Identification of alkali-tolerant candidate genes using the NGS-assisted BSA strategy in rice

Rice (Oryza sativa L.) is a saline-alkali-sensitive crop. Saline-alkali environments can seriously affect the growth, development, and yield of rice. The mechanisms of salt tolerance and alkali tolerance in rice are different; thus, it is very important to study and explore the alkali-tolerant gene loci to improve the saline-alkali tolerance of rice varieties. In this study, the japonica rice varieties Dongnong 425 (DN425) and Changbai 10 (CB10) and a hybridized recombinant inbred line (RIL) population were used as materials to be irrigated with Na₂CO₃ solution under field test conditions. A resistant pool (R-pool) and a sensitive pool (S-pool) were constructed by selecting the lines with extremely high and extremely low 1000-grain weight (TGW), respectively, from the RIL population under alkali treatment. Four candidate TGW regions on chromosomes (Chr.) 2 and 3 were associated using the bulked segregant analysis (BSA) strategy assisted by next-generation sequencing (NGS) technology (NGS-assisted BSA). Using the linkage analysis, QTL-qATGW2-2 in the candidate region was mapped within a range of 116 Kb between the SSR marker RM13592 and the Indel marker Indel3 of Chr. 2, which contained 18 predictive genes. The BSA sequencing results showed that Os02g39884 contained a nonsynonymous substitution mutation SNP (nsSNP), leading to the transformation of a residue from arginine (cGg) to glutamine (cAg); thus, Os02g39884 was inferred to be the candidate gene of qATGW2-2. The results of the qRT-PCR analysis also confirmed this. This paper provides important information for the rapid and accurate identification of the alkali-tolerant gene loci in rice.

The online version contains supplementary material available at 10.1007/s11032-021-01228-x.