Fine Mapping And Functional Analysis Of The Major QTL Affecting Leaf Shape And Yield

Improvement of plant morphology is an important approach to increase rice yield. The proper leaf shape and plant height can increase photosynthetic efficiency of rice, which thus is important target for high yield breeding. QTL mapping is one of the main methods for dissection of the genetic base of complex agronomic traits in crops. In a previous study, through using a backcross recominbant inbred lines (BRILs) derived from a cross of93-11and Zhenshan97, both elite indica hybrid rice parents, we found that about7genomic regions on chromosome1,3,6,7,8,11and12showed the pleiotropy, which were controlling the leaf shape and yield traits simultaneously. To deepen our understanding of the molecular and genetic base of the plant morphology, and to provide desirable genes for marker-assisted breeding for improvement of high-yield potential in rice, two QTL clusters each on chromosomes1and8with large effects controlling the leaf shape and yield traits have been targeted for fine mapping and cloning in our study. The main results are present below:1. To dissect the cluster QTL in the region of RM283—RM8083on the short arm of chromosome1affecting flag leaf length (FL), flag leaf width (FW), primary branch number (PBN), secondary branch number (SBN) and panicle weight (PW), we developed a subset of homologous CSSLs covering the target region, and screened recombinant plants from an advanced backcross population, and employed progeny test for precisely phenotyping the recombinants. The target QTL (qFL1) affecting various traits was narrowed to a31.3kb region that contains four candidate genes. Using conditional QTL analysis, we found that qFL1had a pleiotropic effect on the leaf size and yield related traits; and another minor-effect QTL (qFW1.2) close to qFL1was also detected for flag leaf width. These results suggest that the pleiotropy of qFL1and its closely linked gene affected the leaf size and yield related traits.2. The comparative expression analysis in leaves of a pariwise of near-isogenic lines (NILs) at three leaf developmental phases, which including the young leaf stage of seedlings, about40days after transplantation, and the mature stage about seven days before heading, shows that two annotated genes, OsFTL1a homolog of florigen FT (Flowering locus T) in Arabidopsis, and ATP-binding cassette (ABC) transporter in the31.3kb region are the most likely candidates for qFLl. Particularly, the expression of OsFTL1at all the three stages differed between the near-isogenic lines that carry the alleles of Zhenshan97and93-11respectively.3. For the cluster QTL on the short arm of chromosome8affecting heading date (HD), flag leaf length (FL), flag leaf width (FL), plant height (PH), distance between flag leaf and secondary leaf (FD), panicle length (PL), panicle exsertion (PE), primary branch number (PBN), secondary branch number (SBN) and panicle weight (PW), three heterogeneous inbred families (HIFs) with the heterozygous target region in different genetic backgrounds were used to vadidate the QTL effect and to narrow down the target gene. One of three HIFs with large effect at the QTL was used to construct a large segregative population to screen the recombinant plants for fine-mapping. Through developing a set of SSR, InDel and sequencing markers, and progeny testing of the recombinants, a20kb region containing two ORFs (Open Reading Frames) was determined as candidates for the QTL. The two annotated genes are CCAAT-box binding factor and transferase protein. Complemention test showed that CCAAT-box binding factor is that target gene affecting various traits including grains number, heading date and plant height. We thus renamed it Ghd8.4. The effect magnitudes of Ghd8in the three HIFs depended on the other QTLs in the genetic background, especially qHD6.1and qHD7on chromosomes6and7. When the alleles of qHD7, a QTL corresponding a cloned gene Ghd7, was from93-11, the distribution of heading date in the HIF carrying the alleles of93-11at qHD7showed an obvious segregation of two peaks with the3:1ratio, and the alleles of93-11is complete dominance; but the other two HIFs carrying the alleles of Zhengshan97at qHD7showing normal distribution demonstrated the effect of Ghd8was small. These results indicate that Ghd7might interact with Ghd8.5. Ghd8was constitutively expressed in different tissues, of which the expression level in flag leaf and root were a little higher than other tissues. Through comparative analysis of the expressive profile of several flowering genes of the photoperiod pathway in the Ghd8positive and negative transgenic plants, we found that Ghd8could up-regulate Ehdl, Hd3a and RFT1, and promote flowering in the short-day conditions, and down-regulate Ehdl, Hd3a and RFT1and delay flowering in the long-day conditions; however, the circadian clock gene OsGI and early flowering gene OsMADS50,OsMADS51and RID1were not altered in both conditions. These results indicate that Ghd8has a dual regulatory function in the Ehd1-Hd3a pathway.