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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (10): 2654-2664.doi: 10.3724/SP.J.1006.2024.41008

• RESEARCH NOTES • Previous Articles    

An E3 ubiquitin ligase gene TaSINA-3A is associated with plant height and 1000-grain weight in various environments in wheat

ZHAO Yang1,2(), LI Long2, YANG Jin-Wen1, JING Rui-Lian2, SUN Dai-Zhen1,*(), WANG Jing-Yi2,*()   

  1. 1College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi, China
    2State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2024-02-04 Accepted:2024-05-21 Online:2024-10-12 Published:2024-06-30
  • Contact: *E-mail: sdz64@126.com;E-mail: wangjingyi0507@163.com
  • Supported by:
    National Key R&D Program of China(2022YFD1200201);China Agriculture Research System of MOF and MARA(CARS-03)

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Abstract:

The SINA (seven in absentia) family of E3 ubiquitin ligases is involved in plant growth and development, immune symbiosis and response to stresses. In this study, we cloned the TaSINA-3A gene located on chromosome 3A in wheat. The TaSINA-3A genome sequence spans 3897 bp, including a 2001 bp promoter region and a 1896 bp coding region. The TaSINA-3A genome encods 244 amino acids, and contains a conserved RING (really interesting new gene) domain at amino acids 50-91. Sequence polymorphism analysis revealed the presence of 33 single nucleotide polymorphisms (SNPs) in the promoter region and 4 SNPs in the coding region. Quantitative analysis showed that the TaSINA-3A gene exhibited tissue-specific expression during different developmental stages of wheat. Molecular markers based on the SNP loci SNP-159, SNP-418, and SNP-1286 in the promoter region were developed to genotype the natural population of wheat. Association analysis between genotypes and phenotypic traits revealed significant associations between molecular marker CAPS-159 and penultimate internode length (PIL) and plant height (PH) under various environmental conditions, and Association analysis between genotypes and phenotypic traits revealed significant associations between molecular marker dCAPS-418 and spike length (SL) and 1000-grain weight (TGW) under various environmental conditions. Among these associations, the allelic variant SNP-159-C was associated with shorter PIL and PH, while SNP-418-A was associated with longer SL and higher TGW. TaSINA-3A was found to negatively regulate spike and grain development, and its expression may be suppressed by the MYC transcription factor. In the context of wheat breeding in China, SNP-418-A has been positively selected and its frequency in modern cultivars has gradually increased; however, its full potential has not been fully utilized. These results provide valuable insights for further exploration of the mechanisms underlying penultimate internode length, plant height, spike length, and grain yield. Moreover, they provide genetic resources for breeding new varieties with high yield, stable yield and wide suitability.

Key words: molecular marker, plant height, spike length, 1000-grain weight, association analysis

Table 1

Thirty diverse wheat accessions"

序号Number 材料名称Accession name 序号Number 材料名称Accession name
1 沧麦6001 Cangmai 6001 16 泰山23 Taishan 23
2 冬协2号 Dongxie 2 17 泰山24 Taishan 24
3 丰产1号 Fengchan 1 18 太原566 Taiyuan 566
4 衡5229 Heng 5229 19 温麦6号 Wenmai 6
5 葫芦头 Hulutou 20 西农688 Xinong 688
6 冀麦30 Jimai 30 21 西峰9号 Xifeng 9
7 冀麦6号 Jimai 6 22 小白麦 Xiaobaimai
8 冀麦9号 Jimai 9 23 小山8号 Xiaoshan 8
9 京品3号 Jingpin 3 24 烟农21 Yannong 21
10 京品11 Jingpin 11 25 原冬847 Yuandong 847
11 洛旱11 Luohan 11 26 运旱20410 Yunhan 20410
12 临旱935 Linhan 935 27 运旱23-35 Yunhan 23-35
13 兰天15号 Lantian 15 28 偃展1号 Yanzhan 1
14 秦麦3号 Qinmai 3 29 中7902 Zhong 7902
15 山农优麦2号 Shannongyoumai 2 30 中作60064 Zhongzuo 60064

Table 2

Primers"

