Salinity–alkalinity stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve the tolerance to salinity–alkalinity of rice varieties at the germination stage. Although we have a more comprehensive understanding of salt tolerance in rice, the genetic basis of alkali tolerance in rice is still poorly understood. In this study, we measured seven germination-related traits under alkali stress and control conditions using 428 diverse rice accessions. The alkali tolerance levels of rice germplasms varied considerably during germination. Xian/indica accessions had generally higher tolerance to alkali stress than Geng/japonica accessions at the germination stage. Using genome-wide association analysis, 90 loci were identified as significantly associated with alkali tolerance. Eight genes (LOC_Os01g12000, LOC_Os03g60240, LOC_Os03g08960, LOC_Os04g41410, LOC_Os09g25060, LOC_Os11g35350, LOC_Os12g09350, and LOC_Os12g13300) were selected as important candidate genes for alkali tolerance based on the gene functional annotation and gene-CDS-haplotype analysis. According to the expression levels of LOC_Os09g25060 (OsWRKY76), it is likely to play a negative regulatory role in alkali tolerance during rice germination. An effective strategy for improving rice alkali tolerance may be to pyramid alkali-tolerant haplotypes of multiple candidate genes to obtain the optimal haplotype combination. Our findings may provide valuable genetic information and expand the use of alkali tolerance germplasm resources in rice molecular breeding to improve the alkali tolerance at the germination stage.

The power of selection and phenotypic plasticity of seven rice grain yield (GY) traits was dissected using DNA markers and 226 Minghui86 introgression lines (ILs) phenotyped across four contrast environments of long‐day versus short‐day and drought versus irrigated conditions. Linkage mapping identified 77 main‐effect quantitative trait loci (QTLs) plus 15 groups of epistatic QTLs affecting the GY traits. By characterizing genomic introgression patterns of the donor alleles in ILs selected for high‐ and low‐trait values based on replicated progeny testing across each of the four environments and for high‐ and low‐GY across nine different environmental scenarios, 246 QTLs affecting the seven yield traits were identified. Genetic drag from tight repulsive linkage of genes with opposite effects on the same traits was detected in 45 cases involving 90 (35.8%) QTLs, indicating its wide presence in superior Chinese hybrid parents. The demonstrated selective introgression strategy, including the developed ILs plus the genetic information on the associations of introgressed donor alleles with the yield traits in the ILs would provide a useful platform for future breeding by design.

IntroductionSaline-alkali stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve rice saline-alkali tolerance at the germination stage. MethodsTo understand the genetic basis of saline-alkali tolerance and facilitate breeding efforts for developing saline-alkali tolerant rice varieties, the genetic basis of rice saline-alkali tolerance was dissected by phenotyping seven germination-related traits of 736 diverse rice accessions under the saline-alkali stress and control conditions using genome-wide association and epistasis analysis (GWAES).ResultsTotally, 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified as significantly associated with saline-alkali tolerance, which explained a significant portion of the total phenotypic variation of the saline-alkali tolerance traits in the 736 rice accessions. Most of these QTNs were located in genomic regions either harboring saline-alkali tolerance QTNs or known genes for saline-alkali tolerance reported previously. Epistasis as an important genetic basis of rice saline-alkali tolerance was validated by genomic best linear unbiased prediction in which inclusion of both main-effect and epistatic QTNs showed a consistently better prediction accuracy than either main-effect or epistatic QTNs alone. Candidate genes for two pairs of important epistatic QTNs were suggested based on combined evidence from the high-resolution mapping plus their reported molecular functions. The first pair included a glycosyltransferase gene LOC_Os02g51900 (UGT85E1) and an E3 ligase gene LOC_Os04g01490 (OsSIRP4), while the second pair comprised an ethylene-responsive transcriptional factor, AP59 (LOC_Os02g43790), and a Bcl-2-associated athanogene gene, OsBAG1 (LOC_Os09g35630) for salt tolerance. Detailed haplotype analyses at both gene promoter and CDS regions of these candidate genes for important QTNs identified favorable haplotype combinations with large effects on saline-alkali tolerance, which can be used to improve rice saline-alkali tolerance by selective introgression. DiscussionOur findings provided saline-alkali tolerant germplasm resources and valuable genetic information to be used in future functional genomic and breeding efforts of rice saline-alkali tolerance at the germination stage.