1.38 and dry root mass QTL qDRM1.11, respectively. Analysis of genes present within QTL intervals revealed many potential candidate genes such as laccase, Calvin cycle protein, serine threonine protein kinase, heat shock protein, and WRKY protein. In the reproductive stage drought screening, 21 QTLs were discovered for days to flowering, plant height, leaf rolling score, plant dry matter content, spikelet fertility, grain yield, yield index, and harvest index. A major QTL for plant height qPH1.38 was identified in a narrow confidence interval on chromosome 1. The QTLs, qDTF3.01 and qPH1.38, overlapped with the previously identified QTL qDTY1.1 and Hd9, respectively. A large-effect QTL qLRS1.37 was identified close to the sd1 locus on chromosome 1. A grain yield QTL qGY1.42 located on chromosome 1 contained only 4 candidate genes. There was no overlapping of QTLs for the root traits and the yield attributes. The important candidate genes present within the large effect drought tolerance QTL regions are MYB transcription factors, no apical meristem protein (NAC), potassium channel protein, nuclear matrix protein1, and chlorophyll A-B binding protein. The drought tolerant US rice genotypes identified in the genetic diversity analysis will be valuable for breeding programs whereas the candidate genes and the QTL information will set the foundation for application of marker-assisted pyramiding approach to