Fine Mapping Of Quantitative Trait Loci And Genetic Analysis For Heading Date And Panicle Length In Rice(Oryza Sativa L.)Using Chromosome Segment Substitution Lines

Heading date and panicle length in rice(Oryza sativa L.) are important agronomic traits. Genetic analysis and QTL detection for heading date and panicle length traits would make significant improvement for rice breeding. Common wild rice(Oryza rufipogon Griff.) contains a number of superior genes but with overwhelming complicated genetic background, thus it’s difficult for direct utilization for breeding and genetic analysis. Chromosome segment substitution lines(CSSLs) are prone to the gene separation and identification because they can eliminate the genetic noise and transfer wild rice gene into the relatively homogeneous cultivated rice genetic background, hence they are the ideal materials of genetic analysis and fine mapping. In this study, 200 CSSLs have been obtained from cultivated rice(9311) as the receptor parent and wild rice(BC276) as the donor parent. Among them, CSSL129 which prolong the heading and CSSL39 which prolong the heading date and shorten the panicle length under NLD and NSD conditions were selected as the materials for genetic analysis and QTL detection of heading date and panicle length. The following results were obtained:1. In CSSL129, a HD loci qHd6.1 that can stablely inheritant under NLD and NSD conditions was detected on Chromosome 6. Sequence analysis showed that qHd6.1 from wild rice was the allele of Hd1. It led to early heading in 9311 because of the 4bp deletion in coding region.2. In CSSL39, three heading date QTLs, namely qHD7.1, qHD7.2 and qHd12, that can stablely inheritant were detected under NLD and NSD conditions. They maintained the same genetic effects that prolong heading date. Among those three QTLs, qHD7.1, qHD7.2 were major QTLs because they had the highly explained variance in the two environments.3. In CSSL39, four panicle length QTLs, namely qPL7.1, qPL7.2, qPL10.1 and qPL10.2 were detected. Among those four QTLs, qPL10.1 was only detected in NSD, qPL7.2 was only detected in NLD. qPL7.1 and qPL10.2 can stablely inheritance under both NLD and NSD conditions. Among the four QTLs, only qPL10.2 under NSD conditions had the positive effect on elongating the panicle length, the others had negative effects on shortening the panicle length.4. we located the heading date QTL qHD7.2 to approximately 101.1kb between RM172 and RM22188 by F2 segregation population of CSSL39. There are ten ORFs in this region and the candidate gene ORF7(LOC_Os07g49460) was a response regulator that regulated photoperiod. There was an 8-bp deletion in 9311 coding sequences compared with CSSL39, that made a premature translational-termination and then led to nonfunctional allele, meanwhile there were also many insertion, delection and mutation in promoter sequences between two parents. Those data indicated that both the coding sequences and promoter sequences were selected in the process of domestication. We deduced that the heading date changes caused by the changes of expression quantity and protein functional. The qHD7.2 gene in CSSL39 had the different expression level in different tissues, the highest expression level was found in young leaf blades and the lowest one in roots, this was consistant with the heading date gene expression patterns previously reported.In this study, we selected two CSSLs that had statistically significant heading date and panicle length changes compared with recurrent parent 9311 by investigating 200 CSSLs agronomic traits. The results of fine mapping of QTL and genetic analysis showed that there are four QTLs associated with heading date and four QTLs associated with panicle length. There were many changes in both coding sequences and promoter sequences of qHD7.2 between two parents, and the expression level in CSSL39 was higher than 9311 in every periods. Genetic analysis of high contribution rate qHD7.2 indicated that the heading date changes were caused by the changes of expression quatity and protein functional. qHD7.2 was the allele of OsPRR37 and the constitutive expression pattern conforms to the expression patterns of heading date genes.