Scientia Agricultura Sinica ›› 2025, Vol. 58 ›› Issue (17): 3357-3371.doi: 10.3864/j.issn.0578-1752.2025.17.001

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

Cloning and Genetic Effect Analysis of TaTIFY11c-4A in Wheat

JIA YuJing1,2(), LI ChaoNan2, PAN ZhiXiong1,2, YANG DeLong1,*(), MAO XinGuo2,*(), JING RuiLian2   

  1. 1 College of Life Science and Technology, Gansu Agricultural University/State Key Laboratory of Aridland Crop Science, Lanzhou 730070
    2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081
  • Received:2025-03-14 Accepted:2025-05-09 Online:2025-09-02 Published:2025-09-02
  • Contact: YANG DeLong, MAO XinGuo

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Abstract:

【Objective】The TIFY family, a plant-specific group of transcription factors, plays critical roles in regulating growth, development, and stress responses. This study aimed to clone TaTIFY11c-4A in wheat, validate its genetic effects, and provide a theoretical basis for high-yield molecular breeding of wheat.【Method】The wheat cultivar Hanxuan 10 was used to clone TaTIFY11c-4A and allelic variations were detected in germplasms. The tissue-specific expression patterns of TaTIFY11c-4A and its responses to various hormones and stresses were analyzed via quantitative real-time PCR (qRT-PCR). The subcellular localization of TaTIFY11c-4A was determined through transient expression in tobacco. A molecular marker targeting the polymorphic site in TaTIFY11c-4A was developed to assess the genotypes in the natural population, and association analysis was performed to evaluate the correlations between the genotypes and phenotypes. Additionally, the spatial and temporal distribution of different genotypes were analyzed. Synergistic effects of TaTIFY11c-4A and TaSRL1-4A haplotypes were explored to identify superior genotype.【Result】TaTIFY11c-4A was successfully cloned, comprising three exons and two introns, encoding a 198-amino acid protein with conserved TIFY and Jas domains. TaTIFY11c-4A is expressed in roots, root bases and leaves at the seedling stage, and highly expressed in roots and leaves at the booting stage. There are multiple cis-acting elements related to hormone responses, stress adaptation, and endosperm development in the promoter of TaTIFY11c-4A. Its expression responds to plant hormones (ABA, IAA, MeJA) and abiotic stresses (drought, high salinity, low and high temperature). A SNP (G/A) was identified in its promoter at -405 bp. A molecular marker was developed based on the SNP and association analysis revealed significant correlations between TaTIFY11c-4A alleles and plant height, thousand grain weight under multiple environments such as drought and high temperature, and root depth at tillering stage. Compared with genotype SNP-G, wheat germplasms carrying the SNP-A allele exhibited shorter plants, higher thousand grain weight, and shallower roots at tillering stage, and have been positively selected in the wheat breeding process. TaTIFY11c-4A-SNP-A and TaSRL1-4A-SNP-C genotypes synergistically reduced plant height and enhanced thousand grain weight.【Conclusion】TaTIFY11c-4A encodes a nuclear-localized JAZ protein. It is expressed in various tissues of wheat and involved in responses to ABA, IAA, MeJA, as well as abiotic stresses such as drought, extreme temperature, and high salinity. The TaTIFY11c-4A-SNP is associated with plant height and thousand grain weight under multiple environments, and root depth. SNP-A allele has been positively selected in the wheat breeding process. The superior genotypes and combinations of TaTIFY11c-4A and TaSRL1-4A provide genetic resources for breeding high-yield and stress-resistant wheat cultivars.

Key words: wheat, TaTIFY11c-4A, molecular marker, association analysis, plant height, thousand grain weight, root depth

Table 1

Primers used in this study"

引物名称Primer name 正向引物Forward primer (5′-3′) 反向引物Reverse primer (5′-3′)
TaTIFY11c-4A-qRT CACGTACATACCTCGGCACC CTGCTCCCTCATGTACTGGC
TaTUB-qRT CGTGCTGTCTTTGTAGATCTCG GACCAGTGCAGTTGTCTGAAAG
TaTIFY11c-4A-1300-GFP CCAAATCGACTCTAGAATGGG
AGCCGAGCAGCAGCA		 TGCTCACCATGGTACCGTTGA
GCTGGAGCGCGGG
TaTIFY11c-4A ACCAAGGATAGCAACACTC AACGGCAACAATCAAGGA
TaTIFY11c-4A-SacⅠ ACGAAGTCTCAATGGACGGAGACCTAG GGGGGTGGTGGAAGAAATGCCTGAG

Fig. 1

Sequence and phylogenetic analysis of TaTIFY11c-4A a: TaTIFY11c-4A gene structure diagram; b: Phylogenetic tree of TIFY proteins; c: Amino acid sequence alignment"

Fig. 2

Tissue expression pattern of wheat TaTIFY11c-4A a: Seedling stage; b: Booting stage. L: Leaf; R: Root; RB: Root base; S: Spike; FL: Flag leaf; P: Peduncle; St: Stem; R0-30, R30-60, and R60-90 represent the roots between 0-30, 30-60, and 60-90 cm below the ground"

Fig. 3

Subcellular localization of wheat TaTIFY11c-4A in tobacco leaves"

