Genome-wide association study reveals genetic loci for seed density per silique in rapeseed (Brassica napus L.)

Youjuan Quan, Haidong Liu, Kaixiang Li, Liang Xu, Zhigang Zhao, Lu Xiao, Yanmei Yao & Dezhi Du

Theoretical and Applied Genetics; March 20 2025; vol.138; article 80

Key message

Two stable QTLs controlling seed density per silique were detected on chromosomes A09 and C05 in rapeseed via GWAS, and ARF18 was the only causal gene of QTL qSDPS-A09.

Abstract

Seed density per silique (SDPS) is a key agronomic trait that directly or indirectly affects seed yield in rapeseed (Brassica napus L.). Exploring the genetic control of SDPS is beneficial for increasing rapeseed production. In this study, we evaluated the SDPS phenotypes of 413 rapeseed cultivars (lines) across five natural environments and genotyped them by resequencing. A GWAS analysis was performed using 5,277,554 high-quality variants with the MLM_PCA + K and FarmCPU models. A total of 51 loci were identified to be significantly (p < − log₁₀(1.88 × 10^–6)) associated with SDPS, of which 5 were detected in all environments (except for SNP-2095656) by both GWAS models. Among the five loci, three were located on chromosome A09, whereas the other two loci were located on chromosome C05. The three loci on chromosome A09 and the two loci on chromosome C05 were physically close to each other. Therefore, only the two common candidate QTLs were integrated and named QTL qSDPS-A09 (320 kb) and qSDPS-C05 (331.48 kb), respectively. Sixty-seven and forty-eight candidate genes were initially identified on A09 and C05 and then narrowed down to 17 and 13 candidate genes, respectively, via LD block analyses. Gene-based association studies, haplotype analyses and expression analyses confirmed that three homologs of Arabidopsis auxin-response factor 18 (BnaA09G0559300ZS) was the most likely candidate genes underlying the QTL qSDPS-A09. ARF18^Hap4 was identified as a favorable haplotype for high SDPS. These findings will aid in elucidating the genetic and molecular mechanisms of SDPS and promoting genetic modifications in rapeseed breeding.

See https://link.springer.com/article/10.1007/s00122-025-04857-4