QTL Mapping On Agronomic Traits Using RILs And Identification Of QHD5for Heading Date In Rice(Oryza Sativa L.)

As a complex quantitative trait, rice yield is mainly influenced by the genes controlling heading date, plant type, panicle and grain traits. This thesis presents the comprehensive study of Quantitative Trait Loci (QTL) associated agronomic traits including Heading Date (HD), plant type, panicle and grain traits detected in two environments Hangzhou (2011)/Hainan (2012), using Recombination Inbred Lines (RILs) population derived from two parents BG1and XLG with large differences in agronomic traits. Based on QTL detection, a set of near isogenic lines (NILs) was established through the backcross method. A new QTL qHD5controlling HD was identified. The main results are as follows:1. We selected203markers with polymorphism between parents to identify the genotypes of RILs population. A genetic linkage map with the total distance of1515.8cM and average interval of9.13cM was established, the number of markers on12chromosomes was8-27.2. The QTL for HD and plant type of RILs population were analyzed in two environments Hangzhou/Hainan. Thirty-one QTL on chromosome1,2,3,4,5,8,9and12were identified. Among them, two major QTL qHD5and qHD8controlling HD were reliably detected in two environments. In addition, one Tillering Angle (TA) major QTL qTA9, three Secondary Leaf Length (SLL) QTL qSLL3, qSLL5-2and qSLL8, five Secondary Leaf Width (SLW) QTL qSLW4-1, qSLW4-2, qSLW5, qSLW8-land qSLW8-2, two Flag Leaf Length (FLL) QTL qFLL3and qFLLS, three Flag Leaf Width (FLW) QTL qFLW4, qFLW5and qFLW8-2were detected in two environments.3. The QTL for six panicle traits of RILs population were analyzed in two environments. A total of29QTL on chromosome2,3,4,5,6,7,8and10were detected. The number of QTL for number of tillers per plant, panicle length, grain number per panicle, number of filled grain per panicle, setting rate per panicle and grain density were4,6,6,6,3and4, respectively. Among them, six QTL can be steadily detected in two environments, including Number of Tillers per Plant (NTP) QTL qNTP4, Panicle Length (PL) QTL qPL5-2, Grain Number Per Panicle (GNPP) QTL qGNPP4and qGNPP8, Number of Filled Grain per Panicle (NFGP) QTL qNFGP2-2, Grain Density (GD) QTL qGD5.4. QTL analysis for10grain related traits indicated that58QTL on chromosome2,3,4,5,6,7,8and9were detected. Thirty-seven and thirty-eight QTL were detected in Hangzhou and Hainan, respectively. Among them, sixteen QTL can be detected in both environments, which were located on chromosome2,3,4and5. Sequence alignment analysis showed that Grain Width (GW) QTL qGW2-l, Grain Length (GL) QTL qGL3-2, Grain Thickness (GT) QTL qGT3may have identity with the cloned grain shape genes GW2, GL3and GS3, respectively.5. The interaction with environments for QTL under different conditions were analyzed. The results showed that qHD8, qTA9, qPH5, qGNPP8, qNFGP5-2and qNFGP8had significant interaction with environments, in contrast, all of the QTL controlling grain traits had not. Epistasis analysis results showed that five pairs of QTL intervals controlling plant type and panicle traits, seventeen pairs of QTL intervals controlling grain traits had significant two-factor epistatic effects, but both effect value and contribution rate were low. 6. In this study, some QTL gathering areas affecting plant type and grain traits simultaneously were detected. For example, RM5619-RM5356interval on chromosome2affected GNPP, NFGP, GW, GT and Thousand Grain Weight (TGW). C2-7-RM324interval on chromosome2affected four traits such as GT. RM3687-RM349interval on chromosome4affected seven traits such as SLW. C5-1-RM1200interval on chromosome5contained the QTL controlling HD, GNPP, PL, GT, Setting Rate. RM18457-RM6229interval affected Plant Height (PH), FLL, GL, Milled Grain Length/Width (MGLW).7. Based on the results of QTL detection, combined marker assisted selection and backcross method, a set of NILs was established. A new QTL qHD5controlling HD was identified in RD501-RM6317(～380kb) on the short arm of chromosome5. Nine candidate genes in this interval were further screened from50candidates by prediction analysis of gene function. Among those genes, a gene is related to rice panicle development, and there was sequence differences between two parents. These results can provide references for the fine mapping and cloning of qHD5.