名称Name 序列Sequence (5'-3')
TaSINA-3A-F GCCAAAAAGTGTGTTGACACACGAACAC
TaSINA-3A-R CTTTTTGGCGACTCCACTGGGG
SINA-3A-159-Age I-F CAACCTCCCGCATCGGTGTTC
SINA-3A-159-Age I-R GGAGGTTGACATCCGATGATAGTCGC
TaSINA-3A-418-Sph I-F GACCAACCAGAGGTTCTTAAAAAGGAAAAAG
TaSINA-3A-418-Sph I-R TGCGCTCATGAAGACGACTGATGAAA
TaSINA-3A-1286-Alu I-F CCCGTACAAGCAAAGAATTTATCTAGGCTTTC
TaSINA-3A-1286-Alu I-R TATCTTGACCGTTTCGACGAGACGAAC
TaSINA-3A-RT-F CTTTGCCGGCACAACTGACAAG
TaSINA-3A-RT-R AAAGAAGGGACGTGGGTTCTCCAC
TaSINA-3A-0800-F CGGTATCGATAAGCTTCCAGTGGAGTCGCCAAAAAG
TaSINA-3A-0800-R GCGAGAGGGAGAGGGAAGGGCCATGGAAGACGCCAA
TaTUB-F CGTGCTGTCTTTGTAGATCTCG
TaTUB-R GACCAGTGCAGTTGTCTGAAAG

Fig. 1

Schematic diagram of TaSINA-3A gene and protein sequence A: schematic diagram of gene structure; B: schematic diagram of protein domains."

Fig. 2

Prediction of TaSINA-3A protein properties A: the hydrophilicity analysis; B: phosphorylation site prediction."

Fig. 3

Prediction of cis-acting elements in TaSINA-3A promoter"

Fig. 4

Analysis of expression pattern of TaSINA-3A genes in wheat Expression pattern of TaSINA-3A genes at booting stage (A), heading stage (B), and flowering stage (C). P: peduncle; PI: penultimate inter- node; AI: antepenultimate internode; S: spike; R: root. Values are the means ± SD."

Fig. 5

Polymorphism analysis of TaSINA-3A A: polymorphism sites of TaSINA-3A. B-D: the development of the molecular markers CAPS-159 (B), dCAPS-418 (C), and dCAPS-1286 (D). The red letters represent two bases of the polymorphic sites, red rectangles indicate the restriction sites, and red dots indicate mismatched bases. E-G: gel assay of PCR products with molecular markers CAPS-159 (E), dCAPS-418 (F), and dCAPS-1286 (G)."

Table 3

Analysis of associations between TaSINA-3A marker CAPS-159 and agronomic traits in wheat"

年份
Year		 地点
Site		 处理
Treatment		 性状Trait
倒二节长 PIL 株高 PH
2015 顺义 Shunyi DS 0.00110** 0.00007***
DS+HS 0.01154* 0.00339**
WW 0.00002*** 0.00001***
WW+HS 0.00050*** 0.00092***
2016 顺义 Shunyi DS 0.00003*** 0.00003***
DS+HS 0.00023*** 0.00018***
WW 0.00138** 0.00008***
WW+HS 0.00024*** 0.00004***
昌平 Changping DS 0.00429** 0.00049***
WW 0.00007*** 0.00002***
2017 顺义 Shunyi DS 0.00013*** 0.00008***
DS+HS 0.00140** 0.00006***
WW 0.00025*** 0.00012***
WW+HS 0.00037*** 0.00004***
昌平 Changping DS 0.00605** 0.00067***
WW 0.00069*** 0.00004***

Fig. 6

Comparison of agronomic traits between accessions with two different allelic variations of TaSINA-3A marker CAPS-159 in wheat A-B: comparison of PIL (penultimate internode length) (A) and PH (plant height) (B) between accessions with two different allelic variations identified by marker CAPS-159 in 16 environments. E: environment; E1: 15-SY-DS; E2: 15-SY-DS-HS; E3: 15-SY-WW; E4: 15-SY-WW-HS; E5: 16-SY-DS; E6: 16-SY-DS-HS; E7: 16-SY-WW; E8: 16-SY-WW-HS; E9: 16-CP-DS; E10: 16-CP-WW; E11: 17-SY-DS; E12: 17-SY-DS-HS; E13: 17-SY-WW; E14: 17-SY-WW-HS; E15: 17-CP-DS; E16: 17-CP-WW. 15: 2015; 16: 2016; 17: 2017. SY: Shunyi; CP: Changping. WW: well-watered; DS: drought stress (rainfed); HS: heat stress. Significance of data is tested by Student’s t-test. Values are the means ± SD. *, **, and *** indicate significant differences at the 0.05, 0.01, and 0.001 probability levels, respectively."

