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 ofHATgenes have been performed inArabidopsis thalianaandOryza sativa. However, little information is available on theHATgenes in foxtail millet (Setaria italica[L.] P.Beauv).Results: In this study, 24HATgenes (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 betweenArabidopsis thaliana,Oryza sativa, and foxtail millet; 19 and 2 orthologous gene pairs were individually identified. Moreover, all identifiedHATgene pairs likely underwent purified selection based on their non-synonymous/synonymous nucleotide substitutions. Using published transcriptome data, we found thatSiHATgenes were preferentially expressed in some tissues and organs. Stress responses were also examined, and data showed thatSiHATgene transcription was influenced by drought, salt, low nitrogen, and low phosphorus stress, and that the expression of fourSiHATs was altered as a result of infection bySclerospora graminicola.Conclusions: Results indicated that histone acetylation may play an important role in plant growth and development and stress adaptations. These findings suggest thatSiHATsplay specific roles in the response to abiotic stress and viral infection. This study lays a foundation for further analysis of the biological functions ofSiHATsin foxtail millet.

Sorghum is an important grain, forage, and bioenergy crop. The objective of this study was to identify genetic signals associated with plant architecture and bioenergy traits in sorghum and sudangrass germplasm through a genome-wide association study (GWAS). Plant height (HT), tiller number (TN), internode number (IN), stem diameter (SD), panicle length (PL), panicle weight (PW), reducing sugar (RS) content, Brix, and protein (PRO) content were assessed in 300 germplasm consisting of grain sorghum, sweet sorghum, sudangrass, sweet sorghum-sweet sorghum recombinant inbred lines (RILs) and sudangrass-sudangrass RILs grown in three different environments over two years. Large variations of phenotypic traits were observed in the population panel. The heritability of traits were all higher than 0.5, ranging from 0.52 (PRO) to 0.92 (HT) with an average of 0.76. The population exhibited three population structures (Q) and minor relative kinship (K), assessed by using 7982 single-nucleotide polymorphisms (SNPs). After controlling Q and K, GWAS identified 24 SNPs that were significantly associated with traits, including three SNPs with HT, four with TN, four with PL, three with Brix, and ten with RS. Of them, seven SNPs were novel signals that were not identified previously, including one for HT, one for TN, one for Brix, and four for RS. The putative candidate genes involved in brassinosteroid regulatory pathway, auxin biosynthesis, carbohydrate metabolism, and sugar transport were identified underlying the significant SNPs. Identification of SNP signals and related candidate genes would enrich the current genomic resource for further molecular breeding aimed at improvement of food, feed, and biofuel productions of sorghum.

Enhancing the absorption and utilization of phosphorus by crops is an important aim for ensuring food security worldwide. However, the gene regulatory network underlying phosphorus use in foxtail millet remains unclear. In this study, the molecular mechanism underlying low-phosphorus (LP) responsiveness in foxtail millet was evaluated using a comparative transcriptome analysis. LP reduced the chlorophyll content in shoots, increased the anthocyanin content in roots, and up-regulated purple acid phosphatase and phytase activities as well as antioxidant systems (CAT, POD, and SOD). Finally, 13 differentially expressed genes related to LP response were identified and verified using transcriptomic data and qRT-PCR. Two gene co-expression network modules related to phosphorus responsiveness were positively correlated with POD, CAT, and PAPs. Of these, SiPHR1, functionally annotated as PHOSPHATE STARVATION RESPONSE 1, was identified as an MYB transcription factor related to phosphate responsiveness. SiPHR1 overexpression in Arabidopsis significantly modified the root architecture. LP stress caused cellular, physiological, and phenotypic changes in seedlings. SiPHR1 functioned as a positive regulator by activating downstream genes related to LP tolerance. These results improve our understanding of the molecular mechanism underlying responsiveness to LP stress, thereby laying a theoretical foundation for the genetic modification and breeding of new LP-tolerant foxtail millet varieties.

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 in plant development and stress responses. Histone acetylation is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity plays an essential regulatory role in a variety of 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 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 compositions 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 by Sclerospora graminicola infection. 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.

Phosphorus (P) deficiency severely limits the growth and yield of crop plants, and anthocyanin accumulation is a key adaptive physiological response to low-P stress. However, the role of MYB transcription factors in regulating anthocyanin biosynthesis under P-deficient conditions and the application of favorable haplotypes in foxtail millet low-P tolerance breeding remain unclear. Here, we performed genome-wide identification of SiMYB genes, elucidated their evolutionary characteristics, and identified key members regulating anthocyanin accumulation under P deficiency to provide genetic resources and a theoretical basis for foxtail millet molecular breeding aimed at improving nutrient use efficiency. Specifically, a total of 229 SiMYB genes were identified in the foxtail millet genome and classified into three subgroups, with the R2R3-MYB subfamily accounting for 59.8%. Phylogenetic and synteny analyses across 15 plant species revealed diverse divergence times and complex relationships, with 29 R2R3-MYB genes showing conserved collinearity with rice and maize orthologs. Association analysis using 196 foxtail millet accessions showed that 38 single nucleotide polymorphisms (SNPs) from 16 SiMYB genes were significantly associated with leaf anthocyanin content under P deficiency (p < 0.001). Notably, the SiMYB169 gene exhibited differential tissue expression and was highly upregulated in the leaves of a P-tolerant genotype after 24 h of P deficiency treatment. Furthermore, accessions carrying the favorable G allele of SiMYB169 showed significantly higher anthocyanin accumulation under P deficiency (p < 0.01). Network prediction analysis found that SiMYB169 interacted with key genes and multiple transcription factors in the biosynthesis pathway of anthocyanin. These findings highlight SiMYB169 as an evolutionarily conserved regulator that modulated anthocyanin biosynthesis under P-deficient conditions.