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作物学报 ›› 2025, Vol. 51 ›› Issue (9): 2330-2340.doi: 10.3724/SP.J.1006.2025.53013

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

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 接受日期:2025-06-01 出版日期:2025-09-12 网络出版日期:2025-06-13
  • 通讯作者: *王凤格, E-mail: gege0106@163.com; 杨扬, E-mail: caurwx@163.com
  • 作者简介:朱维佳, E-mail: 2994945163@qq.com;王蕊, E-mail: wangrui@baafs.net.cn
    **同等贡献
  • 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);本研究由北京市农林科学院科技创新能力建设专项(KJCX20230301)

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. 1Maize 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
    2Yangzhou 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 Accepted:2025-06-01 Published:2025-09-12 Published online:2025-06-13
  • Contact: *E-mail: gege0106@163.com; E-mail: caurwx@163.com
  • About author:**Contributed equally to this work
  • Supported by:
    Construction of Scientific and Technological Innovation Capacity of Beijing Academy of Agriculture and Forestry Sciences(KJCX20230303);Construction of Scientific and Technological Innovation Capacity of Beijing Academy of Agriculture and Forestry Sciences(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时, 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可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了有效的方案。

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

图1

玉米糯质基因突变类型及功能标记引物设计示意图 A: 玉米糯质基因突变类型及等位变异图; B: wx-D7、wx-D10功能标记包含3条引物, wx-124、wx-hAT功能标记包含4条引物; 方括号里的序列表示变异序列, 标有不同类型箭头的序列表示引物序列, 其中标有直线箭头的序列代表F1, 标有短划线箭头的序列代表F2, 标有双线箭头的序列代表R1和R2; e1~e10: 玉米糯质基因10个外显子。"

图2

4种糯质基因功能标记在KASP和荧光毛细管电泳平台的基因分型结果 A: 基于KASP平台的wx-D7、wx-D10、wx-124和wx-hAT功能标记基因分型结果。每1个点代表一个玉米材料的基因分型结果, 其中蓝色和红色点分别代表纯合的突变基因型和参考基因型, 黑色点代表空白对照。B: 基于荧光毛细管电泳平台的wx-D7、wx-D10、wx-124和wx-hAT功能标记基因分型峰图。蓝色峰为FAM荧光标记的糯质变异。NTC: 无模板对照。"

表1

糯质基因功能标记引物信息"

变异类型
Variation type		 等位基因
Allele		 荧光修饰
Fluorescence modification		 产物大小
Product size
(bp)		 引物序列
Primer sequence (5′-3′)
wx-D7 wx-D7/non-wxD7 FAM 44 F1: ATCTACAGGGACGCCGT
R1: GACGAGGTATACGAGCATGGA
HEX 48 F2: CTCTGAACTGAACAACGC
R2: GACGAGGTATACGAGCATGGA
wx-D10 wx-D10/non-wxD10 FAM 37 F1: GCCTGCAGCGCCTT
R1: GGTGTCCGGTTCAGGC
HEX 52 F2: GCCTGCAGCGCCTC
R2: GGTGTCCGGTTCAGGC
wx-124 wx-124/non-wx124 FAM 48 F1: TGCTCTTGAGGTAGCACGAGG
R1: CCATCGACAAATTCAGAGGATCCCAA
HEX 64 F2: GTTGCTCTTGAGGTAGCACGAGA
R2: GAGGACGTCGTGTTCGTCTGCAA
wx-hAT wx-hAT/non-wxhAT FAM 59 F1: GTCCCAGGCGTCCTTGTACTC
R1: AGCTCGGCATACTCTAACTTAAAATCCTA
HEX 45 F2: GTCCCAGGCGTCCTTGTACTG
R2: TCATGGTCGTCTCTCCCCGCTA

图3

基于KASP平台的不同类型玉米种质糯质基因类型鉴定 A: 302份玉米种质的4种糯质基因变异的基因分型结果。B: 5份糯×非糯型玉米杂交组合的4种糯质基因变异的基因分型结果。"

表2

302份玉米种质的糯质基因类型统计"

基因型
Genotype		 糯玉米
Waxy maize		 普通玉米
Common maize		 甜玉米自交系
Sweet maize inbred line		 甜糯玉米杂交种
Sweet-waxy maize hybrid		 甜糯双隐基因型玉米自交系
Double recessive sweet-waxy maize inbred line
杂交种
Hybrid		 自交系
Inbred line		 杂交种
Hybrid		 自交系
Inbred line
D7/D7 47 136 0 0 0 3 1
D10/D10 1 7 0 0 0 0 0
124/124 0 1 0 0 0 0 0
hAT/hAT 1 10 0 0 0 0 0
D7/D10 8 0 0 0 0 0 0
Wx/Wx 0 0 10 19 58 0 0
总计Total 57 154 10 19 58 3 1

表3

三联体玉米种质的糯质基因型鉴定"

序号
Number		 三联体
Triplet		 基因型
Genotype
1 京科糯2000 Jingkenuo 2000 D7/D7
京糯6 Jingnuo 6 D7/D7
BN2 D7/D7
2 京科糯623 Jingkenuo 623 D7/D10
京糯2 Jingnuo 2 D10/D10
D6644-2 D7/D7

表4

玉米糯质基因单倍型、基因型、表现型的对应关系"

Waxy基因
Waxy gene		 变异类型
Variation type		 单倍型
Haplotype		 基因型Genotype 表现型
Phenotype
自交系Inbred line 杂交种
Hybrid
隐性基因wx
Recessive gene wx		 wx-D7 wD7WD10W124WhAT (D7) D7/D7
 D7/D7, D7/D10, D7/124, D7/hAT, D7/mut 糯性
Waxy
wx-D10 WD7wD10W124WhAT (D10) D10/D10
 D10/D10, D7/D10, D10/124, D10/hAT, D10/mut
wx-124 WD7WD10w124WhAT (124) 124/124
 124/124, D7/124, D10/124, 124/hAT, 124/mut
wx-hAT WD7WD10W124whAT (hAT) hAT/hAT
 hAT/hAt, D7/hAT, D10/hAT, 124/ hAT, hAT/mut
wx-mut WD7WD10W124WhAT (mut) mut/mut mut/mut, D7/mut, D10/mut, 124/mut, hAT/mut
显性基因Wx
Dominant gene Wx		 Wx WD7WD10W124WhAT (Wx) Wx/Wx Wx/Wx, Wx/D7, Wx/D10, Wx/124, Wx/hAT, Wx/mut 非糯性
Non-waxy

表5

糯玉米糯质基因类型占比"

基因型
Genotype		 糯玉米杂交种
Waxy maize hybrid
(%)		 糯玉米自交系
Waxy maize inbred line (%)
D7/D7 82.46 88.31
D10/D10 1.75 4.55
124/124 0 0.65
hAT/hAT 1.75 6.49
D7/D10 14.04 0
总计Total 100.00 100.00
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