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<p>Chinese cabbage (<i>Brassica rapa</i> L. syn. <i>B. campestris</i> L., AA, 2n = 20) is an important and widely consumed green leafy vegetable in the U triangle of crops, with China being its primary center of origin and diversification. Plant height, rosette leaf diameter &amp; color, and disease resistance have consistently been key selection criteria for Chinese cabbage breeding programs. In this study, we performed re-sequencing on 55 Chinese cabbage accessions collected from China, Japan, and Korea, followed by population genetic evolutionary analysis and genome-wide association studies (GWAS). Our findings revealed a lack of significant population structure among these accessions, suggesting potential evolutionary connections or hybridization events between Japanese and Korean Chinese cabbages and their Chinese counterparts. Results of GWAS identified <i>BrASD1</i>, <i>BrZHD13</i>, <i>BrGH3.3</i>, and <i>BrGH3.6</i> as candidate genes highly associated with plant height in Chinese cabbage. Additionally, we detected two single nucleotide polymorphism (SNP) loci linked to rosette leaf diameter and one SNP locus associated with downy mildew resistance. Furthermore, we developed a novel insertion-deletion (InDel) marker, <i>SMB.4</i>, located at the end of chromosome A04 in <i>B. rapa</i>. This marker can potentially serve as a valuable tool for screening genetic resources with downy mildew resistance and for breeding resistant <i>Brassica</i> crops in the near future.</p>

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Development and application of InDels and SNPs markers based on whole-genome resequencing in Chinese cabbage

  • 期刊论文

  • 发表日期：

    2025年4月8日

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  • Kai-Wen Liu,
  • Wan-Jie Men,
  • Jin-Xia Feng,
  • Iqbal Hussain,
  • Hui Sheng,
  • Li-Wei Zhang,
  • Zhong-Ren Dai,
  • Hai-Jiang Hu,
  • Jian-Hao Yang,
  • Na Lei,
  • Xiao-Lin Yu

摘要

Chinese cabbage (Brassica rapa L. syn. B. campestris L., AA, 2n = 20) is an important and widely consumed green leafy vegetable in the U triangle of crops, with China being its primary center of origin and diversification. Plant height, rosette leaf diameter & color, and disease resistance have consistently been key selection criteria for Chinese cabbage breeding programs. In this study, we performed re-sequencing on 55 Chinese cabbage accessions collected from China, Japan, and Korea, followed by population genetic evolutionary analysis and genome-wide association studies (GWAS). Our findings revealed a lack of significant population structure among these accessions, suggesting potential evolutionary connections or hybridization events between Japanese and Korean Chinese cabbages and their Chinese counterparts. Results of GWAS identified BrASD1, BrZHD13, BrGH3.3, and BrGH3.6 as candidate genes highly associated with plant height in Chinese cabbage. Additionally, we detected two single nucleotide polymorphism (SNP) loci linked to rosette leaf diameter and one SNP locus associated with downy mildew resistance. Furthermore, we developed a novel insertion-deletion (InDel) marker, SMB.4, located at the end of chromosome A04 in B. rapa. This marker can potentially serve as a valuable tool for screening genetic resources with downy mildew resistance and for breeding resistant Brassica crops in the near future.