Genome-wide identification and abiotic stress-responsive pattern of heat shock transcription factor family in Triticum aestivum L.

Abstract

Background Enhancement of crop productivity under various abiotic stresses is a major objective of agronomic research. Wheat ( Triticum aestivum L.) as one of the world’s staple crops is highly sensitive to heat stress, which can adversely affect both yield and quality. Plant heat shock factors (Hsfs) play a crucial role in abiotic and biotic stress response and conferring stress tolerance. Thus, multifunctional Hsfs may be potentially targets in generating novel strains that have the ability to survive environments that feature a combination of stresses. Result In this study, using the released genome sequence of wheat and the novel Hsf protein HMM (Hidden Markov Model) model constructed with the Hsf protein sequence of model monocot ( Oryza sativa ) and dicot ( Arabidopsis thaliana ) plants, genome-wide TaHsfs identification was performed. Eighty-two non-redundant and full-length TaHsfs were randomly located on 21 chromosomes. The structural characteristics and phylogenetic analysis with Arabidopsis thaliana , Oryza sativa and Zea mays were used to classify these genes into three major classes and further into 13 subclasses. A novel subclass, TaHsfC3 was found which had not been documented in wheat or other plants, and did not show any orthologous genes in A. thaliana , O. sativa , or Z. mays Hsf families. The observation of a high proportion of homeologous TaHsf gene groups suggests that the allopolyploid process, which occurred after the fusion of genomes, contributed to the expansion of the TaHsf family. Furthermore, TaHsfs expression profiling by RNA-seq revealed that the TaHsfs could be responsive not only to abiotic stresses but also to phytohormones. Additionally, the TaHsf family genes exhibited class-, subclass- and organ-specific expression patterns in response to various treatments. Conclusions A comprehensive analysis of Hsf genes was performed in wheat, which is useful for better understanding one of the most complex Hsf gene families. Variations in the expression patterns under different abiotic stress and phytohormone treatments provide clues for further analysis of the TaHsfs functions and corresponding signal transduction pathways in wheat. Electronic supplementary material The online version of this article (10.1186/s12864-019-5617-1) contains supplementary material, which is available to authorized users.

Genome-Wide Investigation of Heat Shock Transcription Factor Family in Wheat (Triticum aestivum L.) and Possible Roles in Anther Development

“…The number of HSF family members appears to be unrelated to the genome size, e.g., 35 Hsfs were found in Chinese cabbage (485 Mb) and 137 Hsfs in pear (527 Mb) [21,52]. Previous studies identified 56 and 82 members of the wheat HSF family [32,53], but we identified 61 TaHsfs in this study. To understand these differences in the numbers of wheat HSF members identified, we blasted the protein sequences identified by Xue et al [32] and Duan et al [53] against the latest wheat reference genome (IWGSC V1.1) [43].…”

“…These findings matched with the identification criteria employed in the present study, so they were excluded. In total, 41 common HSFs were identified in all three studies, but the classifications and names of some of these proteins differed in the studies by Xue et al [32] and Duan et al [53]. For example, TraesCS1A02G375600, TraesCS1D02G382900, and TraesCS1B02G396000 were renamed as TaHsfA6a-1, TaHsfA6a-2, and TaHsfA6a-3 in the present study because they belong to a homeologous group and are orthologous to rice Os10g28340 (A6a).…”

“…For example, TraesCS1A02G375600, TraesCS1D02G382900, and TraesCS1B02G396000 were renamed as TaHsfA6a-1, TaHsfA6a-2, and TaHsfA6a-3 in the present study because they belong to a homeologous group and are orthologous to rice Os10g28340 (A6a). However, Duan et al [53] classified these genes in classes A4 and C1, and TraesCS1B02G396000 was not even identified in the study of Xue et al [32]. The main reasons for the differences in the three studies are as follows.…”

“…To understand these differences in the numbers of wheat HSF members identified, we blasted the protein sequences identified by Xue et al [32] and Duan et al [53] against the latest wheat reference genome (IWGSC V1.1) [43]. Using the latest version gene IDs as standards, 77 genes were identified in all three studies, where four unique genes were identified in the present study, whereas six unique genes were identified by Duan et al [53] and one by Xue et al [32] ( Figure S3, Table S11). The 16 protein sequences not identified as HSFs in the present study were analyzed.…”

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“…At least 25 Hsfs were identified in maize in 2011 and the number of ZmHsfs reached 30 in 2016 (Lin et al, 2011;Guo et al, 2016). Xue et al reported that at least 56 Hsfs exist in wheat (Xue et al, 2014), but our recent analysis results suggested a larger amount (Duan et al, 2019). The large number of Hsfs family members in plant mean the complexity and diversity of Hsfs family.…”