Association Mapping Of Yield-related Traits Affecting Harvest Index In Different Environments In Rapeseed (Brassica Napus L.)

Rapeseed is a widely planted oil crop. Improving the seed yield and harvest index has become the focus. Genome-wide association study(GWAS), an accurate and effective method of QTL location, has been widely applied in the research of seed yield and agronomic traits. In our experiment, 520 resource materials collected from all over the world have been planted in Yunnan province and Chongqing, after which GWAS is adopted to search for the markers association to the yield-related traits and harvest index in different environments, using 34103 SNP markers of rapeseed genome sequence and the phenotypic values of 12 traits like the number of siliques on main inflorescence(NSM), number of siliques on branch(NSB), number of siliques on per plant(NSP) 、 seeds weight(SW) 、 seeds per silique(SPS) 、 yield on main inflorescence(MIY)、yield on branch(BRY)、canopy biomass yield(CBY)、stem dry weight(ST)、biomass yield(BY)、seeds yield(SY)and harvest index(HI). Then combine with the transcriptome analysis of various organs of extreme phenotypes material and verifying some genes by quantitative real-time PCR(qRT-PCR), we will filter some candidate genes related to yield and harvest index. The results are as follow.1. Phenotypic variation in different environments: there are extremely significant differences in terms of the traits between environments, materials and interaction of environment and materials. The broad heritability amounts to 70%, and the traits are normally distributed, which indicates that the traits in this experiment are mainly controlled by polygenes, and the traits are inherited stably in one environment but significant differences exist between different environments. The phenotypic data can be used for later analysis.2. Correlation and path analysis of traits in different environments: in the three environments of 2013 in Chongqing, 2014 in Chongqing and 2014 in Yunnan, seed yield has the most significantly positive impact on harvest index while biomass yield exerts the negative impact, which is consistent with the formula of harvest index. canopy biomass yield is most closely related to seed yield. The correlations between NSM and HI, ST and HI are greatly affected by the environments. The above two traits have positive impact on harvest index in Chongqing while they have negative impact in Yunnan. In addition, SPS and NSP have relatively big positive influence on harvest index in Chongqing. However, in Yunnan, BRY and SW have relatively big positive influence on harvest index. The impact of NSP on harvest index varies greatly in different years.3. Genome-wide association study of the traits: different traits in different environments are used with different optimal models to adopted GWAS. 382 SNP markers significantly associated with 12 traits are detected in total(P<1/34103) in three environments and the D-value of 2014 Yunnan and 2014 Chongqing. 290 SNP detected in 2013 in Chongqing, 36 SNP detected in 2014 in Chongqing, 24 SNP detected in 2014 in Yunnan and 32 SNP detected in D-value of 2014 respectively. It can be concluded from the phenotypic variation that relatively great phenotypic variation is explained in Yunnan productive environment.4. Candidate genes prediction of the basic gene cluster:89 significantly SNP markers are detected repeatedly in all environments, which might be the significant markers of the basic gene cluster related to yield.4 Arabidopsis thaliana homologous genes close to these SNP markers are found in the LD confidence intervals, which are MST1 gene associated with SW, TCP12 、 BIG and MBD9 genes collaboratively associated with NSP and NSB, respectively.5. Candidate genes prediction of the yield potential gene cluster: the SNP markers, associated to SY and HI detected in Yunnan productive environment and D-value, might be used to find the yield potential genes. 10 Arabidopsis thaliana homologous genes are found in the LD confidence intervals of the SNP markers associated with SY and HI in Yunnan productive environment, such as APP1, HAM4, ROT3/CYP90C1, STY2, ARAC1/ROP3, TT4/CHS, KAT5, SLY2, CPD and DME. 3 Arabidopsis thaliana homologous genes related to HI are found, like AHK4/CRE1, BIN2 and ARGOS. In addition, GRF3, MBD9 and PIS1 are the genes close to the repeatedly detected SNP markers associated with HI and other traits, which might also be the specific candidate genes.6. Differential expression analysis of two candidate genes: we use 8 organs of extreme phenotypes materials to verify the differential expression of two genes BnaA07gHI-01 and BnaC02gSY-01 by qRT-PCR. The result shows that BnaA07gHI-01 have higher relative expression in master seed inflorescence, collateral seed and main inflorescence bud in Yunnan high yield and high harvest index materials, while lower relative expression in main inflorescence pericarp. BnaC02gSY-01 have higher relative expression in master seed inflorescence, and main inflorescence bud in Yunnan high yield and high harvest index materials, while lower relative expression in collateral pericarp. Excavation of these genes will facilitate marker-assisted breeding and lay the foundation for cloning genes related to high yield and high harvest index of Brassica napus L.