Crops ›› 2024, Vol. 40 ›› Issue (1): 65-72.doi: 10.16035/j.issn.1001-7283.2024.01.009

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Identification of bHLH Family Transcription Factors of Wheat and Expression Analysis under Salt Stress

Lü Baolian1,2(), Yang Yuxin2, Cui Licao2, Shi Feng3, Ma Liang3, Kong Xiuying2, Zhang Lichao2(), Ni Zhiyong1()   

  1. 1College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang 050041, Hebei, China
  • Received:2022-11-07 Revised:2023-11-23 Online:2024-02-15 Published:2024-02-20
  • Contact: Zhang Lichao,Ni Zhiyong E-mail:18099270656@163.com;zhanglichao@caas.cn;nizhiyong@126.com

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Abstract:

Basic helix-loop-helix, or bHLH, is a major family of plant transcription factors that is involved in signal transduction, biosynthesis, abiotic stress response, and plant growth and development. Using the winter wheat cultivar ?Kenong 199? as the experimental material, we systematically analyzed the expression characteristics of wheat bHLH transcription factor under salt stress using transcriptional sequencing and bioinformatics analysis to investigate the functions of common wheat bHLH transcription factors in response to salt stress. According to the findings, wheat contains 489 bHLH transcription factors spreading across 21 chromosomes. Following the construction of the phylogenetic tree, the bHLH family was further subdivided into nine subfamilies, with the VI subfamily having the greatest number of members and the IV subfamily having the least. Wheat roots? transcriptome sequencing revealed 44 differentially expressed genes (DEGs), of which 17 were up-regulated and 27 were down-regulated at one and six hours after salt stress. According to GO analysis, DEGs were more abundant in the regulation of auxin, water and salt stress. According to KEGG annotation analysis, DEGs were primarily enriched in metabolic pathways related to starch and sucrose, amino sugars, nucleotide sugars, and other signaling pathways. The accuracy of the RNA-Seq results was confirmed through qRT-PCR verification of a few DEGs, which revealed that their expression pattern matched the transcriptome sequencing results.

Key words: Wheat, bHLH transcription factor, Salt stress, Bioinformatics analysis

Table 1

Primer information"

引物名称Primer name 正向引物（5’-3’）Forward primer 反向引物（3’-5’）Reverse primer
TraesCS5B01G518800 GATCATGGTAGCCCGTCACC TTCACCATCACGTTCCCCTC
TraesCS1A01G110400 CACCTTGTTAGCTTGTGTGGTG GCAATGGACGGTGATCTCGTTA
TraesCS4A01G408800 GAGGCAAAGCTCTCGGAGG TCTTCCACCTTTGCCATGGT
TraesCS5D01G244000 CCTTTCCTTCCGTTTCTGTCG ATGCGGTAACAACGACGACA
TraesCS2B01G543800 TCGACTTCCTGCACCTTTGG CTGCAGATATAGTCCCGCCG
TraesCS1A01G345200 GCAATCTGTGACGAGTCGGA TACCGCTCTTCCTTGCAGTC
TraesCS7B01G074900 GGATATGACGAACCAAGAACAGC CATCGATGGAGTAACAGCACTG
TraesCS1B01G359000 TGCATCTCGTGATCTCCAAGT TAACCACTCTTCCTAGCGGC
TraesCS6D02G196300 (TaGAPDH) TTAGACTTGCGAAGCCAGCA AAATGCCCTTGAGGTTTCCC

Fig.1

The distribution of the wheat bHLH family transcription factors in the chromosomes"

Table 2

Regulation patterns of 44 common differential expression genes"

基因号
Gene ID		 染色体位置
Chromosome location		 调控模式
Regulation pattern		 基因号
Gene ID		 染色体位置
Chromosome location		 调控模式
Regulation pattern
TraesCS4A01G408800 681653116~681658841 上调 TraesCS4B01G308300 599168078~599170653 上调
TraesCS4B01G308200 598910941~598914019 上调 TraesCS5A01G237500 453519135~453519842 上调
TraesCS5D01G244000 352453691~352454917 上调 TraesCS5A01G401300 594132650~594134217 上调
TraesCS2D01G270300 334040936~334043454 上调 TraesCS4D01G306400 474700560~474701269 上调
TraesCS5B01G518800 681737539~681740186 上调 TraesCS1A01G110400 110072873~110073869 上调
TraesCS2B01G289900 402217632~402220229 上调 TraesCS4B01G304500 592819415~592821925 下调
TraesCS7B01G211600 387160478~387163988 上调 TraesCS2B01G463800 657790256~657793959 下调
TraesCS3B01G002700 2169304~2172368 上调 TraesCS7A01G229900 200230140~200231461 下调
TraesCS5B01G235200 415127011~415128223 上调 TraesCS6B01G244800 437162916~437168918 下调
TraesCS5D01G411600 475000589~475001987 上调 TraesCS4A01G292800 595294248~595297051 下调
TraesCS4D01G306300 474598568~474603146 上调 TraesCS4A01G404700 678217690~678220066 下调
TraesCS2A01G271700 444623265~444626004 上调 TraesCS4D01G328800 487119229~487120910 下调
TraesCS6D01G197500 275152959~275163740 下调 TraesCS2D01G517000 607986836~607997092 下调
TraesCS4D01G302700 470506568~470509154 下调 TraesCS2B01G543800 741241659~741248415 下调
TraesCS6A01G190600 254936294~254937809 下调 TraesCS1A01G345200 532672290~532673440 下调
TraesCS6A01G214900 394613029~394618337 下调 TraesCS2B01G298600 418276647~418278407 下调
TraesCS3B01G550000 785039358~785043172 下调 TraesCS2A01G281200 469810800~469812561 下调
TraesCS4D01G018700 7992189~7995548 下调 TraesCS2D01G280100 351981513~351983269 下调
TraesCS3D01G495700 587745410~587748716 下调 TraesCS5A01G555300 706705261~706706358 下调
TraesCS3B01G550200 785280464~785284379 下调 TraesCS3A01G489600 717006915~717011250 下调
TraesCS3A01G489700 717296946~717300622 下调 TraesCS1B01G359000 588448000~588449096 下调
TraesCS3D01G495600 587644739~587648644 下调 TraesCS7B01G074900 84388710~84389462 下调

Fig.2

GO analysis of differentially expressed genes The dots represent metabolic pathways; The size of the dot represents the number of genes; Rich factor is the ratio of the number of differential genes in this metabolic pathway to the number of genes annotated to this pathway, and the higher values indicate a higher degree of enrichment. The same below."

Fig.3

KEGG analysis of differential expressed genes"

Fig.4

Cluster analysis of wheat bHLH transcription factor genes in response to salt stress"

Fig.5

Real-time PCR validation of part of DEG “*”: the difference is significant (0.05 > P > 0.01);“**”: the difference is significant (P < 0.01)."

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