Molecular Genetics of Salinity Tolerance in Rice (Oryza sativa L.)

Abstract

Due to the threat of salinity stress to Louisiana rice production, an effort was made to understand the molecular genetics of salinity tolerance with the overall goal of developing salt tolerant varieties. The objectives of this study were to 1) determine if salinity tolerance exist in the US rice varieties, 2) map the additive and epistatic QTLs for traits related to seedling salinity tolerance in recombinant inbred lines (RILs) using genotyping-by-sequencing (GBS)-derived SNP markers, and 3) identify and validate stable QTLs and their effects in introgression lines (ILs) of Pokkali in Bengal background. All experiments for phenotypic characterization were conducted in hydroponics at salinity level of 12dSm-1 in the greenhouse. Among the thirty Southern US rice varieties characterized under salt stress, LAH10, R609, and Cheniere were tolerant. Additionally, CL162, Jupiter, Jazzman, Templeton, Cypress, Neptune, and Caffey were identified as moderately tolerant based on clustering and discriminant analyses using the linear combination of six traits. On the other hand, clustering based on DNA profiles did not correspond to the varietal grouping based on salinity responses. Nona Bokra, Pokkali, and Pokkali-derived lines remained the donors of choice for highest salt tolerance. Alternatively, TCCP266, Geumgangbyeo, and R609 with few undesirable agronomic traits were recommended as donors for rice improvement. For QTL mapping, 189 lines of F6 RIL population were phenotyped and characterized by GBS. A total of 9303 SNP markers were used for construction of genetic map. Eighty-five QTLs with small and large effects were identified for nine traits. Of which, 11 QTLs co-localized with 14 reported QTLs. Epistatic QTLs were also mapped and indicated the complexity of salinity tolerance. Based on the annotation of candidate genes within QTL intervals, ion transporters, osmotic regulators, transcription factors, and protein kinases may play important roles in salinity tolerance. On the other hand, at least 14 QTLs in RILs were validated in the IL population. Our study emphasized the importance of salt injury score (SIS) and seedling vigor-QTLs for salinity tolerance. Based on tolerant ILs, the probable mechanisms of tolerance are Na+ dilution in leaves, Na+ ion compartmentation, and by synthesis of compatible solutes. The tolerant ILs will serve as improved variety of Bengal or donor breeding lines for transferring salinity tolerance to other US elite varieties.