紫花苜蓿/豆科植物 BADH基因家族全基因组鉴定

… of this gene family within the species. The … the ALDH gene family. As plants transitioned from aquatic to terrestrial environments, genes associated with aquatic life were lost, while genes …

SQUAMOSA promoter-binding protein-like (SPL) transcription factors are widely present in plants and are involved in signal transduction, the stress response and development. The SPL gene family has been characterized in several model species, such as A. thaliana and G. max. However, there is no in-depth analysis of the SPL gene family in forage, especially alfalfa (Medicago sativa L.), one of the most important forage crops worldwide. In total, 76 putative MsSPL genes were identified in the alfalfa genome with an uneven distribution. Based on their identity and gene structure, these MsSPLs were divided into eight phylogenetic groups. Seventy-three MsSPL gene pairs arose from segmental duplication events, and the MsSPLs on the four subgenomes of individual chromosomes displayed high collinearity with the corresponding M. truncatula genome. The prediction of the cis-elements in the promoter regions of the MsSPLs detected two copies of ABA (abscisic acid)-responsive elements (ABREs) on average, implying their potential involvement in alfalfa adaptation to adverse environments. The transcriptome sequencing of MsSPLs in roots and leaves revealed that 54 MsSPLs were expressed in both tissues. Upon salt treatment, three MsSPLs (MsSPL17, MsSPL23 and MsSPL36) were significantly regulated, and the transcription level of MsSPL36 in leaves was repressed to 46.6% of the control level. In this study, based on sequence homology, we identified 76 SPL genes in the alfalfa. The SPLs with high identity shared similar gene structures and motifs. In total, 71.1% (54 of 76) of the MsSPLs were expressed in both roots and leaves, and the majority (74.1%) preferred underground tissues to aerial tissues. MsSPL36 in leaves was significantly repressed under salt stress. These findings provide comprehensive information regarding the SPB-box gene family for improve alfalfa tolerance to high salinity.

Alfalfa (Medicago sativa) is a high-quality legume forage crop worldwide, and alfalfa production is often threatened by abiotic environmental stresses. GRAS proteins are important transcription factors that play a vital role in plant development, as well as in response to environmental stress. In this study, the availability of alfalfa genome “Zhongmu No.1” allowed us to identify 51 GRAS family members, i.e., MsGRAS. MsGRAS proteins could be classified into nine subgroups with distinct conserved domains, and tandem and segmental duplications were observed as an expansion strategy of this gene family. In RNA-Seq analysis, 14 MsGRAS genes were not expressed in the leaf or root, 6 GRAS genes in 3 differentially expressed gene clusters were involved in the salinity stress response in the leaf. Moreover, qRT-PCR results confirmed that MsGRAS51 expression was induced under drought stress and hormone treatments (ABA, GA and IAA) but down-regulated in salinity stress. Collectively, our genome-wide characterization, evolutionary, and expression analysis suggested that the MsGRAS proteins might play crucial roles in response to abiotic stresses and hormonal cues in alfalfa. For the breeding of alfalfa, it provided important information on stress resistance and functional studies on MsGRAS and hormone signaling.

