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Key message <p>CRISPR/Cas9 mutagenesis and overexpression lines analyses revealed CIPK9 homoeologs function in oil regulation of allotetraploid <i>Brassica napus</i>, cooperative multicopy interactions, and a superior haplotype on chromosome A10.</p> Abstract <p>Rapeseed (<i>Brassica napus</i>, <i>B. napus</i>), a globally significant allopolyploid oilseed crop, fulfills substantial annual vegetable oil demand. Evolutionary adaptation in this species is underpinned by gene duplication and homoeolog retention, enhancing plasticity under dynamic environmental stresses. This study focuses on <i>BnaCIPK9</i>, a regulator of seed oil content. Phylogenomic and structural analyses demonstrate that <i>BnaCIPK9</i> homoeologs underwent duplication followed by consistent evolutionary retention within the <i>Brassica</i> lineage, exhibiting remarkable sequence and structural conservation. Expression profiling revealed tissue-partitioned functional specialization among homoeologs, with <i>BnaA10.CIPK9</i> and <i>BnaC05.CIPK9</i>&#xa0;showing seed-preferential expression. CRISPR/Cas9 knockout in <i>B. napus</i> and heterologous overexpression in <i>Arabidopsis</i> demonstrate these homoeologs act as dosage-dependent regulators of oil accumulation, dependent on their distinct expression patterns. They further exhibit expression-driven functional diversification in abiotic stress responses during seedling development. Population genomics reveal differential evolutionary trajectories among duplicates, with intensified selection on chromosome A10 driving adaptive divergence. Crucially, haplotype–trait association identifies hap.q<i>CIPK9</i>.A10.0 as a major haplotype linked to elevated oil content. This work elucidates how homoeolog subfunctionalization fine-tunes critical agronomic traits, oil biosynthesis, and stress resilience, in polyploid crops, establishing haplotype-assisted breeding as imperative for developing crop cultivars. Favorable haplotypes, exemplified by hap.q<i>CIPK9</i>.A10.0, offer precise targets for high-oil crop breeding improvement.</p>

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BnaCIPK9 homoeologs mediate the dosage-dependent regulation of seed oil in allotetraploid Brassica napus L

  • 期刊论文

  • 发表日期：

    2026年4月6日

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  • Nan Wang,
  • Jingquan Tang,
  • Xianfei Hou,
  • Chengtao Quan,
  • Jiaming Mai,
  • Chao He,
  • Rundong Chen,
  • Baolong Tao,
  • yuanguo Gu,
  • Donghai Jia,
  • Tingdong Fu,
  • Jitao Zou,
  • Lun Zhao,
  • Jing Wen,
  • Jinxiong Shen

摘要

Key message

CRISPR/Cas9 mutagenesis and overexpression lines analyses revealed CIPK9 homoeologs function in oil regulation of allotetraploid Brassica napus, cooperative multicopy interactions, and a superior haplotype on chromosome A10.

Abstract

Rapeseed (Brassica napus, B. napus), a globally significant allopolyploid oilseed crop, fulfills substantial annual vegetable oil demand. Evolutionary adaptation in this species is underpinned by gene duplication and homoeolog retention, enhancing plasticity under dynamic environmental stresses. This study focuses on BnaCIPK9, a regulator of seed oil content. Phylogenomic and structural analyses demonstrate that BnaCIPK9 homoeologs underwent duplication followed by consistent evolutionary retention within the Brassica lineage, exhibiting remarkable sequence and structural conservation. Expression profiling revealed tissue-partitioned functional specialization among homoeologs, with BnaA10.CIPK9 and BnaC05.CIPK9 showing seed-preferential expression. CRISPR/Cas9 knockout in B. napus and heterologous overexpression in Arabidopsis demonstrate these homoeologs act as dosage-dependent regulators of oil accumulation, dependent on their distinct expression patterns. They further exhibit expression-driven functional diversification in abiotic stress responses during seedling development. Population genomics reveal differential evolutionary trajectories among duplicates, with intensified selection on chromosome A10 driving adaptive divergence. Crucially, haplotype–trait association identifies hap.qCIPK9.A10.0 as a major haplotype linked to elevated oil content. This work elucidates how homoeolog subfunctionalization fine-tunes critical agronomic traits, oil biosynthesis, and stress resilience, in polyploid crops, establishing haplotype-assisted breeding as imperative for developing crop cultivars. Favorable haplotypes, exemplified by hap.qCIPK9.A10.0, offer precise targets for high-oil crop breeding improvement.