Genome-Wide Identification of Membrane-Bound Fatty Acid Desaturase Genes in Three Peanut Species and Their Expression in Arachis hypogaea during Drought Stress

As a crop irrigated primarily by rain, the quality and yield of peanuts are significantly limited by drought. To date, many studies have indicated that fatty acid desaturase (FAD) genes enhance plant tolerance to drought stresses. In this study, 16, 15, and 31 FADs were identified in Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. All the FADs were divided into four subfamilies, which had relatively conserved gene structures, motifs, and domains. The synteny relationships and chromosomal position analysis showed that the FADs in subgenome pairs, A. duranensis-A. hypogaea (AA) and A. ipaensis-A. hypogaea (BB), were homologous, and their physical locations were consistent. The Ka/Ks results indicated that nine FAD genes underwent a purifying selection, and Ah|FAD3.2 experienced positive selection during tetraploid peanut speciation. Various cis-acting elements related to hormone signaling and stress responsiveness in promoters and the predicted miRNA targeting Ah|FADs suggested that these genes play crucial roles in drought tolerance. The expression profiles of Ah|FADs in 22 tissues and drought-tolerant and -sensitive cultivars under drought stress suggested that 4 and 6 FADs were putative genes related to oil accumulation and drought, respectively. These findings will help provide insight into the potential functional roles of the FAD genes, which may aid in dealing with plant drought stress

Transcript profiling of Paoenia ostii during artificial chilling induced dormancy release identifies activation of GA pathway and carbohydrate metabolism.

Endo-dormant flower buds must pass through a period of chilling to reinitiate growth and subsequent flowering, which is a major obstacle to the forcing culture of tree peony in winter. Customized cDNA microarray (8×15 K element) was used to investigate gene expression profiling in tree peony 'Feng Dan Bai' buds during 24 d chilling treatment at 0-4°C. According to the morphological changes after the whole plants were transferred to green house, endo-dormancy was released after 18 d chilling treatment, and prolonged chilling treatment increased bud break rate. Pearson correlation hierarchical clustering of sample groups was highly consistent with the dormancy transitions revealed by morphological changes. Totally 3,174 significantly differentially-expressed genes (P<0.05) were observed through endo-dormancy release process, of which the number of up-regulated (1,611) and that of down-regulated (1,563) was almost the same. Functional annotation of differentially-expressed genes revealed that cellular process, metabolic process, response to stimulus, regulation of biological process and development process were well-represented. Hierarchical clustering indicated that activation of genes involved in carbohydrate metabolism (Glycolysis, Citrate cycle and Pentose phosphate pathway), energy metabolism and cell growth. Based on the results of GO analysis, totally 51 probes presented in the microarray were associated with GA response and GA signaling pathway, and 22 of them were differently expressed. The expression profiles also revealed that the genes of GA biosynthesis, signaling and response involved in endo-dormancy release. We hypothesized that activation of GA pathway played a central role in the regulation of dormancy release in tree peony

Evolutionary and Integrative Analysis of the <i>Gibberellin 20-oxidase</i>, <i>3-oxidase</i>, and <i>2-oxidase</i> Gene Family in <i>Paeonia ostii</i>: Insight into Their Roles in Flower Senescence

The brief longevity of tree peony blossoms constrains its ornamental value and economic worth. Gibberellins (GAs) are crucial in the modulation of flower senescence, and GA 20-oxidase (GA20ox), GA 3-oxidase (GA3ox), and GA 2-oxidase (GA2ox) catalyze the synthesis and deactivation of bioactive GAs. In Paeonia ostii, a total of three PoGA20ox, ten PoGA3ox, and twelve PoGA2ox proteins were identified and comprehensively analyzed. The analysis of the gene structures, conserved domains, and motifs revealed structural similarities and variances among the GA20ox, GA3ox, GA2ox-A, and GA2ox-B subfamilies. The synteny analysis indicated a scarcity of collinear blocks within the P. ostii genome, with no tandem or whole-genome duplication/segmental duplications found in PoGAoxs. The investigation into the binding of transcription factors to PoGAox promoters and the assessments of the expression levels suggest that PoGA2ox1 and PoGA2ox8.1 are promising candidate genes implicated in the regulation of floral senescence. Further, Pos.gene61099 (BPC6) and Pos.gene61094 (CIL2) appear to modulate PoGA2ox1 transcription in a positive and negative manner, respectively, while Pos.gene38359 (DDF1) and Pos.gene17639 (DREB1C) likely enhance PoGA2ox8.1’s expression. This study lays a foundation for an in-depth understanding of PoGAox functions and the development of strategies to delay flower senescence in tree peony

Transcriptome profiling and digital gene expression analysis of genes associated with salinity resistance in peanut

Background: Soil salinity can significantly reduce crop production, but the molecular mechanism of salinity tolerance in peanut is poorly understood. A mutant (S1) with higher salinity resistance than its mutagenic parent HY22 (S3) was obtained. Transcriptome sequencing and digital gene expression (DGE) analysis were performed with leaves of S1 and S3 before and after plants were irrigated with 250 mM NaCl. Results: A total of 107,725 comprehensive transcripts were assembled into 67,738 unigenes using TIGR Gene Indices clustering tools (TGICL). All unigenes were searched against the euKaryotic Ortholog Groups (KOG), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and these unigenes were assigned to 26 functional KOG categories, 56 GO terms, 32 KEGG groups, respectively. In total 112 differentially expressed genes (DEGs) between S1 and S3 after salinity stress were screened, among them, 86 were responsive to salinity stress in S1 and/or S3. These 86 DEGs included genes that encoded the following kinds of proteins that are known to be involved in resistance to salinity stress: late embryogenesis abundant proteins (LEAs), major intrinsic proteins (MIPs) or aquaporins, metallothioneins (MTs), lipid transfer protein (LTP), calcineurin B-like protein-interacting protein kinases (CIPKs), 9-cis-epoxycarotenoid dioxygenase (NCED) and oleosins, etc. Of these 86 DEGs, 18 could not be matched with known proteins. Conclusion: The results from this study will be useful for further research on the mechanism of salinity resistance and will provide a useful gene resource for the variety breeding of salinity resistance in peanut. Keywords: Digital gene expression, Gene, Mutant, NaCl, Peanut (Arachis hypogaea L.), RNA-seq, Salinity stress, Salinity tolerance, Soil salinity, Transcripts, Unigene

Functional category distribution of transcriptional changed genes in tree peony using Gene Ontology (GO).

<p>A comparison of 12 d, 15 d, 18 d and 24 d chilling treatment with 6 d chilling treatment yielded 3174 significantly differentially expressed features(<i>P</i><0.05).</p

Heat map diagrams of gene expression detected by microarray analysis and RT-PCR analysis of interested genes.

<p>Green indicates down-regulation and red indicates up-regulation of the gene for particular treatment. Each column represents a treatment of 0 d, 6 d, 12 d, 15 d, 18 d and 24 d chilling. Averages of replicates from MA (left), averages of RTPCR (right).</p

Cluster analysis of expression data from differentially-expressed genes.

<p>Relative gene expression levels shown with high expression are represented by red color and the low expression one are represented by green color.</p

Hypothesis of reprograming during chilling induced dormancy release-model of tree peony.

<p>Red character represents up-regulation.</p

All pairwise comparisons of chilling treatments were computed using Tukey’ HSD Post Hoc test.

<p>Entities found to be differentially expression in the top-right boxes, while entities found not to be differentially expressed represented in the lower-left boxes.</p