Dataset Information

Genome-Wide Identification and Functional Analysis of the TIFY Family Genes in Response to Abiotic Stresses and Hormone Treatments in Tartary Buckwheat (Fagopyrum tataricum).

ABSTRACT: TIFY is a plant-specific gene family with four subfamilies: ZML, TIFY, PPD, and JAZ. Recently, this family was found to have regulatory functions in hormone stimulation, environmental response, and development. However, little is known about the roles of the TIFY family in Tartary buckwheat (Fagopyrum tataricum), a significant crop for both food and medicine. In this study, 18 TIFY family genes (FtTIFYs) in Tartary buckwheat were identified. The characteristics, motif compositions, and evolutionary relationships of the TIFY proteins, as well as the gene structures, cis-acting elements, and synteny of the TIFY genes, are discussed in detail. Moreover, we found that most FtTIFYs responded to various abiotic stresses (cold, heat, salt, or drought) and hormone treatments (ABA, MeJA, or SA). Through yeast two-hybrid assays, we revealed that two FtTIFYs, FtTIFY1 and FtJAZ7, interacted with FtABI5, a homolog protein of AtABI5 involved in ABA-mediated germination and stress responses, implying crosstalk between ABA and JA signaling in Tartary buckwheat. Furthermore, the overexpression of FtJAZ10 and FtJAZ12 enhanced the heat stress tolerance of tobacco. Consequently, our study suggests that the FtTIFY family plays important roles in responses to abiotic stress and provides two candidate genes (FtJAZ10 and FtJAZ12) for the cultivation of stress-resistant crops.

SUBMITTER: Zhao Z

PROVIDER: S-EPMC10341436 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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Genome-Wide Identification and Functional Analysis of the TIFY Family Genes in Response to Abiotic Stresses and Hormone Treatments in Tartary Buckwheat (Fagopyrum tataricum).

Zhao Zhixing Z Meng Guanghua G Zamin Imran I Wei Tao T Ma Dongdi D An Lizhe L Yue Xiule X

International journal of molecular sciences 20230630 13

TIFY is a plant-specific gene family with four subfamilies: ZML, TIFY, PPD, and JAZ. Recently, this family was found to have regulatory functions in hormone stimulation, environmental response, and development. However, little is known about the roles of the TIFY family in Tartary buckwheat (Fagopyrum tataricum), a significant crop for both food and medicine. In this study, 18 TIFY family genes (FtTIFYs) in Tartary buckwheat were ide ...[more]

PMID: 37446090

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Project description:Abscisic acid (ABA) is a plant hormone that plays an important role in plant resistance to drought, salinity, cold, and pathogens. It is also important for regulating plant growth and development. Pyrabactin resistance/pyr1-like/regulatory components of the ABA receptor (PYL/RCAR) are ABA receptor proteins in plants and the core of ABA signal transduction pathways in plant regulatory factors. At present, there are no reports on the PYL family of Tartary buckwheat. In this study, 19 paralogous form PYL genes in buckwheat were identified at the whole-genome level and named FtPYL1-FtPYL19 according to their positions on chromosomes. We further analyzed the gene structure, conserved motifs, cis-acting elements, gene duplication, phylogenetic relationships, and expression patterns under different stress treatments and during grain development of the 19 paralogous form PYL genes in Tartary buckwheat. The FtPYL gene exhibits a single exonic gene structure for about 68.4% of the duplicated forms from the total paralogous forms. The remaining subfamilies, such as I and II, contain three exons and two exons (e.g., FtPYL19), respectively. Nineteen FtPYL genes were evenly distributed across the eight chromosomes, with at least one FtPYL gene on each chromosome. In the FtPYL gene family, there was one tandem repeat event and five gene duplication events. We investigated the gene expression levels of FtPYL gene under four abiotic stresses and different stages of grain development. Under drought stress (PEG6000), the relative expression levels of FtPYL14 and FtPYL15 increased by fourfold. Under high temperature stress (38℃), the relative expression level of FtPYL16 dropped to 0.12, and that of FtPYL17 fell to 0.22. At different stages of grain development, the gene expression level of FtPY15 is extremely high at 19 D. The relative expression level of FtPYL7 in roots and stems reaches up to approximately 450, and the relative expression level of FtPYL10 in 13 D also reaches up to 248. In this study, the PYL gene family of Tartary buckwheat was identified and analyzed based on the whole genome, and 19 paralogous form FtPYL genes of Tartary buckwheat were bioinformatically analyzed. The expression patterns of 19 paralogous form FtPYL genes in Tartary buckwheat cultivars under different stress treatments and during grain development were analyzed. It was found that the FtPYL gene played an important role in grain development.

