Genome-Wide Analysis of the MADS-Box Gene Family in Foxtail Millet (Setaria Italica L.) and Expression Analyses to Reveal Their Role During Drought Stress

Abstract MADS-box gene family is a key regulatory factor family, which controls vegetative growth, reproductive development and can be used to mediate abiotic stresses in many plants. However, Knowledge of this gene family is still limited in Setaria italica. In the present study, a total of 70 SitMADS genes were identified and renamed on the basis of the chromosomal distribution of the SitMADS genes. According to gene structure, conserved motif and phylogenetic feature, the 70 SitMADSs were classified into type-Ⅰ (Mα, Mβ, Mγ) and type-Ⅱ (MIKCC and MIKC*). All of the SitMADS genes were randomly distributed on nine chromosomes, and five tandem duplicated genes and 12 pairs of duplicated gene segments were detected in the SitMADS genes family. Synteny analysis provided a high homology between SitMADS genes and OsMADS genes. A cis-element analysis inferred that SitMADS genes, except for SitMADS23, possessed at least one drought stress response and ABA(Abscisic Acid)-induced response cis-element. Real-time quantitative PCR analysis was used to detect the expression patterns of SitMADS genes in various tissues and demonstrated that the genes responded drought stress and ABA treatments. SitMADS23, SitMADS42, SitMADS51, SitMADS52, SitMADS58 and SitMADS64 were highly expressed in PEG(Polyethylene glycol) and drought stress, which suggested its important role in drought stress response. SitMADS51, SitMADS63 and SitMADS64 seemed to be responsive to ABA hormone signaling, suggesting that they were involved in the ABA signaling pathways. This paper provided a deep insight into the evolutionary characteristics of SitMADS genes. The results provide comprehensive information for further analyses of the molecular functions of the MADS-box gene family in Setaria italica.

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The Responses of the Lipoxygenase Gene Family to Salt and Drought Stress in Foxtail Millet (Setaria italica)

Life ◽

10.3390/life11111169 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1169

Author(s):

Qianxiang Zhang ◽

Yaofei Zhao ◽

Jinli Zhang ◽

Xukai Li ◽

Fangfang Ma ◽

...

Keyword(s):

Drought Stress ◽

Gene Family ◽

Abiotic Stresses ◽

Expression Patterns ◽

Foxtail Millet ◽

Heme Iron ◽

Setaria Italica ◽

Salt And Drought Stress ◽

Plant Lipoxygenases ◽

Lipoxygenase Gene Family

Plant lipoxygenases (LOXs), a kind of non-heme iron-containing dioxygenases, participate plant physiological activities (especially in response to biotic and abiotic stresses) through oxidizing various lipids. However, there was few investigations on LOXs in foxtail millet (Setaria italica). In this study, we identified the LOX gene family in foxtail millet, and divided the total 12 members into three sub-families on the basis of their phylogenetic relationships. Under salt and drought stress, LOX genes showed different expression patterns. Among them, only SiLOX7 showed up-regulated expression in Yugu1 (YG1) and Qinhuang2 (QH2), two stress-tolerant varieties, indicating that SiLOX7 may play an important role in responses to abiotic stress. Our research provides a basis for further investigation of the role of LOX genes in the adaptation to abiotic stresses and other possible biological functions in foxtail millet.

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Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)

International Journal of Molecular Sciences ◽

10.3390/ijms21228520 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8520

Author(s):

Ling Qin ◽

Erying Chen ◽

Feifei Li ◽

Xiao Yu ◽

Zhenyu Liu ◽

...

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Drought Stress ◽

Expression Profiles ◽

Expression Patterns ◽

Foxtail Millet ◽

Gene Expression Profiles ◽

Sugar Metabolism ◽

Setaria Italica ◽

Phenylpropanoid Biosynthesis

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.

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Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽

10.3390/f11030315 ◽

2020 ◽

Vol 11 (3) ◽

pp. 315

Author(s):

Hanzeng Wang ◽

Xue Leng ◽

Xuemei Xu ◽

Chenghao Li

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Expression Profiles ◽

Populus Trichocarpa ◽

Expression Patterns ◽

Interaction Network ◽

Pcr Analysis ◽

Phylogenetic Tree Analysis ◽

Element Analysis ◽

Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

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Genome-Wide Analysis of MADS-Box Genes in Foxtail Millet (Setaria italica L.) and Functional Assessment of the Role of SiMADS51 in the Drought Stress Response

Frontiers in Plant Science ◽

10.3389/fpls.2021.659474 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wan Zhao ◽

Li-Li Zhang ◽

Zhao-Shi Xu ◽

Liang Fu ◽

Hong-Xi Pang ◽

...

