一种新型冬瓜10 K SNP液相芯片及其在杂种优势利用与品种鉴定中的应用

doi:10.1016/j.jia.2025.11.010

Journal of Integrative Agriculture ›› 2026, Vol. 25 ›› Issue (2): 734-743.DOI: 10.1016/j.jia.2025.11.010

一种新型冬瓜10 K SNP液相芯片及其在杂种优势利用与品种鉴定中的应用

收稿日期:2024-10-09 修回日期:2025-11-13 接受日期:2025-09-01 出版日期:2026-02-20 发布日期:2025-11-14

A new 10K liquid SNP genotyping array for wax gourd and its application in heterosis utilization and cultivars identification

Dan Liu^{1, 5*}, Lingling Xie^{1, 5*}, Yuting Lei^{3, 5}, Bingchuan Tian^{3, 5}, Daolong Liao⁴, Fangfang Wu^{2, 5#}, Baobin Mi^{1, 5#}

¹ Hunan Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
² Hunan Agricultural University, Changsha 410128, China
³ Higentec. Co., Ltd., Changsha 410125, China
⁴ Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou 571100, China
⁵ Yuelushan Laboratory, Changsha 410128, China

Received:2024-10-09 Revised:2025-11-13 Accepted:2025-09-01 Online:2026-02-20 Published:2025-11-14
About author:#Correspondence Fangfang Wu, E-mail: wufangfang@hunau.edu.cn; Baobin Mi, E-mail: mibaobin@hunaas.cn * These authors contributed equally to this study.
Supported by:
This work was supported by the Science and Technology Talent Support Project of Hunan Province, China (2022TJ-N15), the Hunan Agricultural Science and Technology Innovation Fund, China (2024CX90 and 2024CX65), the Science and Technology Innovation Program of Hunan Province, China (2021NK1006).

摘要/Abstract

摘要：

高通量单核苷酸多态性（SNP）芯片已成为重要的基因分型工具，可显著加速育种进程并推动基础研究。本研究基于靶向测序基因分型（GBTS）技术，成功开发了用于冬瓜的高通量10 K SNP芯片，其包含的10,722个SNP均匀分布在全部12条染色体上，其中278个是与重要经济性状相关的功能位点。为验证其应用，我们利用该芯片SNP数据计算了19个优良自交系之间的遗传距离，并分析了其与单果重杂种优势的相关性。结果表明，遗传距离越大，单果重的中亲杂种优势（MPH）越高。此外，我们对采集自八个地区的56个商业冬瓜品种进行了基因分型。群体结构、系统进化和主成分分析（PCA）结果一致表明，这些品种可分为两大类群。以黑皮或深绿皮冬瓜为代表的第一类群，其遗传多样性低于由绿皮或浅绿皮品种组成的第二类群，这反映出第一类群内部遗传距离较近。最终，我们筛选出60个多态性SNP位点，构建了可用于区分56个冬瓜品种的DNA指纹图谱。作为首个冬瓜高通量基因分型平台，该SNP芯片为遗传分析提供了高效强大的工具。

Abstract:

High-throughput single nucleotide polymorphism (SNP) arrays have emerged as essential genotyping tools, significantly accelerating breeding programs and advancing basic research. In this study, a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing (GBTS), featuring 10,722 SNPs evenly distributed across all 12 chromosomes, including 278 functional loci associated with key economic traits. To demonstrate its utility, genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight. The results revealed that greater genetic distance was associated with higher middle parent heterosis (MPH) for single fruit weight. Furthermore, 56 commercial wax gourd cultivars collected from eight regions were selected and genotyped. Population structure analysis, phylogenetic analysis, and principal component analysis (PCA) collectively indicated that these cultivars fall into two major groups. Group I, comprising black or dark green skinned wax gourds, exhibited lower genetic diversity than Group II, which includes green or light green skinned varieties, reflecting shorter genetic distances within Group I. Finally, 60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars. As the first high-throughput genotyping platform for wax gourd, this SNP array provides an effective and powerful tool for genetic analysis.

Key words: wax gourd , SNPs genotyping array , heterosis , cultivar identification , DNA fingerprint

. 一种新型冬瓜10 K SNP液相芯片及其在杂种优势利用与品种鉴定中的应用[J]. Journal of Integrative Agriculture, 2026, 25(2): 734-743.

Dan Liu, Lingling Xie, Yuting Lei, Bingchuan Tian, Daolong Liao, Fangfang Wu, Baobin Mi. A new 10K liquid SNP genotyping array for wax gourd and its application in heterosis utilization and cultivars identification[J]. Journal of Integrative Agriculture, 2026, 25(2): 734-743.

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一种新型冬瓜10 K SNP液相芯片及其在杂种优势利用与品种鉴定中的应用

A new 10K liquid SNP genotyping array for wax gourd and its application in heterosis utilization and cultivars identification

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