Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses

Abstract Background In plants, histone modification (HM) genes participate in various developmental and defense processes. Gramineae plants (e.g., Triticum aestivum, Hordeum vulgare, Sorghum bicolor, Setaria italica, Setaria viridis, and Zea mays) are important crop species worldwide. However, littl...

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Autores principales:	Liwei Zheng, Shengjie Ma, Dandan Shen, Hong Fu, Yue Wang, Ying Liu, Kamran Shah, Caipeng Yue, Jinyong Huang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Histone modification Wheat and maize Growth and development Stress Botany QK1-989
Acceso en línea:	https://doaj.org/article/a8fbea4319604ff998339f61f8b109ab
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spelling	oai:doaj.org-article:a8fbea4319604ff998339f61f8b109ab2021-11-21T12:05:49ZGenome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses10.1186/s12870-021-03332-81471-2229https://doaj.org/article/a8fbea4319604ff998339f61f8b109ab2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03332-8https://doaj.org/toc/1471-2229Abstract Background In plants, histone modification (HM) genes participate in various developmental and defense processes. Gramineae plants (e.g., Triticum aestivum, Hordeum vulgare, Sorghum bicolor, Setaria italica, Setaria viridis, and Zea mays) are important crop species worldwide. However, little information on HM genes is in Gramineae species. Results Here, we identified 245 TaHMs, 72 HvHMs, 84 SbHMs, 93 SvHMs, 90 SiHMs, and 90 ZmHMs in the above six Gramineae species, respectively. Detailed information on their chromosome locations, conserved domains, phylogenetic trees, synteny, promoter elements, and gene structures were determined. Among the HMs, most motifs were conserved, but several unique motifs were also identified. Our results also suggested that gene and genome duplications potentially impacted the evolution and expansion of HMs in wheat. The number of orthologous gene pairs between rice (Oryza sativa) and each Gramineae species was much greater than that between Arabidopsis and each Gramineae species, indicating that the dicotyledons shared common ancestors. Moreover, all identified HM gene pairs likely underwent purifying selection based on to their non-synonymous (Ka)/synonymous (Ks) nucleotide substitutions. Using published transcriptome data, changes in TaHM gene expression in developing wheat grains treated with brassinosteroid, brassinazole, or activated charcoal were investigated. In addition, the transcription models of ZmHMs in developing maize seeds and after gibberellin treatment were also identified. We also examined plant stress responses and found that heat, drought, salt, insect feeding, nitrogen, and cadmium stress influenced many TaHMs, and drought altered the expression of several ZmHMs. Thus, these findings indicate their important functions in plant growth and stress adaptations. Conclusions Based on a comprehensive analysis of Gramineae HMs, we found that TaHMs play potential roles in grain development, brassinosteroid- and brassinazole-mediated root growth, activated charcoal-mediated root and leaf growth, and biotic and abiotic adaptations. Furthermore, ZmHMs likely participate in seed development, gibberellin-mediated leaf growth, and drought adaptation.Liwei ZhengShengjie MaDandan ShenHong FuYue WangYing LiuKamran ShahCaipeng YueJinyong HuangBMCarticleHistone modificationWheat and maizeGrowth and developmentStressBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-18 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Histone modification Wheat and maize Growth and development Stress Botany QK1-989
spellingShingle	Histone modification Wheat and maize Growth and development Stress Botany QK1-989 Liwei Zheng Shengjie Ma Dandan Shen Hong Fu Yue Wang Ying Liu Kamran Shah Caipeng Yue Jinyong Huang Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses
description	Abstract Background In plants, histone modification (HM) genes participate in various developmental and defense processes. Gramineae plants (e.g., Triticum aestivum, Hordeum vulgare, Sorghum bicolor, Setaria italica, Setaria viridis, and Zea mays) are important crop species worldwide. However, little information on HM genes is in Gramineae species. Results Here, we identified 245 TaHMs, 72 HvHMs, 84 SbHMs, 93 SvHMs, 90 SiHMs, and 90 ZmHMs in the above six Gramineae species, respectively. Detailed information on their chromosome locations, conserved domains, phylogenetic trees, synteny, promoter elements, and gene structures were determined. Among the HMs, most motifs were conserved, but several unique motifs were also identified. Our results also suggested that gene and genome duplications potentially impacted the evolution and expansion of HMs in wheat. The number of orthologous gene pairs between rice (Oryza sativa) and each Gramineae species was much greater than that between Arabidopsis and each Gramineae species, indicating that the dicotyledons shared common ancestors. Moreover, all identified HM gene pairs likely underwent purifying selection based on to their non-synonymous (Ka)/synonymous (Ks) nucleotide substitutions. Using published transcriptome data, changes in TaHM gene expression in developing wheat grains treated with brassinosteroid, brassinazole, or activated charcoal were investigated. In addition, the transcription models of ZmHMs in developing maize seeds and after gibberellin treatment were also identified. We also examined plant stress responses and found that heat, drought, salt, insect feeding, nitrogen, and cadmium stress influenced many TaHMs, and drought altered the expression of several ZmHMs. Thus, these findings indicate their important functions in plant growth and stress adaptations. Conclusions Based on a comprehensive analysis of Gramineae HMs, we found that TaHMs play potential roles in grain development, brassinosteroid- and brassinazole-mediated root growth, activated charcoal-mediated root and leaf growth, and biotic and abiotic adaptations. Furthermore, ZmHMs likely participate in seed development, gibberellin-mediated leaf growth, and drought adaptation.
format	article
author	Liwei Zheng Shengjie Ma Dandan Shen Hong Fu Yue Wang Ying Liu Kamran Shah Caipeng Yue Jinyong Huang
author_facet	Liwei Zheng Shengjie Ma Dandan Shen Hong Fu Yue Wang Ying Liu Kamran Shah Caipeng Yue Jinyong Huang
author_sort	Liwei Zheng
title	Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses
title_short	Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses
title_full	Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses
title_fullStr	Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses
title_full_unstemmed	Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses
title_sort	genome-wide identification of gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses
publisher	BMC
publishDate	2021
url	https://doaj.org/article/a8fbea4319604ff998339f61f8b109ab
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Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses

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