## 5 Conclusions  
In this study, HI and 13 HI-related traits were investigated in 104 core breeding lines of rapeseed. HI showed a complex network with other traits. We performed genome-wide association analyses using the Bnapus50K array. A total of 212 significant SNPs involved in 324 QTL related to the studied traits, and 22 stable SNPs were identified. Three pleiotropic SNPs were obtained, namely A01_1783685 (PH and SYP), C06_26638717 (PH and NSS), and C03_4731660 (MIL and MINS). Twelve promising novel SNPs were detected that are related to BN (A05_19368584 and A05_19764389), SL (A06_23598999, A06_23608274, and C07_38735522), PH (C04_47349279, C04_47585236, and C09_36899680), MINS (C05_6251826), NSS (C06_22559430 and C06_22570315), and HI (C05_6554451). Meanwhile, 39 candidate genes were predicted in stable SNP intervals by their gene expressions and function annotations. The obtained significant SNPs and candidate genes facilitate the development of molecular markers and casual gene cloning. These results provide further support for the improvement of the harvest index in rapeseed.  
The following supporting information can be downloaded at [[https://www.mdpi.com/article/10.3390/agronomy12040000/s1](https://www.mdpi.com/article/10.3390/agronomy12040000/s1)]([https://www.mdpi.com/article/10.3390/agronomy12040000/s1](https://www.mdpi.com/article/10.3390/agronomy12040000/s1)): Figure S1: Pearson correlation among the branch angles. Figure S2: Partial correlation among the agronomic traits. Figure S3: Population structure variation and phylogeny tree in rapeseed. Figure S4: Manhattan plots and quantile-quantile plots of estimated \(-\)log10 (\(p\)-value) for the test traits using mrMLM. Figure S5: Manhattan plots and quantile-quantile plots of estimated \(-\)log10 (\(p\)-value) for the test traits using TASSEL 5.0. Figure S6: Linkage disequilibrium (LD) block analyses of the stable significant SNPs. Table S1: Phenotypic analyses of 104 rapeseed inbred lines. Table S2: Significant SNPs associated with HI and HI-related traits across four environments. Table S3: Distribution of significant SNPs to environments and chromosomes. Table S4: Candidate gene expression in the BrassicaEDB.  
Conceptualization, A.X.; formal analysis, M.Q., N.G. and J.S.; funding acquisition, A.X.; investigation, N.G., J.S., M.Z. and Y.Z.; project administration, Z.H. and A.X.; resources, A.X.; software, M.Q. and J.S.; supervision, Z.H. and A.X.; visualization, M.Q.; writing--original draft, M.Q.; writing--review & editing, Z.H. and A.X. All authors have read and agreed to the published version of the manuscript.  
This research was jointly supported by the grants from the National Key Research and Development Program of China (2018 YED0100600) and the Key Research and Development Program Yangling Seed Industry Innovation Center (ylzy-yc2021-01).  
Data Availability Statement: Not applicable.  
This research benefited from grants from the Ministry of Science and Technology of China and the Yangling Seed Industry Innovation Center. We would like to thank [PERSON] and [PERSON] of Northwest A&F University who assisted the investigation during the cropping periods.  
The authors declare no conflict of interest.