| The characters related to plant type included plant height,tillering number,tillering angle,flag leaf angle and panicle character.Plant type related traits are important agronomic traits and important components of rice yield factors.The formation of plant type involves the expression of a series of genes and the function of expression products.In this study,295 japonica rice varieties from all over the world were used to investigate the tillering number and tilleringangle of rice in the tillering stage in 2018 and 2019,the flag leaf angle of rice in the panicle stage was measured,and the plant height and panicle angle of rice in the mature stage were investigated.In combination with 788,396 high-quality polymorphism SNPS obtained by high-throughput resequencing,genomewide association analysis was conducted using the MLM model of TASSEL 5.0 software,and the threshold value of effective independent SNPS calculated by GEC software was determined to determine the significance of the association between SNP markers and target traits.According to the peak value of the detected SNP and rice every 2 years chromosomes LD attenuation distance,determine the japonica rice plant-type traits relating main effect QTL,and further to extract total locate QTL range all gene exon region non-synonymous mutation SNPS and promoter region SNP haploid type analysis,combined with gene annotation screening candidate genes influence the japonica rice plant type traits.The main research results are as follows:(1)All the five plant type traits of japonica rice presented extensive phenotypic variation in 2 years,and the general trend of the two years was basically the same.The variation coefficients of 5 plant types in 2018 and 2019 were between 12.41-70.31% and 12.46-79.96%,respectively.The variation coefficient of plant height was the smallest in 2018 and 2019,which were 12.41% and 12.46%,respectively.The flag leaf angle variation coefficient in 2 years was the highest,which was 70.31% and 79.96% respectively.The 2-year coefficient of variation of tillering number was 32.58% and 29.55%,respectively.The 2-year tillering angle variation coefficients were 21.75% and 28.76%,respectively.The coefficient of variation of panicle angle in 2018 and 2019 was 30.84% and 29.51%,respectively.Phenotypic correlation analysis showed that there was a significant negative correlation between tillering number and plant height,a significant negative correlation between flag leaf angle and tillering number,a significant or extremely significant positive correlation between tillering angle and tillering number,a significant positive correlation between flag leaf angle and panicle angle,a significant positive correlation between flag leaf angle and plant height,a significant positive correlation between panicle angle and plant height.(2)The MLM model of TASSEL 5.0 software was used to perform genome-wide association analysis of plant height,tillering number,tillering angle,flag leaf angle and panicle angle of japonica rice,under the threshold of P <5.46 × 10-6,2018-2019 A total of 54 QTLs affecting plant type traits in rice were detected,including 11 QTL(q PH2.4,q PH4,q PH6.1,q PH7.1,q TN9,q TA4,q FLA1,q FLA3,q PA1,q PA2 and q PA5)can stable expression in two years.(3)Use this test to locate QTL associated with previous QTL and the plant type traits compared to,the results showed that q TN9,q PH2.4,q PH6.1 and q PH7.1 located in rice plant type has been positioning related traits QTL interval,Os RLCK107,a flag leaf angle gene,and Os PHR2,a plant height development gene were detected in q FLA3 and q PH7.1,respectively,at the same time identify new plant type 6 total positioning related QTL(q PH4,q TA4,q FLA1,q PA1,q PA2 and q PA5).Haplotype analysis was performed on all genes in 9 important QTLS(q PH2.4,q PH4,q PH6.1,q TN9,q TA4,q FLA1,q PA1,q PA2,and q PA5).Ten candidate genes that may affect rice plant type related traits were predicted by combining with gene function annotation.This study analyzed the five of the genetic basis of rice plant type development related traits,predict the impact of 10 candidate genes of rice plant type traits QTL related,the results will provide breeding by molecular design breeding super-high-yield rice varieties with excellent genes with independent intellectual property rights,at the same time for subsequent plant type related gene cloning to lay the solid foundation. |
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