Table 4

Analysis of associations between TaSINA-3A marker dCAPS-418 and agronomic traits in wheat"

年份
Year		 地点
Site		 处理
Treatment		 性状Trait
穗长 SL 千粒重 TGW
2015 顺义 Shunyi DS 0.01312* 0.03559*
DS+HS 0.00318** ns
WW 0.00152** 0.00433**
WW+HS 0.02498* 0.01210*
2016 顺义 Shunyi DS 0.01424* 0.00031***
DS+HS 0.01662* 0.02247*
WW 0.00451** 0.00016***
WW+HS 0.00847** 0.00442**
昌平 Changping DS 0.02585* 0.00138**
WW 0.00098*** 0.04618*
2017 顺义 Shunyi DS 0.02237* 0.00993**
DS+HS ns 0.03062*
WW 0.02425* 0.00097***
WW+HS 0.00494** 0.03238*
昌平 Changping DS 0.03690* 0.00095***
WW 0.00218** 0.01735*

Fig. 7

Comparison of agronomic traits between accessions with two different allelic variations of TaSINA-3A marker dCAPS-418 in wheat A-B: comparison of spike length (SL) (A) and 1000-grain weight (TGW) (B) between accessions with two different allelic variations identi- fied by marker dCAPS-418 in 16 environments. *, **, and *** indicate significant differences at the 0.05, 0.01, and 0.001 probability levels, respectively."

Fig. 8

Expression patterns of different allelic variants of TaSINA-3A A: Expression levels of two allelic-variant wheat corresponding to the TaSINA-3A gene marker CAPS-159; B: Expression levels of two allelic-variant wheat corresponding to the TaSINA-3A gene marker dCAPS-418. Values are the means ± SD. ** indicates significant difference at the 0.01 probability level."

Fig. 9

Promoter activity analysis of different allelic variants of TaSINA-3A A: LUC activity of TaSINA-3A promoter in two allelic variants of SNP-159; B: LUC activity of TaSINA-3A promoter in two allelic variants of SNP-418. Values are the means ± SD. Different letters (a, b, c) above the bars indicate significant difference at the 0.05 probability level."

Fig. 10

Distribution of allelic variations of TaSINA-3A gene in ten wheat production zones of China A-B: the distribution of two allelic variations detected by CAPS-159 marker of TaSINA-3A gene in 157 landraces (A) and 394 modern culti-vars (B) across ten Chinese wheat production zones. C-D: the distribution of two allelic variations detected by dCAPS-418 marker of TaSINA-3A gene in 157 landraces (C) and 394 modern cultivars (D) across ten Chinese wheat production zones. I: Northern Winter Wheat Zone; II: Yellow and Huai River Valleys Facultative Wheat Zone; III: Middle and Low Yangtze Valleys Autumn-Sown Spring Wheat Zone; IV: Southwestern Autumn-Sown Spring Wheat Zone; V: Southern Autumn-Sown Spring Wheat Zone; VI: Northeastern Spring Wheat Zone; VII: Northern Spring Wheat Zone; VIII: Northwestern Spring Wheat Zone; IX: Qinghai-Tibetan Plateau Spring-Winter Wheat Zone; X: Xinjiang Winter-Spring Wheat Zone."

Fig. 11

Utilization trend of superior allelic variation of dCAP-418 in Chinese modern cultivars A: 1000-grain weight (TGW) and spike length (SL) of modern cultivars released in different decades. B: the frequency of two allelic varia-tions in varieties of different decades. Pre-1950: Before the 1950s; 1950: During the 1950s. 1960: During the 1960s; 1970: During the 1970s; 1980: During the 1980s; 1990: During the 1990s."

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