BACKGROUND: Alfalfa (Medicago sativa) is the most widely planted legume forage and one of the most economically valuable crops in the world. The periodic changes in its growth and development and abiotic stress determine its yield and economic benefits. Auxin controls many aspects of alfalfa growth by regulating gene expression, including organ differentiation and stress response. Auxin response factors (ARF) are transcription factors that play an essential role in auxin signal transduction and regulate the expression of auxin-responsive genes. However, the function of ARF transcription factors is unclear in autotetraploid-cultivated alfalfa. RESULT: A total of 81 ARF were identified in the alfalfa genome in this study. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, identifying that ARF genes are mainly involved in transcriptional regulation and plant hormone signal transduction pathways. Phylogenetic analysis showed that MsARF was divided into four clades: I, II, III, and IV, each containing 52, 13, 7, and 9 genes, respectively. The promoter region of the MsARF gene contained stress-related elements, such as ABRE, TC-rich repeats, MBS, LTR. Proteins encoded by 50 ARF genes were localized in the nucleus without guide peptides, signal peptides, or transmembrane structures, indicating that most MsARF genes are not secreted or transported but only function in the nucleus. Protein structure analysis revealed that the secondary and tertiary structures of the 81 MsARF genes varied. Chromosomal localization analysis showed 81 MsARF genes were unevenly distributed on 25 chromosomes, with the highest distribution on chromosome 5. Furthermore, 14 segmental duplications and two sets of tandem repeats were identified. Expression analysis indicated that the MsARF was differentially expressed in different tissues and under various abiotic stressors. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that the expression profiles of 23 MsARF genes were specific to abiotic stresses such as drought, salt, high temperature, and low temperature, as well as tissue-specific and closely related to the duration of stress. CONCLUSION: This study identified MsARF in the cultivated alfalfa genome based on the autotetraploid level, which GO, KEGG analysis, phylogenetic analysis, sequence characteristics, and expression pattern analysis further confirmed. Together, these findings provide clues for further investigation of MsARF functional verification and molecular breeding of alfalfa. This study provides a novel approach to systematically identify and characterize ARF transcription factors in autotetraploid cultivated alfalfa, revealing 23 MsARF genes significantly involved in response to various stresses.

… Betaine aldehyde dehydrogenase (BADH) is among the genes that encode the enzymes involved in … In this study, through phylogenetic analysis, we found DtBADH2 had high homology …

Aldehyde dehydrogenases (ALDHs) are members of NAD(P) + -dependent protein superfamily that catalyze the oxidation of a wide range of endogenous and exogenous highly …

… Interestingly, many ALDH10 homologues show preference for aminoaldehyde substrates over betaine aldehyde (BAL). Numerous studies have shown that some ALDH10 isoforms act …

Betaine aldehyde dehydrogenase (BADH), mitogen-activated protein kinase (MAPK) and sodium/hydrogen exchanger (NHX) play important roles in the response to salt stress. This is the first study to identify the BADH and NHX genes in maize (Zea mays) via genome-wide analysis. The qRT‒PCR results indicated that ZmNHX was upregulated by 4.38-fold, while a significant difference was not observed in ZmBADH or ZmMAPK, with fold changes of 0.96 and 1.06, respectively, under salinity stress. Genome-wide analysis revealed 8 ZmBADH, 19 ZmMAPK and 11 ZmNHX proteins in Z. mays. Domain analysis confirmed the presence of the aldehyde dehydrogenase superfamily (ALDH-SF), protein kinase and Na_H_Exchanger domains in the ZmBADH, ZmMAPK and ZmNHX proteins, respectively. Motif analysis indicated that the phylogenetic relationships were similar to the conserved motif distributions within the clade. The Ka/Ks ratio indicated that the ZmBADH, ZmMAPK and ZmNHX genes were influenced primarily by purifying selection. This study provides comprehensive identification, characterization, and evolutionary analysis for a better understanding of the ZmBADH, ZmMAPK and ZmNHX genes in maize.

… a syntenic … acid BADH isoform with 10 amino acid substitutions compared to AHYBADH4, sharing 98% identity. Expression analysis revealed that ahybadh17 mRNA and BADH protein …

