Primary Mapping Of Genes For Grain Length Using The Bulked Segregant Analysis Method And Analysis Of Candidate Genes In Rice(Oryza Sativa L.)

Rice（Oryza sativa L.）is one of the most major cereal crops and its grains is the major economic products.Grain shape of rice is a critical and direct trait for grain yield and grain quality.To excavate the new genes controlling the grains,which could provide fundamental basis for increasing the yield and improving the quality of rice.In this study,we constructed a F₁ population derived from a cross between a small dwarf stalks wild rice line S18 and a long grain cultivates line KJ01,and obtainted a segregation population of F₂.Then two DNA bulking tanks were conducted respectively for extreme short grains and extreme long grains.The results of BSA and bioinformatics analysis of the candidate genes are as follows:（1）The phenotype of F₁ was intermediate type deviation to short-grain parent,and the frequency of grains length showed for normal continuous distribution in the F₂ population.Which demonstrated that the grain shape was a typical quantitative traits.There were some major genes that controlled the length of grains in the group.（2）Evaluation and filteration of high-throughput sequencing data and SNP annotation.After quality assessment of the high-throughput sequencing and filteration of the low quality data,we obtained a total of 100.22G high-quality bases cover degree of genome is96.51%of the reference N ipponbare genome with 55X average coverage dept h.And the Q30 is more than 93.88%,the average ratio on rate is 96.64%.Compare with the reference Nipponbare genome,single nucleotide polymorphisms（SNPs）were detected in long grain bulked DNA pool and short grain bulked DN A pool.The numbers of SNPs were 2136482and 2216645,SNP heterozygosity were 72.35%and 79.63%,SNP homozygosity were590657 and 451419,respectively.It indicates that the differences between the F₂ group and the N ipponbare genome were smaller than the two parents.（3）The BSAresults showed that:The genes controlling grains length were primary mapping a hot region of 0.34 Mb on Chromosome 03,containing 57 candidate genes,which have not been reported about fine mapping and cloning.37 genes were nonsynonymous mutation in the hot region of 0.34 Mb.Hencewe chose the 37 genes for further research.From GO and top GO annotation,3 genes（LOC_Os03g42020,LOC_Os03g42010andLOC_Os03g42830）were annotated about plasma membrane of cellular component,and plasma membranewas the highest significance.In addition,compared withSwissprot database found that LOC_Os03g43030 was relevant with extensin protein.Besides that,LOC_Os03g42790 and LOC_Os03g42040were searched on Rice XPro website.Therefore,6 genes might be striking candidate genes that are closely tied to grain length.（4）The expression for different length of the young panicles and different tissues were conducted at RNA level,which were respectively of the young panicles of³cm、5cm、7cm、10cm、13cm and stems,and roots.The results showed that:LOC_Os03g43030 was expressed strongly in³cm and 7cm long panicles and stem tissue.LOC_Os03g42010 and LOC_Os03g42020expressed both highly in³cm、5cm、10cm and 13cm long panicles.The expression of LOC_Os03g42830、LOC_Os03g42790 and LOC_Os03g42040 were below in the panicles and stem,and were not detected in root.These suggested thatthe highly expression levels of grain length genes in paniclesdevelopment could increase the grain length.LOC_Os03g43030、LOC_Os03g42010 and LOC_Os03g42020 may be the grain length.The purpose of this study is to find the candidate genes of regulating rice grain length,and to provide theory basis for cloning the grain-length genes and molecular breeding on grain shape in rice.