| The ideotype is the foundation for rice high-yielding. The development and cultivation of varieties with erect or semierect panicles is considered as the third landmark after dwarfing breeding and hybrid rice in the history of Chinese rice breeding. PE (Panicle erectness) varieties show increased lodging and fertilizer resistance, benefit ventilation and light penetration of population, higher photosynthetic rates and grain yield. Therefore, the nature of panicle erect not only makes us deeply understand the mechanisms of panicle development, but also facilitate the plant architecture improvement by molecular design breeding.Grain shape is closely connected with rice yield and directly determines rice quality. The genetics and molecular basis is essential for the improvement of rice varieties.In this study, the genetic effects of panicle erectness gene (qPE9-1) and grain shape gene (qGS7-1) were analyzed with near-isogenic lines. Map-based cloning of qPE9-1 and fine mapping of qGS7-1 was conducted. The main results are as follows:Part 1:Map-based cloning of qPE9-1 for rice panicle erectness.1. Three pairs of near-isogenic lines (NILs) with different backgrounds (R6547, Wuyujing 3 and Wuyunjing 8) were constructed by cross, backcross and MAS. An array of panicle architecture, plant architecture and yield traits were systematically analyzed using the NILs. The allele from panicle drooping variety had positive effects on panicle curvature, panicle length, grain length, length of leaf,1,000-grain weight and grain yield per plant, but had no effect on the number of spikelets on the main panicle, number of primary branch and secondary branch. The allele from PE varieties had negative effects.2. The bimodal distributions of the panicle curvature, panicle length, and grain length and 1,000-grain weight in the BC3F2 population with R6547 background suggested that these traits were likely controlled by a semi-dominant QTL.3. Fine mapping allowed us to delimit qPE9-1 within a～32-kb window defined by the markers S919 and S927 on PAC AP005419. Three genes, Os09g26999, Os09g27010 and Os09g27020, located in this region according to the TIGR Rice genome Annotation Database. And Os09g26999 was considered as the strongest candidate gene for qPE9-1 because of its large genetic effect on grain length. The hypothesis that Os09g26999 equaled to qPE9-1 was further confirmed by complementary test, RNAi and overexpression experiments. The allele from R6547 (qPE9-1) is functional, and the loss-of-function allele in Wuyunjing 8 (qpe9-1) resulted in the PE trait.4. The qPE9-1 allele from R6547 contains five exons and four introns and encodes a protein of 426 amino acid residues. The qPE9-1 protein contains three Von Willebrand Factor Type C (VWFC) domains, a transmembrane domain and a one 4-disulfide-core domain (http://www.ebi.ac.uk/InterProScan/). Thirteen single nucleotide polymorphisms (SNP1-SNP13) and four insertion-deletion polymorphisms (InDel1-InDe14) were found on qPE9-1 locus between R6547 and Wuyunjing 8. Except for SNP13 and InDe14, all the sequence polymorphisms were found in non-coding regions. SNP13 results in a Cystine to Tyrosine substitution at the site 105 (C105Y). The Wuyunjing 8 allele, due to its InDe14 (637-bp deletion and 12-bp insertion) in exon 5, encodes a presumably truncated protein that lacks 231 C-terminal residues. The recessive allele at qPE9-1 locus is a loss-of-function mutation that leads to the PE trait.5. GUS activity was detected mainly in elongating and dividing tissues, including the shoot apical meristem, the divisional and elongating zones of stem and knot. Real-time PCR analysis was consistent with GUS staining and suggested that the genomic sequence changes did not affect expression level.Part 2:Identification and fine mapping of a major quantitative trait loci, qGS7-1, controlling grain shape in rice. 1. C1044 is a chromosome segment substitution line derived from 132 introgression lines by introgressing chromosomal segments from a japonica doner cultivar, Nipponbare, into an indica recurrent cultivar, Guangluai 4. This line displayed obviously large grain length than Guangluai 4 based on phenotypic examination at two sites in two years. There were significant differences in plant height, main panicle length and grains per main panicle, while no significant difference in number of panicles per plant, seed set rate and days to heading between them.2. An F2 population was generated for genetic analysis by selfing the F1 plants of C1044 and Guangluai 4. Grain length, grain width and grain length-width ratio simultaneously showed as a single locus Mendelian segregation. F3 family analysis also supported this conclusion. QTL analysis indicated that qGS7-1 had effects on grain length, grain width, grain length-width ratio and grain thickness, and contributed 40.8%, 53.1%,60.2% and 8.1%of the phenotypic variation to these traits, respectively. The Nipponbare allele increases grain length and length-width ratio, but decreases grain width and grain thickness. Thus, QTL qGS7-1 was a major QTL for grain length, width and length-width ratio but a minor QTL for grain thickness and weight.3. In addition, grain length and length-width ratio showed significantly negative correlation with grain width and thickness, respectively. But grain length-width ratio showed positive correlation with grain length. Grain width and grain thickness was also highly significant positive correlation. Long grains were more narrow and thinner than short grains, or vice visa. That is reason why the grain weight did not change with grain shape.4. Using excessive plants with extreme short grains in F2/F3 populations, the qGS7-1 was finally delimited to a 87.6-Kb genomic DNA region between S7-45 and S7-115 and co-segregated with S7-179.
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