Fine Mapping And Cloning Analysis Of Grain Shape Locus QGS7 In Rice

Rice is the main food for nearly half of the world’s population. The improvement of yield and quality has been the goal for genetics and breeding researchers. Grain weight is an important factor determining rice yield. Grain shape not only affects grain weight but also an important factor of the appearance quality of rice. Therefore, the research of grain shape has an important theoretical and practical value of breeding on rice yield and quality improvement.In the early, we choose an indica cultivar, N643 (large grain), and a japonica cultivar Longliheinuo-Dwarf (small grain) as the parental lines. And detected a major QTL qGS7 controlling grain width and grain length on chromosome 7 in backcross inbred. On this basis, we use the interval hybrids to construct secondary population, linkage analysis with high accuracy between the mark and the phenotype, fine mapping qGS7, predict and analyze candidate gene. Results are as follows:Construct populations and fine mapping of qGS7:Building large separate groups to fine maping with the recurrent parent N643 and heterozygous individuals of BC2 of Longliheinuo. Screening recombinant individuals in the positioning with clear qGS7 flanking markers In3 and In4 and 12 single exchange individuals were obtained finally. Encrypted tag of exchange lines and combined with grain aspect ratio phenotypic data to linkage analyze with high precision and mapped qGS7 between InDel markers In 13 and C4-47 with the genetic distances of 52.8kb. Progenies of exchange lines verified the interval of qGS7.Candidate gene prediction and screening:According to Nipponbare sequence of the target range, we predicted eight ORFs (ORF1-ORF8):ORF1 encodes DNA-directed RNA polymerase; ORF2 and ORF8 encodes transposon protein; ORF3 and ORF5 encodes an unknown protein. ORF4 encodes a putative 3-oxoacyl-synthase; ORF6 encodes a peroxisome (S)-2-hydroxy-acid oxidase GLO4 protein; ORF7 encodes a 40S ribosomal S2 protein, transposon. Tissues prediction results show that ORF6 and ORF7 highest expression in infloresence, spikelets or shells.Cloning and divergence analysis of qGS7 candidate gene sequence:The sequences of the candidate will be separated by PCR amplification from the template DNA of the parents, and the sequence differences will be analyzed. cDNA sequence of ORF1 has no difference in the two parents, SNPs of ORF4 do not cause amino acid residue changes. A single nucleotide T is insert in sequence of ORF3, resulting in the amino acid encoded protein frameshift, there are two nucleotide substitutions leding to amino acid changes, and three nucleotide substitutions don’t. A SNP of ORF4 do not cause amino acid residue changes, and a mutations makes translation termination in advance with the gene encoding the protein at the C-terminal lost two amino acids. The other two ORFs are transposons. ORF6, ORF7 has nucleotide substitutions leading to amino acid changes. Combine ORFs structure and function notes and expression information, we hold ORF3, ORF5, ORF6 and ORF7 as candidate gene for subsequent studies.