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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (9): 2330-2340.doi: 10.3724/SP.J.1006.2025.53013

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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 Online:2025-09-12 Published:2025-06-13
  • Contact: *E-mail: gege0106@163.com; E-mail: caurwx@163.com E-mail:2994945163@qq.com;wangrui@baafs.net.cn;gege0106@163.com;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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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

Fig. 1

Schematic diagram of variation types and functional marker primers of maize Waxy gene A: variation types and allelic variations of maize Waxy gene; B: wx-D7 and wx-D10 associated functional markers contain three primers, wx-124 and wx-hAT associated functional marker contains four primers; Sequences in square brackets represent variation sequences, sequences marked with different types of arrows represent primer sequences, where sequences marked with straight arrows represent F1, sequences marked with dash arrows represent F2, and sequences marked with double-line arrows represent R1 and R2. e1-e10: 10 exons of maize Waxy gene."

Fig. 2

Genotyping results of four functional markers of Waxy gene based on KASP and fluorescence capillary electrophoresis platforms A: genotyping results of the wx-D7, wx-D10, wx-124 and wx-hAT functional markers on the KASP platform. Each dot represents the genotyping result of each maize material. Blue and red dots represent homozygous mutation genotype and reference genotype, respectively, while black dots represent blank control. B: the genotypic peaks of wx-D7, wx-D10, wx-124 and wx-hAT associated functional markers based on the fluorescence capillary electrophoresis platform. Blue peak is the waxy variant with FAM fluorescent label. NTC: no template control."

Table 1

Primer information of Waxy gene functional markers"

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

Fig. 3

Identification of Waxy genotypes in various types of maize germplasms based on the KASP platform A: genotyping results of four Waxy variations in 302 maize germplasms. B: genotyping results of four Waxy variations in 5 maize hybrids combination with waxy × non-waxy."

Table 2

Statistic of Waxy genotypes in 302 maize germplasms"

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

Table 3

Identification of Waxy genotypes in maize triplets"

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

Table 4

Correspondence of haplotypes, genotypes, and phenotypes of Waxy genes in maize"

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

Table 5

Proportions of waxy genotype in waxy maize"

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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[1] WANG Li-Yan;ZHAO Ke-Fu. Some Physiological Response of Zea mays under Salt-stress[J]. Acta Agron Sin, 2005, 31(02): 264 -268 .
[2] Qi Zhixiang;Yang Youming;Zhang Cunhua;Xu Chunian;Zhai Zhixi. Cloning and Analysis of cDNA Related to the Genes of Secondary Wall Thickening of Cotton (Gossypium hirsutum L.) Fiber[J]. Acta Agron Sin, 2003, 29(06): 860 -866 .
[3] NI Da-Hu;YI Cheng-Xin;LI Li;WANG Xiu-Feng;ZHANG Yi;ZHAO Kai-Jun;WANG Chun-Lian;ZHANG Qi;WANG Wen-Xiang;YANG Jian-Bo. Developing Rice Lines Resistant to Bacterial Blight and Blast with Molecular Marker-Assisted Selection[J]. Acta Agron Sin, 2008, 34(01): 100 -105 .
[4] DAI Xiao-Jun;LIANG Man-Zhong;CHEN Liang-Bi. Comparison of rDNA Internal Transcribed Spacer Sequences in Oryza sativa L.[J]. Acta Agron Sin, 2007, 33(11): 1874 -1878 .
[5] WANG Bao-Hua;WU Yao-Ting;HUANG Nai-Tai;GUO Wang-Zhen;ZHU Xie-Fei;ZHANG Tian-Zhen. QTL Analysis of Epistatic Effects on Yield and Yield Component Traits for Elite Hybrid Derived-RILs in Upland Cotton[J]. Acta Agron Sin, 2007, 33(11): 1755 -1762 .
[6] WANG Chun-Mei;FENG Yi-Gao;ZHUANG Li-Fang;CAO Ya-Ping;QI Zeng-Jun;BIE Tong-De;CAO Ai-Zhong;CHEN Pei-Du. Screening of Chromosome-Specific Markers for Chromosome 1R of Secale cereale, 1V of Haynaldia villosa and 1Rk#1 of Roegneria kamoji[J]. Acta Agron Sin, 2007, 33(11): 1741 -1747 .
[7] Zhao Qinghua;Huang Jianhua;Yan Changjing. A STUDY ON THE POLLEN GERMINATION OF BRASSICA NAPUS L.[J]. Acta Agron Sin, 1986, (01): 15 -20 .
[8] ZHOU Lu-Ying;LI Xiang-Dong;WANG Li-Li;TANG Xiao;LIN Ying-Jie. Effects of Different Ca Applications on Physiological Characteristics, Yield and Quality in Peanut[J]. Acta Agron Sin, 2008, 34(05): 879 -885 .
[9] WANG Li-Xin; LI Yun-Fu; CHANG Li-Fang; HUANG Lan ;; LI Hong-Bo ; GE Ling-Ling; Liu Li-Hua ;; YAO Ji ;; ZHAO Chang-Ping ;. Method of ID Constitution for Wheat Cultivars[J]. Acta Agron Sin, 2007, 33(10): 1738 -1740 .
[10] ZHENG Tian-Qing;XU Jian-Long;FU Bing-Ying;GAO Yong-Ming;Satish VERUKA;Renee LAFITTE;ZHAI Hu-Qu;WAN Jian-Min;ZHU Ling-Hua;LI Zhi-Kang. Preliminary Identification of Genetic Overlaps between Sheath Blight Resistance and Drought Tolerance in the Introgression Lines from Directional Selection[J]. Acta Agron Sin, 2007, 33(08): 1380 -1384 .
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