QTL Mapping And Candidate Gene Discovery For Cold Tolerance At Different Growth And Development Stages In Rice

Cold injury is one of the important critical limiting factors impacting rice production and planting area.It is an effective way to improve cold tolerance of rice by exploring cold-tolerance varieties and cold-tolerance genes.In this study,RIL populations and associated populations were used as test materials to identify cold-tolerance QTL at the germination,bud burst,seedling,booting and flowering stages.High density map was constructed by SNP markers detected by whole-genome re-sequencing technology to detect cold-tolerance QTL loci.Candidate genes were predicted from detected QTL by various methods or environments.The conclusions are as follow:1 An RIL population obtained by crossing Jileng1 hao and Milyang23 was use for QTL mapping.A genetic map containing 2921 Bin markers was constructed by re-sequencing data.This map was used to QTL mapping analysis,and significant cold-tolerance QTL were screened with LOD ≥ 2.5.The results showed that 32 QTLs for cold tolerance were identified at the germination stage;Three QTLs for cold tolerance were identified at bud burst stage;Eight QTLs for cold tolerance were identified at the seedling stage;13 cold-tolerance QTLs were identified at the booting and flowering stages.2 Tolerance and sensitivity mixing pool was constructed for BSA analysis with 0.99 as the threshold,four cold-tolerance loci were detected at the germination stage;23 cold-tolerance loci were identified at the bud burst stages;20 cold-tolerance loci were identified at the seedling stage.3 According to the results of QTL and BSA mapping,the candidate genes for cold-tolerance loci were predicted.At the germination stage,five candidate genes were screened: Os03g0806700,Os03g081155,Os03g0809800,Os03g0812200 and Os03g0809200;At the bud burst stage,three candidate genes,Os07g0619100,Os07g0619500 and Os07g0620400,were screened;At the seedling stage,12 candidate genes,Os07g0517100,Os07g0521500,Os07g05542000,Os07g0521800,Os07g0516300,Os07g0517300,Os07g0545100,Os07g0517700,Os07g0546800,Os07g0547100,Os07g0549800 and Os07g0553633,were predicted.4 The G1004 population of 1004 japonica rice varieties from 11 provinces in China was constructed for cold-tolerance QTL identification at booting and flowering stages,and 287 of them(G287)were selected for cold-tolerance QTL identification at the germination,bud burst and seedling stage.Combined with SNP markers obtained from re-sequencing data,GWAS was carried out at four growth stages,and the significant SNP associated with cold tolerance were screened with-log10(P)≥5as threshold.After significant SNP merging based on LD decay,37 cold-tolerance loci were identified at the germination stage;13 cold-tolerance loci were screened at the bud burst stage;29 cold-tolerance loci were identified at the seedling stage;74 cold-tolerance loci were identified at the booting and flowering stages.5 Qd7ILCG6 identified at the germination stage,QCTS9-1 and QCTS12 detected at bud burst stage,QLTL7 and QLTL3-1 identified at the seedling stage,overlapped with linkage population loci.6 The reliable cold-tolerance loci detected by GWAS analysis were used to predict candidate genes.At the germination stage,four candidate genes,Os07g0490100,Os07g0497500,Os07g0498800 and Os07G0498900,were screened;At the bud burst stage,ten candidate genes,Os03g0233000,Os03g0233500,Os03g0233800,Os03g0235200,Os03g0236675,Os03g0239300,Os03g0240600,Os03g0241600,Os03g0245200 and Os03G0254000,were screened;At the seedling stage,four candidate genes,Os07g0517300,Os07g0519450,Os07g0521500 and Os07g0521800 were screened;At the booting and flowering stage,six candidate genes,Os11g0474500,Os11g0481150,Os11g0481200,Os11g0482400,Os11g0483950 and Os11g0482500,were screened.Three dominant haplotypes of candidate genes for cold tolerance were identified at the bud burst stage.7 Thirty-three,25,10 and 38 cold-tolerant germplasm were screened after low temperature treatment at the germination stage,at bud burst stage,at the seedling stage and at booting and flowering stages,respectively.Four varieties with strong comprehensive cold tolerance were selected,including Hejiang17,Meifeng1 hao,Huangjinxiu and Xinfeng039.