Abstract:

Drought is one of the key factors limiting the yield of japonica rice.Exploring the genetic mechanism of drought tolerance in japonica rice at the germination stage,screening drought-tolerant candidate genes,and identifying their superior haplotypes provide a theoretical basis for deciphering the drought tolerance mechanism of japonica rice at the germination stage and developing related molecular markers.139 core germplasm resources of japonica rice from Northwest China were used as materials.Japonica rice seeds after radicle emergence were subjected to simulated drought stress using 15% PEG-6000.Six drought tolerance-related traits,including relative germination rate(RGR)and relative root length(RRL),were determined.Combined with 255 501 high-quality single nucleotide polymorphisms(SNPs),genome-wide association studies(GWAS)were conducted using the general linear model(GLM),mixed linear model(MLM),and fixed and random model circulating probability unification(FarmCPU)model.Haplotype analysis was further performed based on drought tolerance phenotypic data to identify potential candidate genes.The results showed that the mean values of the six drought tolerance traits followed a normal distribution,with coefficients of variation(CV)ranging from 3.43% to 56.25%.Among these traits,the relative root and shoot dry weight(RRSDW)exhibited the largest CV and showed a significantly positive correlation with relative root length(RRL),relative shoot length(RSL),and relative root and shoot fresh weight(RRSFW).GWAS for the six drought tolerance traits using high-density SNPs detected a total of 1 164 distinct SNPs,among which 379 were regarded as high-confidence SNPs loci and 6 as quantitative trait nucleotides(QTNs).By integrating the 50 kb upstream and downstream regions of these loci,14 significant SNPs loci were screened out,corresponding to 14 reliable quantitative trait loci(QTL)candidate intervals,which were mainly significantly associated with RRSDW.Genes within these 14 intervals were further predicted and analyzed using databases.With missense mutations in exons as the criterion,the gene LOC_Os03g56130,which encodes lichenase-2 precursor,was identified.Combined with drought tolerance phenotypes,haplotype analysis of this gene revealed that 5 missense mutations in exons constituted 4 haplotypes.Among them,Hap.2 showed a significantly higher RRSDW than the other haplotypes,being identified as the superior haplotype.These findings indicate that LOC_Os03g56130 is a potential candidate gene associated with drought tolerance in japonica rice at the germination stage.

Key words: Japonica rice, Genome-wide association study, Drought tolerance, Germination stage, Gene mining

CLC Number: 

• S511.22

• Q943.2植物基因工程