Genetic Dissection of Alkalinity Tolerance at the Seedling Stage in Rice (Oryza sativa) Using a High-Resolution Linkage Map

Abstract

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.

Comparison of the Morpho-Physiological and Molecular Responses to Salinity and Alkalinity Stresses in Rice

“…Due to the co-occurrence of alkaline and saline stress in coastal and arid regions, understanding the genotype-specific tolerance mechanisms can provide guidance in breeding rice varieties with improved adaptation under stressful environments. Investigating the impacts of only one type of stress, as performed in previous studies [ 32 , 33 , 40 ], limits our ability to develop varieties tolerant to multiple stresses. This study addressed this research gap through gaining an understanding of both common and distinctive adaptive mechanisms of tolerance to both stresses in rice.…”

“…A transcriptomic study suggested that alkalinity-responsive genes at the early seedling stage were associated with hormone signal transduction and secondary metabolite biosynthesis [ 5 ]. Both QTL mapping and genome-wide association studies identified candidate genes for traits associated with alkali tolerance [ 31 , 32 , 33 ]. In alkaline soils, Fe deficiency is due to its insoluble hydroxide and oxide forms in soil under high-pH conditions [ 34 ].…”