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<p>Chinese yam (<i>Dioscorea opposita</i> Thunb.) has a long history of cultivation and application, and is an important medicinal and edible plant in China. However, the lack of molecular markers limits the efficiency and accuracy of the genetic breeding of yam. In the current study, 216,009 simple sequence repeat (SSR) loci were mined and identified based on whole-genome sequence information of Chinese yam. Dinucleotides were the major repeat motif, and (AT)n (AAT)n (AAAT)n (AAAAT)n (AAAAAT)n (AAAAAT)n was the most common repeat motif, which corresponded to dinucleotide to hexanucleotide repeats. This study successfully developed 44 novel polymorphic SSR markers that were distributed on most of the chromosomes. Neighbor-joining (NJ) clustering, principal coordinate analysis (PCoA), and genetic structure analysis showed that the genetic structure of 101 accessions was closely related to that of their germplasm origin. These 101 Chinese yam accessions were then used to investigate 14 phenotypic characteristics, which presented Shannon–Wiener index (<i>H</i>′) values of 0.36–2.03. Cluster and principal component analyses revealed that the 101 Chinese yam accessions exhibited significant genetic diversity. Association analyses revealed that one, one, one, four, one, three, one, and three markers were highly significantly (<i>p</i> &lt; 0.01) correlated with stem thickness, leaf shape, leaf length, leaf width, petiole length, petiole color, sexual type, and single bulb weight, respectively. The results of these analyses not only lay the foundation for a comprehensive evaluation of yam germplasm resources but also provide a valuable scientific basis for future breeding strategies using molecular markers. Through these analyses, we could more accurately identify and exploit genetic variation in Chinese yams, thereby improving the efficiency of breeding and the success rate of cultivar improvement.</p>

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Development of high-throughput simple sequence repeat (SSR) markers for Chinese yam (Dioscorea opposita Thunb.) and genetic diversity and association analysis using phenotypic and genotypic traits

  • 期刊论文

  • 发表日期：

    2025年3月22日

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  • Qiang Zhang,
  • Hongling Tian,
  • Shuhong Guo,
  • Yaoqin Wang,
  • Shuaishuai Pei,
  • Changjuan Wu,
  • Qiubao Wang,
  • Xianqiang Zuo

摘要

Chinese yam (Dioscorea opposita Thunb.) has a long history of cultivation and application, and is an important medicinal and edible plant in China. However, the lack of molecular markers limits the efficiency and accuracy of the genetic breeding of yam. In the current study, 216,009 simple sequence repeat (SSR) loci were mined and identified based on whole-genome sequence information of Chinese yam. Dinucleotides were the major repeat motif, and (AT)n (AAT)n (AAAT)n (AAAAT)n (AAAAAT)n (AAAAAT)n was the most common repeat motif, which corresponded to dinucleotide to hexanucleotide repeats. This study successfully developed 44 novel polymorphic SSR markers that were distributed on most of the chromosomes. Neighbor-joining (NJ) clustering, principal coordinate analysis (PCoA), and genetic structure analysis showed that the genetic structure of 101 accessions was closely related to that of their germplasm origin. These 101 Chinese yam accessions were then used to investigate 14 phenotypic characteristics, which presented Shannon–Wiener index (H′) values of 0.36–2.03. Cluster and principal component analyses revealed that the 101 Chinese yam accessions exhibited significant genetic diversity. Association analyses revealed that one, one, one, four, one, three, one, and three markers were highly significantly (p < 0.01) correlated with stem thickness, leaf shape, leaf length, leaf width, petiole length, petiole color, sexual type, and single bulb weight, respectively. The results of these analyses not only lay the foundation for a comprehensive evaluation of yam germplasm resources but also provide a valuable scientific basis for future breeding strategies using molecular markers. Through these analyses, we could more accurately identify and exploit genetic variation in Chinese yams, thereby improving the efficiency of breeding and the success rate of cultivar improvement.