Fig. 4

Expression patterns of TaTIFY11c-4A in wheat seedlings treated with hormones and abiotic stresses a: Cis-acting element prediction in TaTIFY11c-4A promoter region. DRE core: Drought responsive element. ARE: cis-element essential for the anaerobic induction; WUN-motif, WRE: Wound responsive element; STRE: Stress responsive element; LTR: Low temperature responsive element; Sp1, GT1-motif, Box 4, G-box: Light responsive element; ABRE: ABA responsive element; CGTCA-motif, TGACG-motif: MeJA responsive element; TGA element: Auxin responsive element; GCN4_motif: cis-element involved in endosperm expression. b and d: Expression levels of TaTIFY11c-4A in leaves; c and e: Expression levels of TaTIFY11c-4A in roots"

Fig. 5

Sequence polymorphism and dCAPS molecular marker of TaTIFY11c-4A a: The schematic diagram of SNPs and molecular marker in the promoter region of TaTIFY11c-4A. Red box indicates digestion site, red letter indicates variation site, and red dot indicates mismatched base; b: The agarose gel electrophoresis of two genotypes. M: 100 bp DNA ladder; G: SNP-G genotype; A: SNP-A genotype"

Table 2

TaTIFY11c-4A genotype in wheat material of Group 1"

编号 Number 材料名称 Accession name 基因型 Genotype 编号 Number 材料名称 Accession name 基因型 Genotype
1 PANDAS SNP-A 17 临抗5108 Linkang 5108 SNP-G
2 安85中124-1 An 85 Zhong 124-1 SNP-G 18 白齐麦 Baiqimai SNP-G
3 偃展1号 Yanzhan 1 SNP-A 19 昌乐5号 Changle 5 SNP-G
4 霸王鞭 Bawangbian SNP-G 20 红和尚 Hongheshang SNP-G
5 北京10号 Beijing 10 SNP-G 21 北京8686 Beijing 8686 SNP-G
6 北京14号 Beijing 14 SNP-G 22 04-044 SNP-G
7 沧州小麦 Cangzhouxiaomai SNP-G 23 04-030 SNP-G
8 长武131 Changwu 131 SNP-A 24 春22 9th-25 Chun 22 9th-25 SNP-G
9 长6878 Chang 6878 SNP-G 25 紫秆白芒先 Ziganbaimangxian SNP-G
10 大荔1号 Dali 1 SNP-G 26 京品10号 Jingpin 10 SNP-G
11 单R8093 Dan R8093 SNP-G 27 春04 9th-5-1 Chun 04 9th-5-1 SNP-G
12 丰抗13 Fengkang 13 SNP-G 28 春45 9th-50-1 Chun 45 9th-50-1 SNP-G
13 冀麦41 Jimai 41 SNP-G 29 内乡188 Neixiang 188 SNP-G
14 冀麦6号 Jimai 6 SNP-G 30 京411 Jing 411 SNP-G
15 晋2148-7 Jin 2148-7 SNP-G 31 中国春 Chinese Spring SNP-G
16 京核8922 Jinghe 8922 SNP-A 32 白糙麦 Baicaomai SNP-G

Table 3

Association analysis between TaTIFY11c-4A and thousand grain weight and plant height in 16 environments"

环境
Environment		 P(千粒重）
P-value
(Thousand grain weight)		 P(株高）
P-value
(Plant height)		 环境
Environment		 P(千粒重）
P-value
(Thousand grain weight)		 P(株高）
P-value
(Plant height)
E1 0.03915* 0.00599** E9 0.02229* 0.01174*
E2 0.01354* 0.00141** E10 0.03127* 0.00881**
E3 0.00081*** 0.01997* E11 0.32457 0.00192**
E4 0.03561* 0.00371** E12 0.00305** 0.00783**
E5 0.04201* 0.02537* E13 0.00097*** 0.00555**
E6 0.10469 0.00875** E14 0.00169** 0.00637**
E7 0.04312* 0.0136* E15 0.05409 0.01093*
E8 0.02590* 0.01771* E16 0.13964 0.00726**

Fig. 6

Spatiotemporal distribution of two genotypes of TaTIFY11c-4A in Chinese wheat a, b, c: Comparison of the thousand grain weight, plant height, and root depth of the two genotypes of TaTIFY11c-4A in the wheat Population 2. d, e: The distribution frequencies of the two genotypes of TaTIFY11c-4A in landraces and modern cultivars across the ten major wheat-growing zones in China. Ⅰ: Northern Winter Wheat Zone; Ⅱ: Huang-Huai Winter Wheat Zone; Ⅲ: Middle and Lower Yangtze River Wheat Zone; Ⅳ: Southwest Winter Wheat Zone; Ⅴ: South China Winter Wheat Zone; Ⅵ: Northeast Spring Wheat Zone; Ⅶ: Northern Spring Wheat Zone; Ⅷ: Northwest Spring Wheat Zone; Ⅸ: Qinghai-Tibet Spring and Winter Wheat Zone; Ⅹ: Xinjiang Winter and Spring Wheat Zone. f: Plant height and thousand grain weight of cultivars released in different decades in wheat Population 2 under 16 environments. g: Frequency of two TaTIFY11c-4A genotypes of cultivars released in different decades in wheat Population 2"

Fig. 7

Differences in plant height, thousand grain weight and root depth among the haplotype combinations of TaTIFY11c-4A and TaSRL1-4A a: The genotypic combinations of TaTIFY11c-4A and TaSRL1-4A; b: Plant height; c: Thousand grain weight; d: Root depth at tillering stage. Different lowercase letters indicate significant differences between haplotypes within the same environment (P<0.05)"

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