Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (15): 3237-3251.doi: 10.3864/j.issn.0578-1752.2026.15.001

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

Functional Characterization and Molecular Marker Development of the Wheat Transcription Factor Gene TaWRKY65-3A

ZHANG YanFei1(), WU ZiYue1, XUE ZhiWei4, MA DongYun1, KANG GuoZhang1, FENG Wei1, XIE YingXin1, JING RuiLian2, WANG WanZhang3, MAO XinGuo2(), WANG ChenYang1()   

  1. 1 College of Agriculture, Henan Agricultural University/National Wheat Engineering Technology Research Center, Zhengzhou 450046
    2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081
    3 College of Mechanical & Electrical Engineering, Henan Agricultural University, Zhengzhou 450046
    4 Anyang Academy of Agricultural Sciences, Anyang 455000, Henan
  • Received:2025-12-12 Accepted:2026-02-06 Online:2026-08-01 Published:2026-08-03
  • Contact: MAO XinGuo, WANG ChenYang

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Abstract:

【Objective】WRKY transcription factors are the plant-specific transcription factor families, and play a crucial role in plant growth, development, nutrient uptake, and response to biotic and abiotic stresses. Characterized the function of the wheat transcription factor gene TaWRKY65-3A and developed the molecular markers, providing genetic resources for wheat germplasm improvement through molecular breeding in this research.【Method】The sequence of TaWRKY65-3A was cloned from the cDNA of wheat variety Hanxuan 10. The domains were analyzed via the SMART website. The expression patterns of TaWRKY65-3A gene were analyzed by qRT-PCR under phytohormone ABA treatments, PEG and NaCl stresses. Predicted the polymorphisms of TaWRKY65-3A through the Wheat Genome Variation Joint Database, and validated them by using 21 wheat germplasms with rich genetic diversity and further developed molecular markers. Association analysis between TaWRKY65-3A haplotypes and phenotypic traits was carried out in a natural population consisting of 323 wheat accessions. The haplotype of 189 modern wheat cultivars from different released years were analyzed, aiming to clarify the selection trends of superior haplotypes during wheat breeding in China.【Result】TaWRKY65-3A is 1 998 bp in full length, comprising 2 exons and 1 intron, and harbors the characteristic WRKY domain and a C2H2-type zinc finger motif typical of the WRKY transcription factor family. The promoter region of TaWRKY65-3A contains a variety of cis-acting elements, including hormone-responsive elements, (e.g., to abscisic acid and methyl jasmonate) and stress-responsive elements (e.g., to drought and low temperature). Moreover, the expressions of TaWRKY65-3A was influenced by ABA, PEG and NaCl stresses. Six SNPs were identified in the TaWRKY65-3A region, forming three haplotypes: Hap-3A-1, Hap-3A-2, and Hap-3A-3. dCAPS markers were developed at positions of 1 265 bp (G/C) in the coding sequence and 1 658 bp (T/C) in the non-coding sequence, which were significantly associated with thousand-kernel weight, yield per plant, spikelet number per spike, and kernel number per spike across multiple environments. Notably, the haplotype Hap-3A-2 was demonstrated to be significantly correlated with higher spikelet number per spike, a great kernel number per spike, a higher thousand-kernel weight, and a higher yield per plant in multiple environments, including drought, high temperature, and the combined stress of drought and high temperature, and it was positively selected during wheat breeding in China.【Conclusion】TaWRKY65-3A gene responded to phytohormones ABA, PEG and NaCl stress, and were significantly correlated with spikelet number per spike, kernel number per spike, thousand-kernel weight and yield per plant under various environments such as drought, high temperature, and the combined stress of drought and high temperature. Hap-3A-2 is the favorable haplotype with higher spikelet number per spike, more kernel number per spike, higher thousand-kernel weight, and higher yield per plant. The molecular markers of dCAPS developed in this study provide valuable tools for marker-assisted breeding, facilitating the selection of germplasm with superior yield-related traits.

Key words: wheat, transcription factor, TaWRKY65-3A, yield, dCAPS marker, haplotype

Table 1

Primers used in this study"

引物名称 Prime name 引物序列 Sequences (5´-3´) 用途 Usage
TaWRKY65-qF CATCGAGGTGCACGACGAT TaWRKY65表达
Expression of TaWRKY65
TaWRKY65-qR GCGGCCGTGTCGACCTC
TaActin-qF CTCCCTCACAACAACAACCGC
TaActin-qR TACCAGGAACTTCCATACCAAC
OsActin-qF AGTAGTCTCGCCCTGCTTCA
OsActin-qR TTCGCCACTTTGTTCTCAACT
TaWRKY65-1300GFP-F CCAAATCGACTCTAGAATGGACGGCGAGTGGAGC 亚细胞定位
Subcellular localization
TaWRKY65-1300GFP-R TGCTCACCATGGTACCCGTCATGGCTGTGCCCTC
TaWRKY65-3A-1265F TTGACCCCTCCTGCCATT 开发分子标记
Developing the molecular markers
TaWRKY65-3A-1265R GCTCGTTCTTCCGACTCCAT
TaWRKY65-3A-1658F GCTTTTGTTGGTTAGTTTTCTCAC
TaWRKY65-3A-1658R GGGTTTGTATCCCTCTCAATCTC
TaWRKY65-3A-dCAPS-Sma I-1265F CTCGTCCGGAAGGAGCCCGG
TaWRKY65-3A-dCAPS-Sma I-1265R GTCGCCCGAGCCAGC
TaWRKY65-3A-dCAPS-Sac I-1658F AAGCATCTTAGAGGCGGAGCT
TaWRKY65-3A-dCAPS-Sac I-1658R TGGTCCAAACAAATGAATAAAAAC

