Rapid Identification Critical Genes For Controlling Panicle Length,Grain Shape And Tiller In Rice By Using BSA-seq Analysis

Rice is the most important cereal food crop in China.Panicle shape,grain shape and tillering are three important agronomic traits in rice,and it is also the key point of rice genetics and breeding research.Using radiation mutagenesis,our research group isolated three mutant from indica restorer Minghui86.Taking this three attributes this project aims to observe the morphological changes and genetic analysis of these three kinds of mutant.BSA-Seq analysis which can rapid identify the related genes controlling these three agronomic traits in rice was applied.The results of this study laid a foundation for further understanding of the regulation mechanism on panicle length,grain shape and tiller formation in rice.The main results are as follows;Two mutants showed similar traits of short phenotypes with the following morphology;short and small panicle shape,reduction of panicle number and grain number per spike,and shortened rachis branch length which caused by shortening the branch spacing between spikelet.However the panicle length in the regeneration rice of the two mutants could be partially restored,thus the difference of the panicle length between the mutant and the wild type was significantly decreased.Genetic analysis and allele test showed that the two mutants were caused by allele mutation of the same gene.Based on the BSA-seq analysis,a single nucleotide substitution was detected in one of the short panicle mutants as LOC_Os11g12740(SP1)gene,which resulted in the change of splicing site.Sequencing of the other mutants revealed that the SP1 gene was completely deleted.Therefore,the two mutants were new alleles of SP1,designated as sp1-4 and sp1-5.The morphology of the other mutant designated as round kernel showed short and wide grain shape.At the same time the mutant showed significant dwarfism,reduction in the length of panicle,flag leaf,the number of primary and secondary rachis branches.The basal internode remained the same,however the other internodes length of main stem were significantly shortened.When we checked the resin slices they showed that the stem cell size did not show significant difference between wild type and mutant,suggesting that reduction of the cells number were probably the main reason for dwarf phenotype in mutant.Genetic analysis showed that the mutant phenotype was controlled by a single recessive gene.BSA-seq analysis and sequencing results showed that there were five base deletion.The deletion was detected in eleventh exon of LOC_Os05g06280 gene(SRS3)in the mutant.Therefore,round kernel mutant is the new allele mutant of SRS3,and was named as srs3-2.mlf1-1(monoculm and lated flowering)mutant displayed significant reduction in tiller number,expansion leaf angle,delaying heading stage and enlarging flag leaf length with a characteristic slightly drooping phenotype.Genetic analysis showed that the mutant phenotype was controlled by a single recessive gene.BSA-seq analysis and sequencing results detected an inversion in chromosome 2 in the tiller mutant and resulted in the loss-of-function of LOC_Os02g08350.Therefore,the gene was taken as a the candidate gene of MLF1.LOC_Os02g08350 encodes an expressed protein,and its detail function is unknown at present.