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Key message <p>GWAS of eight silique-related traits identified 28 stable quantitative trait loci (QTLs). By integrating GWAS results with haplotype analysis, transcriptomic data, and functional annotation, four candidate genes potentially regulating silique trait were pinpointed.</p> Abstract <p>Silique-related traits are key agronomic characteristics that directly or indirectly influence seed yield in rapeseed (<i>Brassica napus</i> L.). Understanding the genetic basis underlying these traits is essential for the development of high-yielding rapeseed cultivars. In this study, we evaluated eight silique-related traits silique length (SL), silique width (SWH), silique thickness (STK), beak length (HL), thousand-seed weight (SW), number of seeds per silique (SP), number of siliques per plant (SN), and yield per plant (YP) across 200 rapeseed accessions under three natural field environments. Using whole-genome resequencing data, genome-wide association study (GWAS) and linkage analyses were performed to identify loci associated with these traits. Candidate genes were screened within significant SNPs and InDels, resulting in the identification of four potential genes <i>BnaA03G0288100ZS</i> (<i>BnaA03.GRF7</i>), <i>BnaA06G0148300ZS</i> (<i>BnaA06.SPL14</i>), <i>BnaC03G0346100ZS</i> (<i>BnaC03.GRF7</i>), and <i>BnaC07G0456000ZS</i> (<i>BnaC07.DOF4.6</i>). Haplotype analysis of nine traits, including SL, SWH, STK, HL, SW, SP, SN, seed density (SD), and YP, together with gene expression profiling, further supported their potential roles in regulating silique traits. In addition, three kompetitive allele-specific PCR (KASP) markers were developed and validated in a natural population comprising 150 diverse rapeseed accessions. These findings provide new insights into the genetic and molecular mechanisms underlying silique-related traits and offer valuable resources for the genetic improvement of rapeseed yield through molecular breeding.</p>

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Dissecting the genetic architecture of silique-related traits in rapeseed (Brassica napus L.) through genome-wide association studies and transcriptome analysis

  • 期刊论文

  • 发表日期：

    2026年4月18日

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  • Cuiping Zhang,
  • Guangze Li,
  • Ruolin Gong,
  • Yunfei Zhang,
  • Pan Lu,
  • Chunyan Dai,
  • Niannian Fan,
  • Wu Yao,
  • Xue Shi,
  • Jungang Dong,
  • Jihong Hu

摘要

Key message

GWAS of eight silique-related traits identified 28 stable quantitative trait loci (QTLs). By integrating GWAS results with haplotype analysis, transcriptomic data, and functional annotation, four candidate genes potentially regulating silique trait were pinpointed.

Abstract

Silique-related traits are key agronomic characteristics that directly or indirectly influence seed yield in rapeseed (Brassica napus L.). Understanding the genetic basis underlying these traits is essential for the development of high-yielding rapeseed cultivars. In this study, we evaluated eight silique-related traits silique length (SL), silique width (SWH), silique thickness (STK), beak length (HL), thousand-seed weight (SW), number of seeds per silique (SP), number of siliques per plant (SN), and yield per plant (YP) across 200 rapeseed accessions under three natural field environments. Using whole-genome resequencing data, genome-wide association study (GWAS) and linkage analyses were performed to identify loci associated with these traits. Candidate genes were screened within significant SNPs and InDels, resulting in the identification of four potential genes BnaA03G0288100ZS (BnaA03.GRF7), BnaA06G0148300ZS (BnaA06.SPL14), BnaC03G0346100ZS (BnaC03.GRF7), and BnaC07G0456000ZS (BnaC07.DOF4.6). Haplotype analysis of nine traits, including SL, SWH, STK, HL, SW, SP, SN, seed density (SD), and YP, together with gene expression profiling, further supported their potential roles in regulating silique traits. In addition, three kompetitive allele-specific PCR (KASP) markers were developed and validated in a natural population comprising 150 diverse rapeseed accessions. These findings provide new insights into the genetic and molecular mechanisms underlying silique-related traits and offer valuable resources for the genetic improvement of rapeseed yield through molecular breeding.