Journal of Integrative Agriculture ›› 2025, Vol. 24 ›› Issue (7): 2655-2669.DOI: 10.1016/j.jia.2024.11.039

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板栗全基因组微卫星分子标记的开发与鉴定

  

  • 收稿日期:2024-02-28 修回日期:2024-11-28 接受日期:2024-10-17 出版日期:2025-07-20 发布日期:2024-11-29

Development and characterization of genome-wide microsatellite molecular markers for Chinese chestnut

Shihui Chu1*, Xinghua Nie1*, Chaoxin Li1, Wenyan Sun2, Yang Liu1, Kefeng Fang2, Ling Qin1, Yu Xing1#   

  1. 1 College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China

    2 College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China

  • Received:2024-02-28 Revised:2024-11-28 Accepted:2024-10-17 Online:2025-07-20 Published:2024-11-29
  • About author:Shihui Chu, E-mail: shihuichul@163.com; Xinghua Nie, E-mail: niexinghuabua@163.com; #Correspondence Yu Xing, E-mail: xingyu@bua.edu.cn * These authors contributed equally to this study.
  • Supported by:

    This work was supported by the National Key Research & Development Program of China (2024YFD2200602) and the National Natural Science Foundation of China (32471917).  

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摘要：

板栗是重要的经济树种，在木材、医药和化学工业领域都有重要的应用价值。目前，缺少全基因组 SSR 分子标记信息在很大程度上限制了栗属植物遗传多样性研究和种质资源的鉴定。为了解决这个问题，我们利用 GMATA 软件对板栗基因组中的简单序列重复（SSR）标记进行了筛选，共获得了 312,302 个分子标记，密度为 434.38/Mb。并且使用 HipSTR 程序对所有的 SSR 标记进行了多态性检测，最终获得 138,208 个多态性位点。为了验证所开发的 SSR 的鉴定能力，我们从12 条染色体上随机地选取了36个标记，构建了96个燕山板栗古树种质资源的指纹图谱。结果表明，只需要6对引物就能为供试古树建立DNA指纹，证明所开发的标记具有很高的识别潜力。随后我们利用栗属植物三个种总共91份种质资源对这些标记的种间通用性和多态性进行了评估。所开发的分子标记在种间有 94% 的扩增，PIC 值为 0.859。聚类分析结果显示新开发的标记能够用于种内和跨种间材料的区分。结果表明，所开发的分子标记具有基因型多样性的潜力，可为板栗的遗传多样性研究、品种鉴定、亲缘关系分析、优良产品选择和核心种质资源构建提供参考，也可为栗类的分子设计、改良育种和开发种质资源奠定了坚实的基础。

Abstract:

Chestnuts are important economic forest tree species with enormous application value in the wood, medicine, and chemical industries. Currently, the limited genome-wide SSR molecular marker information on chestnut resources significantly limits research on genetic diversity and identification of chestnut resources. To address this issue, we used GMATA to screen simple sequence repeat (SSR) markers throughout the Chinese chestnut genome. A total of 312,302 molecular markers were obtained with a density of 434.38/Mb. Subsequently, all SSR markers were examined for polymorphism using the HipSTR program and 138,208 polymorphic loci were finally obtained. To verify the identification ability of the developed SSR, we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient chestnut resources from the Yanshan Mountains. The results showed that only 6 pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees, showing that the developed markers have high identification potential. We then evaluated the inter-specific universality and polymorphism of these markers using three species, including 91 chestnut plants. The molecular markers amplified 94% of the interspecies with a PIC value of 0.859. Cluster analysis revealed that testing resources using these developed markers can be well differentiated and these markers have been widely used to identify interspecific boundaries. These results proved that the developed molecular markers have the potential for genotypic diversity, which can provide references for genetic diversity research, variety identification, kinship analysis, selection of good products, and construction of core germplasm resources of chestnut and even chestnut plants. They lay a solid foundation for the molecular design of hybrids to improve breeding and develop germplasm resources.

Key words: Chinese chestnut , molecular marker ,  genomic SSRs