Rapid Mapping And Candidate Gene Prediction Of QTL For Defective Kernel In Bread Wheat

Normal development of grain is an essential guarantee for wheat yield formation.The genetic study of grain phenotype is of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield formation.We identified a set of wheat materials with defective-kernel phenotype（Dek）in wheat breeding process.In this study,146 F₂ individuals and 146 F_2:3 lines derived from the cross of a pair of near-isogenic lines for Dek were used to QTL mapping.A QTL mapping for Dek was achieved through SNP chip combining with SSR markers and the candidate genes for the resultant Dek QTLs were also predicted,which lays good foundation for map-based cloning.The main results are listed as follows:1.Grain phenotype was scored using the percentages of defective kernels（defined as Dek rate）.The correlation coefficients of Dek rate had a range of 0.70–0.92 across environments.Variance analysis showed that both genotypes and environments significantly affected the target trait.The broad-sense heritability of Dek rate was 0.95,indicating that the Dek rate was mainly controlled by genotypes.Additionally,the phenotype histograms showed abnormal distributions with“valley-peak”pattern,suggesting the presence of major QTL controlling Dek in the population.2.Ten chromosomes,1A,1B,2A,3A,3B,4A,4B,5A,6B,and 7B,had higher frequency of polymorphic single nucleotide polymorphism（SNP）between BL31 and BL33 using Wheat660K chip.Totally 783 simple sequence repeat（SSR）markers distributed on above chromosomes were screened,and 35 of them showed consistent polymorphisms between two groups of lines with contrasting phenotypes.Fifteen SSR markers were integrated into two linkage groups using the genetic population.Three stable QTLs for Dek were identified on chromosomes 3BS and 4AL,designated as QDek.caas-3BS.1,QDek.caas-3BS.2,and QDek.caas-4AL,explaining 14.78–18.17%,16.61–21.83%,and 19.08–28.19%of the phenotypic variance,respectively.3.Five polymorphic SNP from Wheat66K chips,AX-109027972,AX-109516011,AX-110042240,AX-109301653,and AX-108996126,were transferred into cleaved amplified polymorphism sequences（CAPS）marker and successfully mapped in the linkage groups.QDek.caas-3BS.2 and QDek.caas-4AL were narrowed to 14.01-and 13.18-cM intervals,respectively.AX-108996126 and AX-110042240further saturated the genetic interval of QDek.caas-3BS.1 and QDek.caas-4AL.4.The biochemical analysis revealed that BL33 had lower starch contents in mature grain and higher sucrose contents in developing grains than BL31,indicating that the Dek QTL may be involved in carbohydrate metabolism.The physical region of QDek.caas-3BS.1 is 11.24 Mb,whereas those of QDek.caas-3BS.2 and QDeg.caas-4AL were 1.16 and 1.13 Mb according to IWGSC RefSeq v1.0,and206,14,13 genes were present in corresponding physical intervals of the three QTL.Of them,nine genes were involved in the carbohydrate metabolism.Transcriptome and qPCR analyses showed that four of these genes were highly expressed in grains and thus were predicted as candidate genes for Dek QTL,and designated as TaFba-3B,TaBff-3B,TaABA4-3B,and TaSus-4A,respectively.