## 4 Discussion  
HI was found to be one of the crucial factors for enhancing biomass and seed yield [32; 33]. However, the harvest index shows a big difference among different crops and is sensitive to environmental factors. In the present study, the correlation coefficient and heritability of HI in different years are relatively low, consistent with previous reports [2; 11]. Population genetic structure refers to a non-random distribution of genetic variation in a species or population. In previous studies, _B. napus_ accessions were generally divided into three subgroups, which were mainly contributed to their cetypes [34; 35; 36]. There were also reports that GWAS groups were divided into other numbers of subgroups, such as five subgroups [31]. In this study, the ADMIXTURE and STRUCTURE software were used for determining the population structure, results of which were more than three subgroups, probably because 104 inbred lines were mainly semi-winter ecotypes. Combined with the population evolution tree and PCA, the top five principal components were used for the correction of the population structure to control the false-positive results. For a complex trait, it should take associated traits into consideration, which could provide a better understanding of complex traits for crop [13]. In this study, a total of 14 major agronomic traits were measured that involved plant architecture and economic traits. The partial correlations among HI and the other traits indicated that HI was negatively correlated with BYP and positively correlated with SYP, while some specific traits could connect to HI indirectly by interacting with other traits (Figure S2). In addition, we constructed the association networks across different traits and SNPs (Figure 4). It revealed the complex genetic connections among the agronomic traits. In breeding practice, to improve target traits, favorable alleles of other traits in recipient varieties should be maintained as possible. The network could help to establish a strategy for variety development. For instance, NSS and PH showed the highest connectivity with the most edges linked to other traits, indicating they should be vital traits. If HI is improved by NSS, this should increase SYP and avoid the BYP benefited to break the heritable covariations. Thus, C06_2259430 and A03_10522683 could be the best ones chosen. The same goes for the other traits. Three hundred and twenty-four SNPs related to 212 SNPs were identified to be involved in the 14 traits. Since the increase of the HI of rice is due to the integration of semi-dwarf genes [6; 37], breeders have been working to reduce the plant height of rapeseed to increase the HI of rapeseed. However, the PH usually shows positive correlations with the seed yield and biomass [13; 33], indicating PH may be genetically linked to seed yield and biomass. We identified one stable SNPs C09_36899682 detected by PH, which was also related to BYP but had no correlation with SYP. This result provides a novel locus for dwarfing the plant to improve HI. Plant architecture improvement plays an important role in the increase of crop yield. Several related QTLs of agronomic traits on rapeseed have been reported. Compared to previous reports [10; 12; 13; 30; 31; 36; 38; 39; 40; 41; 42; 43; 44], 49 of 212 loci shared an overlapped region for the same traits based on the reference genome of Darmor-_b2h_[23] (Figure 5), including PH (11 loci), TSW (9 loci), BAI (7 loci), NSP (6 loci), NSS (5 loci), SL (4 loci), BN (3 loci), MINS (2 loci), SYP (1 locus), and BYP (1 locus). It implied that the significant SNPs of our study were dependable compared with previous results. From the location of the significant SNP, some SNPs for different traits were linked in a certain segment, such as 12.4-13.9 Mb on A10 and 26.6-28.2 Mb on C06. Due to the linkage of the trait locus and the locus pleiotropism, it is challenging to decipher the genetic network of agronomic traits.