Project description:BackgroundHeat shock transcription factor (Hsfs) is widely found in eukaryotes and prokaryotes. Hsfs can not only help organisms resist high temperature, but also participate in the regulation of plant growth and development (such as involved in the regulation of seed maturity and affects the root length of plants). The Hsf gene was first isolated from yeast and then gradually found in plants and sequenced, such as Arabidopsis thaliana, rice, maize. Tartary buckwheat is a rutin-rich crop, and its nutritional value and medicinal value are receiving more and more attention. However, there are few studies on the Hsf genes in Tartary buckwheat. With the whole genome sequence of Tartary buckwheat, we can effectively study the Hsf gene family in Tartary buckwheat.ResultsAccording to the study, 29 Hsf genes of Tartary buckwheat (FtHsf) were identified and renamed according to location of FtHsf genes on chromosome after removing a redundant gene. Therefore, only 29 FtHsf genes truly had the functional characteristics of the FtHsf family. The 29 FtHsf genes were located on 8 chromosomes of Tartary buckwheat, and we found gene duplication events in the FtHsf gene family, which may promote the expansion of the FtHsf gene family. Then, the motif compositions and the evolutionary relationship of FtHsf proteins and the gene structures, cis-acting elements in the promoter, synteny analysis of FtHsf genes were discussed in detail. What's more, we found that the transcription levels of FtHsf in different tissues and fruit development stages were significantly different by quantitative real-time PCR (qRT-PCR), implied that FtHsf may differ in function.ConclusionsIn this study, only 29 Hsf genes were identified in Tartary buckwheat. Meanwhile, we also classified the FtHsf genes, and studied their structure, evolutionary relationship and the expression pattern. This series of studies has certain reference value for the study of the specific functional characteristics of Tartary buckwheat Hsf genes and to improve the yield and quality of Tartary buckwheat in the future.

Project description:BackgroundIn the study, the trihelix family, also referred to as GT factors, is one of the transcription factor families. Trihelix genes play roles in the light response, seed maturation, leaf development, abiotic and biological stress and other biological activities. However, the trihelix family in tartary buckwheat (Fagopyrum tataricum), an important usable medicinal crop, has not yet been thoroughly studied. The genome of tartary buckwheat has recently been reported and provides a theoretical basis for our research on the characteristics and expression of trihelix genes in tartary buckwheat based at the whole level.ResultsIn the present study, a total of 31 FtTH genes were identified based on the buckwheat genome. They were named from FtTH1 to FtTH31 and grouped into 5 groups (GT-1, GT-2, SH4, GTγ and SIP1). FtTH genes are not evenly distributed on the chromosomes, and we found segmental duplication events of FtTH genes on tartary buckwheat chromosomes. According to the results of gene and motif composition, FtTH located in the same group contained analogous intron/exon organizations and motif organizations. qRT-PCR showed that FtTH family members have multiple expression patterns in stems, roots, leaves, fruits, and flowers and during fruit development.ConclusionsThrough our study, we identified 31 FtTH genes in tartary buckwheat and synthetically further analyzed the evolution and expression pattern of FtTH proteins. The structure and motif organizations of most genes are conserved in each subfamily, suggesting that they may be functionally conserved. The FtTH characteristics of the gene expression patterns indicate functional diversity in the time and space in the tartary buckwheat life process. Based on the discussion and analysis of FtTH gene function, we screened some genes closely related to the growth and development of tartary buckwheat. This will help us to further study the function of FtTH genes through experimental exploration in tartary buckwheat growth and improve the fruit of tartary buckwheat.

Project description:BackgroundPlant AT-rich sequence and zinc-binding (PLATZ) proteins belong to a novel class of plant-specific zinc-finger-dependent DNA-binding proteins that play essential roles in plant growth and development. Although the PLATZ gene family has been identified in several species, systematic identification and characterization of this gene family has not yet been carried out for Tartary buckwheat, which is an important medicinal and edible crop with high nutritional value. The recent completion of Tartary buckwheat genome sequencing has laid the foundation for this study.ResultsA total of 14 FtPLATZ proteins were identified in Tartary buckwheat and were classified into four phylogenetic groups. The gene structure and motif composition were similar within the same group, and evident distinctions among different groups were detected. Gene duplication, particularly segmental duplication, was the main driving force in the evolution of FtPLATZs. Synteny analysis revealed that Tartary buckwheat shares more orthologous PLATZ genes with dicotyledons, particularly soybean. In addition, the expression of FtPLATZs in different tissues and developmental stages of grains showed evident specificity and preference. FtPLATZ3 may be involved in the regulation of grain size, and FtPLATZ4 and FtPLATZ11 may participate in root development. Abundant and variable hormone-responsive cis-acting elements were distributed in the promoter regions of FtPLATZs, and almost all FtPLATZs were significantly regulated after exogenous hormone treatments, particularly methyl jasmonate treatment. Moreover, FtPLATZ6 was significantly upregulated under all exogenous hormone treatments, which may indicate that this gene plays a critical role in the hormone response of Tartary buckwheat.ConclusionsThis study lays a foundation for further exploration of the function of FtPLATZ proteins and their roles in the growth and development of Tartary buckwheat and contributes to the genetic improvement of Tartary buckwheat.

Dataset Information

Genome-Wide Identification and Functional Analysis of the TIFY Family Genes in Response to Abiotic Stresses and Hormone Treatments in Tartary Buckwheat (Fagopyrum tataricum).

Publications

Genome-Wide Identification and Functional Analysis of the <i>TIFY</i> Family Genes in Response to Abiotic Stresses and Hormone Treatments in Tartary Buckwheat (<i>Fagopyrum tataricum</i>).

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