Fine Mapping Of QTLs Associated With Salt Tolerance From O.rufipogon Using Chromosome Segment Substitution Lines

Common wild rice?Oryza rufipogon Griff.?is the primary genetic resource for improving cultivated rice?Oryza sativa L.?.Examining the lost excellent alleles during the domestication of cultivated rice from wild rice could provide important genetic information and materials for rice breeding.In this study,QTLs associated with salt tolerance were identied in wild rice using a set of chromosome segment substitution lines?CSSL?,which was constructed by our laboratory.Meanwhile,new salt-tolerant germplasm resources were identified.The results were obtained as bellow:1.Identification of suitable CSSLs and applicable molecular markers for QTL mapping:based on genome sequence results of 214 CSSLs,13022 SNPs were obtained,which were used to assess the CSSLs with Identity-By-State?IBS?.Based on the degree of difference between CSSL and 93-11?0.8<IBS<1?and between CSSLs?IBS<1?,200 CSSLs with moderately sized replacement fragments were selected for subsequent studies.At the same time,2880 genetic markers,which covered and randomly distributed in all chromosomes,were selected for QTL mapping,including 2722 SNPs,98 SSRs and 60InDels.2.Salt-tolerant QTL mapping for germination:with 1.3%NaCl solution treatment in germination period of CSSLs,the germination rate of CSSLs decreased by 25.77%-100%compared with the controls.According to the linkage analysis based on 2880 molecular markers,four salt tolerance-related QTLs were obtained.These QTLs were located on chromosome 4,7 and 11,respectively,with the contribution rates of 4.59%-12.45%.Among CSSLs,CSSL72 is the best salt tolerant line with 74.23%germination rate with salt treatment,it habors three salt tolerant QTLs?qGR7.1,qGR11.1 and qGR11.2?.3.Salt-tolerant QTL mapping for seedling:0.7%NaCl solution treatment was used for CSSL population at seedling stage.Combined with the salt tolerance evaluation index at seedling stage,18QTLs were mapped,including 7 related to the survival days,5 related to the survival rate,4 for dry weight of roots correlation and 3 for salt tolerance.Among them,qSSR5.1 and qSSG5.1 were located at the same locus of S5₂7886769,which had synergistic effects on seedling survival rate and salt tolerance grade,and their contribution rates were 6.36%and 8.13%,respectively.Screening the candidate genes within this QTL,it was found that gene OsDi19-1 is associated with abiotic stress.The survival rates of CSSL23 and CSSL153 under salt treatment were still above 80%,and the survival days were significantly higher than other CSSLs.Base on sequence alignment,we found the promoter region of OsDi19-1 was significantly different between 9311 and wild rice,and the expression of OsDi19-1 in9311 was higher than CSSL23 and CSSL153 under salt treatment condition.Combining with physiological experiment data of salt tolerance,it could be concluded that CSSL23 and CSSL153 could improve salt tolerance at seedling stage by reducing K⁺loss and increasing POD and SOD contents in vivo.4.Salt-tolerant QTL mapping during the whole growth period:the CSSLs were tested for salt tolerance in the whole growth period in Dongying's Saline-alkali experiment station.According to the survival rate of the CSSLs,five loci?qWSR1.1,qWSR2.1,qWSR5.1,qWSR7.1,qWSR10.1?related to survival rate were identified during the whole growth period.In this study,four salt tolerance-related QTLs in germination stage,18 QTLs related to salt tolerance in seedling stage and 5 QTLs related to salt-tolerant during the whole growth period were identified by 200 CSSLs.Meanwhile,CSSL72 with higher germination rate,CSSL23 and CSSL153with higher seedling rates were identified as elite germplasm resources for salt tolerance.They could contribute for improvement of rice breeding of salt tolerance as new germplasm resources.