Abstract
BackgroundSalinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in japonica rice at the bud stage.ResultsA population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage, qAT11, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in qAT11 that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390). In addition, we performed phenotype verification on the CRISPR/Cas9 mutant of LOC_Os11g37390.ConclusionBased on these results, LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390 were the candidate genes contributing to alkaline tolerance in japonica rice. This study provides resources for breeding aimed at improving rice responses to alkalinity stress.
Highlights
Salinity-alkalinity stress is one of the major factors limiting rice production
Based on these results, LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390 were the candidate genes contributing to alkaline tolerance in japonica rice
The mean Root length under alkali stress (ARL) were lower than root lengths (RL), indicating that alkali stress depressed the growth and development of japonica rice at the bud stage
Summary
Salinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. Genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. Soil salinity-alkalinity is one of the most important abiotic stresses limiting agricultural production. About 80 million hectares of irrigated soil worldwide are damaged by saline and alkaline stress, accounting for about 40% of the total irrigated area. Soluble salts in saline-alkali soil mainly include cations, such as Na+, Ca2+, Mg2+, and K+, and anions, such as CO32−, HCO3−, Cl−, SO42−, and NO3−, all of which come from neutral or alkaline salts. The development of rice production on saline-alkali land has great significance for improving saline-alkali land and food security
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