Genome-wide investigation of histone acetyltransferase gene family and its responses to biotic and abiotic stress in foxtail millet (Setaria italica [L.] P. Beauv)

Abstract

Background Modification of histone acetylation is a ubiquitous and reversible process in eukaryotes and prokaryotes and plays crucial roles in the regulation of gene expression during plant development and stress responses. Histone acetylation is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT plays an essential regulatory role in various growth and development processes by modifying the chromatin structure through interactions with other histone modifications and transcription factors in eukaryotic cells, affecting the transcription of genes. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana and Oryza sativa. However, little information is available on the HAT genes in foxtail millet (Setaria italica [L.] P. Beauv). Results In this study, 24 HAT genes (SiHATs) were identified and divided into four groups with conserved gene structures via motif composition analysis. Phylogenetic analysis of the genes was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa, and foxtail millet; 19 and 2 orthologous gene pairs were individually identified. Moreover, all identified HAT gene pairs likely underwent purified selection based on their non-synonymous/synonymous nucleotide substitutions. Using published transcriptome data, we found that SiHAT genes were preferentially expressed in some tissues and organs. Stress responses were also examined, and data showed that SiHAT gene transcription was influenced by drought, salt, low nitrogen, and low phosphorus stress, and that the expression of four SiHATs was altered as a result of infection by Sclerospora graminicola. Conclusions Results indicated that histone acetylation may play an important role in plant growth and development and stress adaptations. These findings suggest that SiHATs play specific roles in the response to abiotic stress and viral infection. This study lays a foundation for further analysis of the biological functions of SiHATs in foxtail millet.

Identification of histone acetyltransferase genes responsible for cannabinoid synthesis in hemp

“…The expression patterns of HATs in different organs have been described in many species, including Triticum aestivum , cotton, and foxtail millet [ 33 , 50 , 51 ]. For example, TaHAT genes were highly expressed in wheat leaves [ 33 ].…”

“…GhHATs were widely expressed in the vegetative (root, stem, and leaf) and reproductive (torus, petal, stamen, pistil and calyx) parts [ 50 ]. SiHAT2 was highly expressed in leaves and stems, but the transcript levels of SiHAT4 , SiHAT15 , and SiHAT18 were very low [ 51 ]. In addition, Yang et al found that CsHDACs were expressed in roots, stems, leaves, and flowers to different degrees [ 37 ].…”

QTL analysis of important agronomic traits and metabolites in foxtail millet (Setaria italica) by RIL population and widely targeted metabolome

“…Millet has the characteristics of wide adaptability and yield stability, and it adapt to high temperature and arid environment well ( Yuan et al., 2021 ; Han et al., 2022 ). In addition to its high nutritional value ( Li et al., 2018 ; Ma et al., 2022 ), millet is also an ideal model crop for studying grass crops due to its small genome and close relatedness to many important grass crops, such as switchgrass ( Panicum virgatum ), napiergrass( Pennisetum purpureum ), pearl millet ( Li et al., 2022 ; Xing et al., 2022 ). Therefore, the research on the formation of millet phenotype, genetic mechanism and molecular breeding is of great significance.…”

Molecular genetics and phenotypic assessment of foxtail millet (Setaria italica (L.) P. Beauv.) landraces revealed remarkable variability of morpho-physiological, yield, and yield‐related traits

“…Globally it is cultivated in marginal and resource poor soils and is an ideal crop for sustainable agriculture ( Meng et al, 2020 ). The short life cycle, high breeding rate and minimal water for rapid maturation ( Doust et al, 2009 ; Xing et al, 2022 ) make foxtail millet a farmer’s favorite. In addition, the hardiness of this plant makes it an excellent model crop for genetic and molecular research on water use efficiency and drought tolerance, especially in the context of C4 metabolism ( Doust et al, 2009 ; Li and Brutnell, 2011 ).…”