Fig. 1

Analysis of TaWRKY65-3A gene sequence and protein structure A: Diagram of TaWRKY65-3A gene structure. Black rectangles indicate exons; B: Alignment of TaWRKY65-3A proteins. The red rectangular box indicates the WRKY Domain and C2H2 finger domain; C: The prediction of TaWRKY65-3A secondary structure; D: Phylogenetic tree of plant WRKYs. TaWRKY65-3A is labeled with blue square. At: Arabidopsis thaliana; Do: Dichanthelium oligosanthes; Hv: Hordeum vulgare; Lp: Lolium perenne; Ob: Oryza brachyantha; Os: Oryza sativa; Pt: Populus trichocarpa; Pm: Panicum miliaceum; Pv: Panicum virgatum; Sb: Sorghum bicolor; Si: Setaria italica; Ta: Triticum aestivum; Td: T. dicoccoides; Tu: T. urartu; Zm: Zea mays; E: Subcellular localization of TaWRKY65-3A in tobacco leaves"

Table 2

Putative cis-acting regulatory elements in the promoter region of TaWRKY65-3A"

顺式作用元件 Cis-acting element 数量 Numbers 生物学功能 Biological function
TGACG-motif 5 茉莉酸甲酯应答元件Cis-acting regulatory element involved in the MeJA-responsiveness
CGTCA-motif 5 茉莉酸甲酯应答元件Cis-acting regulatory element involved in the MeJA-responsiveness
ABRE 2 脱落酸应答元件Cis-acting element involved in the abscisic acid responsiveness
TC-rich repeats 1 防御和胁迫应答元件Cis-acting element involved in defense and stress responsiveness
LTR 1 低温应答元件Cis-acting element involved in low-temperature responsiveness
MBS 1 MYB蛋白结合元件MYB protein binding element

Fig. 2

The cis-acting elements in the TaWRKY65-3A promoter and expression patterns of TaWRKY65-3A under different stress conditions A: Distributions of various cis-acting regulatory elements in the promoter regions of TaWRKY65-3A in the reference genome of Chinese Spring; B, C: 50 µmol·L-1 ABA treatment. D, E: 16.1% PEG6000 treatment; F, G: 250 mmol·L-1 NaCl treatment. L: leaf, R: Root. *: P<0.05; **: P<0.01; ***: P<0.001. The same as below"

Table 3

Prediction of variation information in the TaWRKY65-3A gene"

位置Sites (bp) 样本数量
Number of samples		 占总样本百分比
Percentage of total samples (%)
809 1265 1658 1684 1758 1887
T G T T G A 40 27.6
T C T C A A 58 40.0
C G C C G G 24 16.6
T C T C G A 4 2.8
T C T T G A 2 1.4
T C T T A A 2 1.4
C G T T G G 2 1.4
T G C C G G 1 0.7
C G T C G G 1 0.7
C G C C G A 1 0.7
/ / / / / / 10 6.9
合计Total 145 100

Fig. 3

Allelic variation and dCAPS marker genotyping of TaWRKY65-3A A: The allelic variations and haplotypes of TaWRKY65-3A. Black rectangles represent exons, and black lines indicate intron or UTR sequences; B: dCAPS marker dCAPS-1265 at 1265 bp; C: dCAPS marker dCAPS-1658 at 1658 bp; D: The number of samples per genotype within a natural population of 323 individuals"

Table 4

Association analysis between TaWRKY65-3A marker and the yield traits in a natural population of wheat"

环境
Environments		 年份
Years		 地点
Sites		 处理
Treatments		 性状（P值）Traits (P value)
dCAPS-1265 dCAPS-1658
千粒重
Thousand grain weight		 单株产量
Grain yield per plant		 穗粒数
Grain number per spike		 每穗小穗数
Spikelets per spike
E1 2015 顺义
SY		 DS+HT 0.0030** 0.6016ns 0.1759ns 0.0005***
E2 DS 0.0107* 0.5323ns 0.0043** 0.0035**
E3 WW+HT 0.0772ns 0.3067ns 0.0002*** 0.0007***
E4 WW 0.0001*** 0.1644ns 0.0347* 0.0008***
E5 2016 顺义
SY		 DS+HT 0.0433* 0.0001*** 0.0086** 0.0006***
E6 DS 0.0007*** 0.0019** 0.0044** 0.0013**
E7 WW+HT 0.0624ns 0.0075** 0.0547ns 0.0037**
E8 WW 0.5628ns 0.0274* 0.2390ns 0.0179*
E9 昌平
CP		 WW 0.0003*** 0.0088** 0.0053** 0.0149*
E10 DS 0.0010** 0.1856ns 0.0260* 0.1182ns
E11 2017 顺义
SY		 DS+HT 0.3325ns 0.0035** 0.0011** 0.0032**
E12 DS 0.0010** 0.0055** 0.1369ns 0.0069**
E13 WW+HT 0.1806ns 0.0054** 0.0025** 0.0133*
E14 WW 0.0001*** 0.0549ns 0.0040** 0.1279ns
E15 昌平
CP		 DS 0.0017** 0.0169* 0.0008*** 0.0020**
E16 WW 0.0001*** 0.0264* 0.0104* 0.0072**

Fig. 4

Association analysis between dCAPS-1265 and dCAPS-1658 markers and yield trait comparisons under 16 environments"

Fig. 5

Association analysis between the three haplotypes of TaWRKY65-3A and yield trait comparisons under 16 environments The different lowercase letters indicate that significant differences under the same environment at P<0.05 level"

Fig. 6

Frequency distribution of three TaWRKY65-3A haplotypes in modern varieties released in different decades"

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