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.

Keywords: Na+/K+ ratio; Oryza sativa; abiotic stress; candidate genes; genotyping-by-sequencing; quantitative trait loci; salinity; single nucleotide polymorphism.

Figure 1

Frequency distribution of various morphological and physiological traits of Cocodrie × Dular RILs for alkalinity tolerance at the seedling stage with arrowheads indicating the trait means of Cocodrie (C), Dular (D), and RIL population (R). LCHL-log chlorophyll content; LSHL-log shoot length.

Figure 2

Performance of Cocodrie and Dular under control (A) and alkaline stress environments (B).

Figure 3

Comparison of Cocodrie and Dular under stress and control environment for alkalinity tolerance traits. Asterisks indicate significant difference between the means of Cocodrie and Dular under control and alkaline stress environment at 0.05 level of probability.

Figure 4

Positions of the QTLs on the linkage map for alkalinity tolerance traits in the Cocodrie × Dular RIL population. Red and blue fonts represent Cocodrie and Dular alleles for the increased means, respectively. Dark regions on the genetic map are the marker saturated regions and light regions represent gaps between the markers.

Figure 5

The expression level of selected genes in Cocodrie and Dular 6 h after exposure to alkalinity stress. EF1α was used as the reference gene. Log2 fold change was calculated for gene expression analysis under alkaline stress compared with control. 1–10 represents the genes used for expression analysis. 1-LOC_Os03g59730; 2-LOC_Os03g62430; 3-LOC_Os03g62370; 4-LOC_Os03g62379; 5-LOC_Os08g02050; 6-LOC_Os08g44690; 7-LOC_Os09g39100; 8-LOC_Os10g34650; 9-LOC_Os10g34490; 10-LOC_Os10g35170.