Genome-Wide Association Study Of Anaerobic And Salt Stress Tolerance During Germination And Early Growth In Rice

Multiple stress tolerance at seed germination stage is crucial for better crop establishment in the direct seeded rice ecosystem.Therefore,identification the tolerant germplasms and candidate gene,understanding of the molecular mechanisms of multi-stress tolerance in rice is essential for adapting breeding.The utilization of diverse plant materials,high-throughput single nucleotide polymorphism(SNP)genotyping platforms and advanced statistical data analyses made a powerful platform for understanding molecular mechanisms(gene/QTL mapping)and adapting breeding strategy.In this study,genome-wide association analysis(GWAS)was carried out using the SNP data for 434 HHZ IB ILs and 498 germplasm accessions to identify the stably QTL/gene for anaerobic,salinity and combined anaerobic-saline tolerance at germination and early growth stages of rice.Phenotyping of the mapping population against anaerobic,saline and combined anaerobic-saline stresses were carried out to identify novel QTL/genes for respective traits following standard protocols.Of phenotypic traits,seedling survival percent(SP)and anaerobic response index(ARI)for anaerobic stress,germination percent(GP),shoot and root length(SL,RL),and biomass(BM)for salt stress and anaerobic-saline response index(ASRI)for combined anaerobic-saline stresses.All traits were positively correlated in respective stress and showed significant variation.Through GWAS using CMLM,a total of82 significant loci were detected,7 for SP,15 for ARI,17 for GP,12 for SL,12 for RL,11 for BM and 8 for ASRI,and these loci explained phenotypic variance an average 8.38 %,5.48% and 5.86 % in anaerobic,salt,and anaerobic-saline stress,respectively.Among them,35 were previously reported and 47 were newly identified QTL,only 26 QTL were in HHZ IB and 48 in germplasm,and overall 17 genetic overlaps were between traits or mapping population in three stresses.Expression patterns with functional activities of candidate genes in GO(Gene ontology)enrichment analysis indicating that detected QTL/genes were highly related with stress,‘lipid binding(MF)’ in anaerobic germination,‘response to stimulus(BP)’ in salt germination and ‘kinase activity(MF)’ in anaerobic-saline germination.We demonstrated one locus mapped on Chromosome 3,9 and 1 for anaerobic,salt and anaerobic-saline stress,respectively.These regions contained four putative candidate genes LOC_Os03g52450 and LOC_Os03g52475,LOC_Os09g21810 and LOC_Os01g47050,which were strongly expressed under stress and showed significant haplotype differences with phenotypic value.Among the candidate genes,LOC_Os03g52450(C/T)is annotated as ’GATA transcription factor 25’ involving in plant developmental control and responses to the environment;and LOC_Os03g52475(T/C)is as ’pentatricopeptide’ acts for embryodevelopment,hypersensitivity to abiotic stress under anaerobic stress.LOC_Os09g21810(C/T)is annotated as ’retrotransposon protein’ involving in host functional plasticity and able to redirect stress stimuli for salt tolerance.LOC_Os01g47050(A/C)is the member of’F-box domain’ and involving multicellular organismal development,protein modification process and catalytic activity under anaerobic-saline stress.The identified candidate genes/SNP in this study could be directly used to accelerate marker-assisted selection(MAS)in rice breeding programs for anaerobic,saline and combined anaerobic-saline tolerance.However,it needs to be verified and functionally characterized in isogenic background.Reverse genetic studies are therefore defensible.Together,these efforts will contribute to the breeding of more adapted cultivars and a better understanding of multiple stress tolerance mechanisms in rice.