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Although both salinity and alkalinity result from accumulation of soluble salts in soil, high pH and ionic imbalance make alkaline stress more harmful to plants. This study aimed to provide molecular insights into the alkalinity tolerance using a recombinant inbred line (RIL) population developed from a cross between Cocodrie and Dular with contrasting response to alkalinity stress. Forty-six additive QTLs for nine morpho-physiological traits were mapped on to a linkage map of 4679 SNPs under alkalinity stress at the seedling stage and seven major-effect QTLs were for alkalinity tolerance scoring, Na + and K + concentrations and Na + :K + ratio. The candidate genes were identified based on the comparison of the impacts of variants of genes present in five QTL intervals using the whole genome sequences of both parents. Differential expression of no apical meristem protein, cysteine protease precursor, retrotransposon protein, OsWAK28 , MYB transcription factor, protein kinase, ubiquitin-carboxyl protein, and NAD binding protein genes in parents indicated their role in response to alkali stress. Our study suggests that the genetic basis of tolerance to alkalinity stress is most likely different from that of salinity stress. Introgression and validation of the QTLs and genes can be useful for improving alkalinity tolerance in rice at the seedling stage and advancing understanding of the molecular genetic basis of alkalinity stress adaptation.

Drought is a major constraint in some rice-growing areas of the United States. Its impact is most severe at the reproductive stage resulting in low grain yield. Therefore, assessment of genetic and phenotypic variation for drought tolerance in US rice germplasm is necessary to accelerate the breeding effort. Evaluation of 205 US rice genotypes for drought tolerance at the reproductive stage revealed tolerant response in rice genotypes Bengal, Jupiter, Cypress, Jazzman, Caffey, and Trenasse. Harvest index and fresh shoot weight were identified as important traits to explain the majority of variability among the genotypes under drought tolerance. Genotyping with 80 SSR markers indicated a low level of genetic diversity in US germplasm. Population structure analysis grouped the genotypes into eight clusters. The genotypes from California, Louisiana, and Arkansas formed distinct subgroups. Texas genotypes were similar to those from Louisiana and Arkansas. Marker-trait association analysis showed significant association of RM570 and RM351 with grain yield, spikelet fertility, and harvest index whereas shoot dry weight showed association with RM302 and RM461. The drought-tolerant genotypes identified in this study and the SSR markers associated with drought tolerance attributes will be helpful for development of improved drought-tolerant rice varieties through marker assisted selection.