Genome-wide analysis of TALE superfamily in Triticum aestivum reveals TaKNOX11-A is involved in abiotic stress response

Abstract

Background Three-amino-loop-extension (TALE) superfamily genes are widely present in plants and function directly in plant growth and development and abiotic stress response. Although TALE genes have been studied in many plant species, members of the TALE family have not been identified in wheat. Results In this study, we identified 70 wheat TALE protein candidate genes divided into two subfamilies, KNOX (KNOTTED-like homeodomain) and BEL1-like (BLH/BELL homeodomain). Genes in the same subfamily or branch in the phylogenetic tree are similar in structure, and their encoded proteins have similar motifs and conserved structures. Wheat TALE genes are unevenly distributed on 21 chromosomes and expanded on the fourth chromosome. Through gene duplication analysis, 53 pairs of wheat TALE genes were determined to result from segmental duplication events, and five pairs were caused by tandem duplication events. The Ka/Ks between TALE gene pairs indicates a strong purification and selection effect. There are multiple cis-elements in the 2000 bp promoter sequence that respond to hormones and abiotic stress, indicating that most wheat TALE genes are involved in the growth, development, and stress response of wheat. We also studied the expression profiles of wheat TALE genes in different developmental stages and tissues and under different stress treatments. We detected the expression levels of four TALE genes by qRT-PCR, and selected TaKNOX11-A for further downstream analysis. TaKNOX11-A enhanced the drought and salt tolerances of Arabidopsis thaliana. TaKNOX11-A overexpressing plants had decreased malondialdehyde content and increased proline content, allowing for more effective adaptation of plants to unfavorable environments. Conclusions We identified TALE superfamily members in wheat and conducted a comprehensive bioinformatics analysis. The discovery of the potential role of TaKNOX11-A in drought resistance and salt tolerance provides a basis for follow-up studies of wheat TALE family members, and also provides new genetic resources for improving the stress resistance of wheat.

Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat

“…The cation proton antiporter (CPA) superfamily, including K + efflux antiporter (KEA) and cation/H + exchanger (CHX) family proteins as well as the Na + /H + exchanger (NHX), TaNHX4-B.1, and TaNHX4-B.4, facilitated differential drought, salt, and heat stress tolerance to Escherichia coli [64]. A similar phenomenon occurs with transcription factors, in which orthologous or paralogue genes that are produced via gene duplication exhibit identical or opposite expression patterns when subjected to abiotic stress, including NAC [71][72][73][74], DREB [75], Hsf [76][77][78][79], MYB [80,81], bZIP [82,83], WRKY [84,85], AP2/ERF [86], GRF [87], and the homeobox genes HD-Zip [88], TALE [89,90], ZF-HD [91], and WOX [92,93]. Taking TaTAIL as an example, Rathour et al systemically identified and analyzed TAIL family members in wheat, including gene and protein structural properties, phylogeny, and expression patterns.…”

“…In addition to the above cases, a list of duplicate genes is provided in Table 1, including homologous and paralogous genes with structural and functional differences that contribute to wheat response to abiotic stress. A few such examples include drought-responsive TaHVA1, TaRAV, and TaNAC [72,73,160,161]; salt-responsive TaCHYR, TaWRKY75, and TaKNOX11 [84,90,129]; cold-responsive TaEXPA, TaICE, and TaAREB [108,162,163]; and heat-responsive TaMYB, TabZIP, and TaHAG [80,82,83,164,165]. Histone demethylase drought stress [190] TaSIRFP-3A,TaSIRFP-3B RING-HC-type E3 ligases cold stress [191] Plants 2023, 12, 2465 9 of 21…”

TALE gene family: identification, evolutionary and expression analysis under various exogenous hormones and waterlogging stress in Cucumis sativus L.

“…We built an unrooted phylogenetic tree to investigate the evolutionary relationships of the proteins encoded by the 21 genes. In contrast to earlier research, we categorized these proteins into seven distinct groups [ 29 , 30 ]. The KNOX genes are categorized into two groups, whereas the BELL genes are further classified into five groups (Fig.…”

Genome-wide identification, characterization, and evolutionary analysis of the barley TALE gene family and its expression profiles in response to exogenous hormones

“…Required barley TALE CDs and genomic DNA sequences were downloaded from the Ensembl Plants database. TALE protein sequences of T. aestivum , G. max , and P. trichocarpa were obtained from published papers ( Zhao et al., 2019 ; Wang et al., 2021 ; Han et al., 2022 ). Arabidopsis protein sequences were obtained from TAIR ( https://www.arabidopsis.org/ ), while TALE protein sequences of Oryza sativa and Zea mays were obtained from PlantTFDB v4.0 ( http://planttfdb.gao-lab.org/ ) ( Jin et al., 2017 ).…”

“…At present, genome-wide analysis of the TALE family has been completed in many plants such as Arabidopsis thaliana ( Hamant and Pautot, 2010 ), Populus trichocarpa ( Zhao et al., 2019 ), Glycine max ( Wang et al., 2021 ), and Triticum aestivum ( Han et al., 2022 ). Meanwhile, considering the importance of this family in the development of flowers and leaves in the Poaceae family, it is urgent and necessary to conduct research on the barley TALE gene family.…”