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兼容双平台的玉米糯质基因InDel功能标记开发与应用

朱维佳1,2,**，王蕊1,**，薛英杰1，田红丽1，范亚明1，王璐1，李松1，徐丽1，卢柏山1，史亚兴1，易红梅1，陆大雷2，杨扬1,*，王凤格1,*   

  1. 1北京市农林科学院玉米研究所 / 农业农村部农作物DNA指纹创新利用重点实验室(部省共建) / 玉米DNA指纹及分子育种北京市重点实验室, 北京100097; 2扬州大学 / 江苏省作物遗传生理国家重点实验室培育点 / 粮食作物现代产业技术协同创新中心, 江苏扬州225009 
  • 收稿日期:2025-02-25 修回日期:2025-06-01 接受日期:2025-06-01 出版日期:2025-06-13 网络出版日期:2025-06-13
  • 基金资助:
    本研究由北京市农林科学院科技创新能力建设专项(KJCX20230303, KJCX20230301)资助。

Development and application of functional insertion and deletion (indel) markers associated with maize Waxy gene compatible with dual-platform

ZHU Wei-Jia1,2,**,WANG Rui1,**,XUE Ying-Jie1,TIAN Hong-Li1,FAN Ya-Ming1,WANG Lu1,LI Song1,XU Li1,LU Bai-Shan1,SHI Ya-Xing1,YI Hong-Mei1,LU Da-Lei2,YANG Yang1,*,WANG Feng-Ge1,*   

  1. 1 Maize Research Institute, Beijing Academy of Agricultural and Forestry Sciences / Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province) / Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing 100097, China; 2 Yangzhou University /Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou 225009, Jiangsu, China
  • Received:2025-02-25 Revised:2025-06-01 Accepted:2025-06-01 Published:2025-06-13 Published online:2025-06-13
  • Supported by:
    The study was supported by the Construction of Scientific and Technological Innovation Capacity of Beijing Academy of Agriculture and Forestry Sciences (KJCX20230303, KJCX20230301).

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摘要：

为了实现糯玉米中糯质基因变异类型的快速鉴定、了解其在现代糯玉米育种中的应用情况，本研究针对wx-D7、wx-D10、wx-124、wx-hAT等4种常见的糯质基因InDel变异开发功能标记，以普通玉米、糯玉米、甜玉米和甜糯玉米为研究对象，通过多种分子检测平台验证糯质功能标记的特异性和有效性。结果显示，4种Waxy功能标记在KASP平台和荧光毛细管电泳平台均能够实现特异性基因分型，且能够有效区分普通玉米与糯质玉米，并确定糯玉米中Waxy基因的变异类型。针对玉米自交系，当检出特异性糯质功能标记时，可依据4种糯质变异类型确定待测样品的糯质基因单倍型并判断其糯质表型，对于未检测到4种糯质变异的玉米种质则为非糯性或糯质稀有突变。当待测样本为玉米杂交种，可能存在隐性纯合基因型、隐性等位糯性杂合基因型、糯/非糯杂合基因型及显性纯合基因型等4种情况，依据糯质单倍型结果判定。在检测出的糯玉米中85%以上为wx-D7变异类型，表明wx-D7为我国当前糯玉米育种中主要的应用类型。同时，在糯玉米杂交种中发现有D7/D10两种糯质变异类型同时存在的现象，但糯质自交系中仅存在单一的糯质变异类型，意味着在糯玉米杂交育种中通过聚合不同类型的糯质变异实现遗传改良。本研究为糯质基因设计了一套适用于多种分子检测平台的功能标记组合，为鉴定、筛选玉米糯质性状提供有效的方案。


关键词: 糯玉米, 糯质基因, 功能标记, InDel, KASP, 荧光毛细管电泳

Abstract:

To enable rapid identification of variation types associated with the Waxy gene in waxy maize and to support its application in modern waxy maize breeding, we developed functional markers targeting four common InDel variations of the Waxy gene: wx-D7, wx-D10, wx-124, and wx-hAT. The specificity and effectiveness of these markers were validated across multiple molecular detection platforms, including in common maize, waxy maize, sweet maize, and sweet-waxy maize. Results showed that the four Waxy-associated functional markers enabled specific genotyping on both the KASP and fluorescence capillary electrophoresis platforms. These markers effectively distinguished common maize from waxy maize and identified the Waxy gene variation types in waxy maize lines. The waxy phenotype could be inferred based on the Waxy gene haplotype when specific functional markers were detected in inbred lines. Maize germplasms lacking these four waxy variations exhibited either non-waxy phenotypes or rare waxy variants. For hybrid maize samples, four possible genotypic combinations were observed based on Waxy haplotype analysis: recessive homozygous, recessive allele heterozygous, waxy/non-waxy heterozygous, and dominant homozygous genotypes. Notably, over 85% of waxy maize carried the wx-D7 variation, indicating that wx-D7 is the predominant allele used in modern waxy maize breeding in China. Additionally, we found that multiple Waxy gene variations, such as D7/D10, coexisted in waxy maize hybrids, while only a single variation type was present in waxy inbred lines. This suggests that the aggregation of different Waxy variations may contribute to genetic improvement in waxy maize breeding. In summary, we developed a set of functional markers for the Waxy gene that are compatible with multiple molecular detection platforms, providing an efficient tool for the identification and screening of waxy maize germplasm.

Key words: waxy maize, Waxy gene, functional marker, indel, KASP, fluorescence capillary electrophoresis

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