Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice

Abstract

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.

Genome-wide association studies identified OsTMF as a gene regulating rice seed germination under salt stress

“…In the qGRG4 locus, OsHAK1, a well-characterized high-affinity K + transporter that promotes rice seedling growth under salt stress, is present (Chen et al, 2015(Chen et al, , 2018. The OsHAK1 gene was also reported before in the q4.8 locus (Zhang et al, 2023), and is associated with relative germination rate on the 3 rd day under saline-alkali stress. In addition, other HAK genes such as OsHAK12 (Zhang et al, 2021), OsHAK16 (Feng et al, 2019) and OsHAK21 (He et al, 2019;Song et al, 2021) are implicated in salt tolerance in rice.…”

“…qGRG3-1 overlaps with the reported 16.66−17.02 Mbp region on chromosome 3, which is associated with shoot fresh weight under salt stress (Yu et al, 2023). qGRG3-2 overlaps with the reported q5.11 locus that is associated with the relative germination rate under saline-alkali stress (Zhang et al, 2023). However, no salt tolerance-related gene has been reported in these regions.…”

SNP Loci and Favorable Haplotype Mining for Alkalinity Tolerance in the Rice Bud Stage

“…Rice alkalinity tolerance is a complex trait controlled by multiple genes [11]. To date, approximately 182 quantitative trait loci (QTLs) related to alkalinity tolerance have been identified [12][13][14][15][16][17]. Li et al [1] analyzed 295 japonica rice varieties and found that qSNK3-1 (15.0 Mb), which is located on chromosome 3, was correlated with ion homeostasis under salinity-alkalinity stress.…”