Dataset Information

Analysis of bHLH genes from foxtail millet (Setaria italica) and their potential relevance to drought stress.

ABSTRACT: Foxtail millet is very a drought-tolerant crop. Basic helix-loop-helix (bHLH) transcription factors are involved in many drought-stress responses, but foxtail millet bHLH genes have been scarcely examined. We identified 149 foxtail millet bHLH genes in a genome-wide analysis and performed Swiss-Prot, GO, and KEGG pathway analyses for these genes. Phylogenetic analyses placed the genes into 25 clades, with some remaining orphans. We identified homologs based on gene trees and Swiss-Prot annotation. We also inferred that some homologs underwent positive selection in foxtail millet ancestors, and selected motifs differed among homologs. Expression of eight foxtail millet bHLH genes varied with drought stress. One of these genes was localized to a QTL that contributes to drought tolerance in foxtail millet. We also perform a cis-acting regulatory element analysis on foxtail millet bHLH genes and some drought-induced genes. Foxtail millet bHLH genes were inferred to have a possible key role in drought tolerance. This study clarifies both the function of foxtail millet bHLH genes and drought tolerance in foxtail millet.

SUBMITTER: Wang P

PROVIDER: S-EPMC6226204 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Analysis of bHLH genes from foxtail millet (Setaria italica) and their potential relevance to drought stress.

Wang Pengfei P Wang Haili H Wang Yongmei Y Ren Fengshan F Liu Wei W

PloS one 20181109 11

Foxtail millet is very a drought-tolerant crop. Basic helix-loop-helix (bHLH) transcription factors are involved in many drought-stress responses, but foxtail millet bHLH genes have been scarcely examined. We identified 149 foxtail millet bHLH genes in a genome-wide analysis and performed Swiss-Prot, GO, and KEGG pathway analyses for these genes. Phylogenetic analyses placed the genes into 25 clades, with some remaining orphans. We identified homologs based on gene trees and Swiss-Prot annotatio ...[more]

PMID: 30412624

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Project description:Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08095-y.

Dataset Information

Analysis of bHLH genes from foxtail millet (Setaria italica) and their potential relevance to drought stress.

Publications

Analysis of bHLH genes from foxtail millet (Setaria italica) and their potential relevance to drought stress.

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