Mapping And Characterization Of The Major Quantitative Trait Locus QSS7Controlling Rice Seed Shape

Rice is one of the most important crops. With the population growing, food shortage becomes the main problem in most countries. With the improvement of people’s living standard, rice quality has been paid more attention by consumers. Seed shape, consisting of seed length, seed width and length to width ratio, is the determinant of grain weight and one of important appearance quality traits. It’s considered an effective method to improve grain yield and quality by improving seed shape. Characterization and identification of novel genes for seed shape can help facilitate the improvement of grain yield and quality by marker-assisted selection in rice breeding program. In this study, using a chromosome segment substitution line derived from a cross between a tropical japonica variety Cypress and an indica variety ZS97B, a major quantitative trait locus qSS7controlling seed shape was identified. Candidate genes for qSS7were characterized by sequencing, expression and bioinformatics analysis. The grain filling rate, grain yield and quality were also surveyed in the near-isogenic line (NIL) developed for qSS7. The main results are as follows:1. One line with long seeds, named as08Q043, was selected from the chromosome segment substitution lines in which they have the similar genetic background of ZS97B.08Q043has significantly longer and slender seeds than that of ZS97B. Graphic genotype of08Q043showed at least8Cypress chromosomal segments introduced, which located on the chromosomes1,4,5,6,7,12, respectively.2. The major quantitative trait locus (QTL) for seed shape in the F2and F23populations derived from08Q043and ZS97B was initially mapped to the interval of RM21930-RM21936on the long arm of chromosome7by BSA method The Cypress allele increased seed length and the ratio of seed length to width, and decreased seed width, but did not significantly change seed weight. The QTL was thus designed as qSS7.3. A large segregating population that was developed by selfing an introgression line heterozygous at qSS7locus was used for fine mapping. The genotype analysis of1025 plants in the population using several markers surrounding the QTL region identified18recombinant individuals. qSS7was then finely mapped to a23kb region by progeny test. Further analysis of the most important recombinant plants and thier derived segregation populations suggested at least two genes in this region affecting seed shape.4. By sequencing the small region, numerous polymorphic variations were identified between ZS97B and08Q043. There were four predicted genes predicted in the small region of23kb in length. Among them, two genes have no differences in the sequences between the two parents, and the other two genes (LOC_Os07g41200and LOC_Os07g41210) have several sequence differences. There are26and14SNPs or InDels between the two parents in the promoter and encoding region of LOC_Os07g41200, respectively, of which two SNPs might change amino acids. There are30and9SNPs or InDels between the two parents in the promoter and encoding region of LOC_Os07g41210, respectively, of which three SNPs changed amino acids, specifically one SNP resulting in a premature termination of the gene in ZS97B. These two predicted genes were thus considered as the most likely candidates for qSS7.5. The expression levels of the candidate genes were analyzed at various stages of panicle development. LOC_Os07g41200in08Q043expressed at higher levels than in ZS97B through almost the entire panicle development stage (panicles ranging3-23cm in length), except the early stage (panicles2cm in length). In contrast, the expression levels of LOC_Os07g41210in ZS97B were higher at most of the panicle development stages except the late one (panicles reaching23cm in length) than those in08Q043.6. Ten haplotypes were revealed by two InDel markers and coding sequence of LOC_Os07gg41210. ZS97B haplotype (HI) exists mainly in indica,08Q043haplotype (H2) exists mainly in tropical japonica, and Nipponbare haplotype (H3) exists mainly in temporal japonica. Seed length of H4is longer than that of H1and H5; seed width of H2is wider than that of H3and H5, and ratio of length to width of H2is larger than that of H3and H5. 7. To characterize the qSS7effect in details, a pair of NIL (NTL-08Q043and NIL-ZS97B) with different alleles at the qSS7were developed. The length and width of the inner epidermal cells of the outer glume (lemma) was measured by SEM, showing that the cell length was13.7%longer and the cell width was11.8%narrower in NIL-08Q043than in ZS97B. These differences are consistent with that of seed shape, showing that qSS7controls seed shape possibly by affecting cell shape of spikelets.8. The dynamics of seed development and grain filling rate were surveyed using the NILs. The seed shape was significantly different between the two NILs after panicle8cm in length. This result consisted with the expression levels during the panicle development stage. However, no difference in grain filling rate between two the NILs was observed at entire grain-filling stage.9. Yield and quality-related traits in the NILs were investigated as well. There were differences in heading date, panicle length, spikelet density, grain chalk percentage and grain chalk degree between the two NILs (NIL-08Q043and NIL-ZS97B), but no difference in grain yield and grain quality.