BACKGROUND: Alfalfa (Medicago sativa) is a perennial high-quality legume forage widely cultivated worldwide, but drought stress severely restrict its growth and development. Plant homeodomain finger (PHD) family genes are a type of zinc finger transcription factors widely distributed in eukaryotes. They act as histone code identifier to regulate the expression of downstream genes and play important biological roles in plant growth, development, and stress response. However, information about the PHD family genes in alfalfa remains limited at present. RESULTS: We identified 56 MsPHD genes containing 67 PHD domains in the alfalfa, and these genes were unevenly distributed on 8 chromosomes of alfalfa. There are 9 pairs of gene fragment duplicates in the MsPHD family. The 56 MsPHD genes are evolutionarily divided into 14 subgroups. There are differences in the conservative motifs and gene structure composition patterns of MsPHD among different subgroups. In addition, we identified 11 MsPHD genes related to drought stress, and their promoter regions all contained elements related to stress response. Quantitative Real-time PCR (QRT-PCR) further verified that the expression levels of these 11 MsPHD genes were significantly up-regulated in both roots and leaves, with MsPHD9 showing the highest upregulation. 57.14% of MsPHD proteins were predicted to be located in the nucleus, and the co-localization analysis of MsPHD9 protein confirmed that it was primarily located in the nucleus. CONCLUSIONS: The identification of alfalfa PHD family genes not only provides important genetic resources for in-depth analysis of the molecular mechanism of alfalfa drought resistance, but also lays a foundation for creating new germplasm of alfalfa with strong drought resistance through genetic engineering technology.

The PLATZ family is a novel class of plant-specific zinc finger transcription factors with important roles in plant growth and development and abiotic stress responses. PLATZ members have been identified in many plants, including Oryza sativa, Zea mays, Triticum aestivum, Fagopyrum tataricum, and Arabidopsis thaliana; however, due to the complexity of the alfalfa reference genome, the members of the PLATZ gene family in alfalfa (Medicago sativa L.) have not been systematically identified and analyzed. In this study, 55 Medicago sativa PLATZ genes (MsPLATZs) were identified in the alfalfa “Xinjiangdaye” reference genome. Basic bioinformatic analysis was performed, including the characterization of sequence lengths, protein molecular weights, genomic positions, and conserved motifs. Expression analysis reveals that 7 MsPLATZs are tissue-specifically expressed, and 10 MsPLATZs are expressed in all examined tissues. The transcriptomic expression of these genes is obvious, indicating that these MsPLATZs have different functions in the growth and development of alfalfa. Based on transcriptome data analysis and real-time quantitative PCR (RT-qPCR), we identified 22, 22, and 21 MsPLATZ genes that responded to salt, cold, and drought stress, respectively, with 20 MsPLATZs responding to all three stresses. This study lays a foundation for further exploring the functions of MsPLATZs, and provides ideas for the improvement of alfalfa varieties and germplasm innovation.

The B3 family genes constitute a pivotal group of transcription factors that assume diverse roles in the growth, development, and response to both biotic and abiotic stresses in plants. Medicago truncatula is a diploid plant with a relatively small genome, adopted as a model species for legumes genetics and functional genomic research. In this study, 173 B3 genes were identified in the M. truncatula genome, and classified into seven subgroups by phylogenetic analysis. Collinearity analysis revealed that 18 MtB3 gene pairs arose from segmented replication events. Analysis of expression patterns disclosed that 61 MtB3s exhibited a spectrum of expression profiles across various tissues and in the response to salt stress, indicating their potential involvement in salt stress signaling response. Among these genes, MtB3-53 exhibited tissue-specific differential expression and demonstrated a rapid response to salt stress induction. Overexpression of MtB3-53 gene in Arabidopsis improves salt stress tolerance by increasing plant biomass and chlorophyll content, while reducing leaf cell membrane damage. Moreover, salt treatment resulted in more up-regulation of AtABF1, AtABI3, AtHKT1, AtKIN1, AtNHX1, and AtRD29A in MtB3-53 transgenic Arabidopsis plants compared to the wild type, providing evidences that MtB3-53 enhances plant salt tolerance not only by modulating ion homeostasis but also by stimulating the production of antioxidants, which leads to the alleviation of cellular damage caused by salt stress. In conclusion, this study provides a fundamental basis for future investigations into the B3 gene family and its capacity to regulate plant responses to environmental stressors.