Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench

Kuiyin Li,Miaoxiao Shi,Zhenhua Li,Hao Yang,Lili Duan,Songshu Chen,Yashu Peng,Liyi Zhang,Yu Fan,Mingfang Yang,Yubo Zhang,Mingjian Ren,Yabing Dong,Yanqing Ding

doi:10.1186/s12864-021-08000-7

Kuiyin Li, Miaoxiao Shi + Show 12 more

Open Access

https://doi.org/10.1186/s12864-021-08000-7

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Abstract

BackgroundTranscription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. The trihelix gene has been systematically studied in some dicots and monocots, including Arabidopsis, tomato, chrysanthemum, soybean, wheat, corn, rice, and buckwheat. However, there are no related studies on sorghum.ResultsIn this study, a total of 40 sorghum trihelix (SbTH) genes were identified based on the sorghum genome, among which 34 were located in the nucleus, 5 in the chloroplast, 1 (SbTH38) in the cytoplasm, and 1 (SbTH23) in the extracellular membrane. Phylogenetic analysis of the SbTH genes and Arabidopsis and rice trihelix genes indicated that the genes were clustered into seven subfamilies: SIP1, GTγ, GT1, GT2, SH4, GTSb8, and orphan genes. The SbTH genes were located in nine chromosomes and none on chromosome 10. One pair of tandem duplication gene and seven pairs of segmental duplication genes were identified in the SbTH gene family. By qPCR, the expression of 14 SbTH members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. Except for the leaves in which the genes were upregulated after only 2 h exposure to high temperature, the 12 SbTH genes were significantly upregulated in the stems of sorghum seedlings after 24 h under the other abiotic stress conditions. Among the selected genes, SbTH10/37/39 were significantly upregulated, whereas SbTH32 was significantly downregulated under different stress conditions.ConclusionsIn this study, we identified 40 trihelix genes in sorghum and found that gene duplication was the main force driving trihelix gene evolution in sorghum. The findings of our study serve as a basis for further investigation of the functions of SbTH genes and providing candidate genes for stress-resistant sorghum breeding programmes and increasing sorghum yield.

Highlights

Transcription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants
The Pfam and InterPro databases were used to confirm that the putative genes contained the Myb/SANT-LIKE domain
The results of subcellular localization prediction of Sorghum bicolor Trihelix (SbTH) proteins showed that 34 SbTH genes were located in the nucleus, 5 in the chloroplast, and 1 (SbTH23) in the extracellular membrane

Summary

Introduction

Transcription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. Transcription factors are ubiquitous in plants and play important roles in various growth and developmental processes and abiotic stress response [4]. In the 1980s, the trihelix transcription factors exist only in plants and separated from the pea (Pisum sativum) for the first time [7] They bind to the core sequence of 5 ‘-G-Pu- (T / A) -A- (T / A) -3 ‘of the promoter region of rbcS-3A gene to regulate lightdependent expression [8]. Studies have shown that the trihelix structure of GT factors is highly similar to the structure of Myb/SANT-LIKE DNA-binding domains [9]. The gaps between helix pairs result in different recognition sequences between GT factors and Myb/SANT-LIKE proteins [9, 10]

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