Keyword(s):

Drought Stress ◽

Stress Tolerance ◽

Abiotic Stresses ◽

Survival Rates ◽

Foxtail Millet ◽

Negative Regulator ◽

Setaria Italica ◽

Mads Box ◽

Drought Stress Tolerance ◽

Genome Wide

MADS-box transcription factors play vital roles in multiple biological processes in plants. At present, a comprehensive investigation into the genome-wide identification and classification of MADS-box genes in foxtail millet (Setaria italica L.) has not been reported. In this study, we identified 72 MADS-box genes in the foxtail millet genome and give an overview of the phylogeny, chromosomal location, gene structures, and potential functions of the proteins encoded by these genes. We also found that the expression of 10 MIKC-type MADS-box genes was induced by abiotic stresses (PEG-6000 and NaCl) and exogenous hormones (ABA and GA), which suggests that these genes may play important regulatory roles in response to different stresses. Further studies showed that transgenic Arabidopsis and rice (Oryza sativa L.) plants overexpressing SiMADS51 had reduced drought stress tolerance as revealed by lower survival rates and poorer growth performance under drought stress conditions, which demonstrated that SiMADS51 is a negative regulator of drought stress tolerance in plants. Moreover, expression of some stress-related genes were down-regulated in the SiMADS51-overexpressing plants. The results of our study provide an overall picture of the MADS-box gene family in foxtail millet and establish a foundation for further research on the mechanisms of action of MADS-box proteins with respect to abiotic stresses.

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Genome-wide Characterization and Expression Analysis of YABBY Gene Family in Three Cultivars of Cucurbita Linn. And Their Response of Salt Stress in Cucurbita Moschata

10.21203/rs.3.rs-121953/v1 ◽

2020 ◽

Author(s):

Jingping Yuan ◽

Changwei Shen ◽

Jingjing Xin ◽

Zhenxia Li ◽

Xinzheng Li ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Plant Growth ◽

Gene Family ◽

Expression Analysis ◽

Expression Patterns ◽

Pcr Analysis ◽

Abiotic Stress Response ◽

Element Analysis ◽

Qrt Pcr

Abstract BackgroundPlant specific YABBY transcription factors have important biological roles in plant growth and abiotic stress. However, the identification of Cucurbita Linn. YABBY and their response to salt stress have not yet been reported. The gene number, gene distribution on chromosome, gene structure, protein conserved structure, protein motif and the cis-acting element of YABBY in three cultivars of Cucurbita Linn. were analyzed by bioinformatics tools, and their tissue expression patterns and expression profile under salt stress were analyzed.ResultsIn this study, 34 YABBY genes (11 CmoYABBYs in Cucurbita moschata, 12 CmaYABBYs in Cucurbita maxima, and 11 CpeYABBYs in Cucurbita pepo) were identified and they were divided into five subfamilies (YAB1/YAB3, YAB2, INO, CRC and YAB5). YABBYs in the same subfamily usually have similar gene structures (intron-exon distribution) and conserved domains. Chromosomal localization analysis showed that these CmoYABBYs, CmaYABBYs, and CpeYABBYs were unevenly distributed in 8, 9, and 9 chromosomes of 21 chromosomes, respectively. Total of 6 duplicated gene pairs, and they all experienced segmental duplication events. Cis-acting element analysis showed that some Cucurbita Linn. YABBYs were associated with at least one of plant hormone response, plant growth, and abiotic stress response. Transcriptional profiles of CmoYABBYs and CmaYABBYs in roots, stems, leaves, and fruits, and CpeYABBYs in seed and fruit mesocarp showed that YABBYs of Cucurbita Linn. had tissue specificity. Finally, the transcriptional profile of 11 CmoYABBYs in leaf and qRT-PCR analysis of CmoYABBYs in root under salt stress indicated that some genes may play an important role in salt stress.ConclusionsGenome-wide identification and expression analysis of YABBYs revealed the characteristics of YABBY gene family in three cultivars of Cucurbita Linn.. Transcriptome and qRT-PCR analysis revealed the response of the CmoYABBYs to salt stress.This provides a theoretical basis for the functional research and utilization of YABBY genes in Cucurbita Linn..

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Foxtail Millet Stress Associated Protein Gene SiSAP4 Enhances Drought Stress Tolerance in Transgenic Arabidopsis

International Journal of Agriculture and Biology ◽

10.17957/ijab/15.1686 ◽

2021 ◽

Vol 25 (02) ◽

pp. 441-449

Author(s):

Wenlu Li

Keyword(s):

Drought Stress ◽

Stress Response ◽

Stress Tolerance ◽

Transcriptional Activation ◽

Transgenic Arabidopsis ◽

Expression Patterns ◽

Foxtail Millet ◽

Expression Level ◽

Drought Stress Tolerance ◽

Transgenic Breeding

Abiotic stresses like drought affect plant growth and crop yield with climate change worsening. Stress associated proteins (SAPs), as the zinc finger proteins with A20/AN1 domain, play an important role in regulating abiotic stress response. As a typical summer dryland grain crop in the north of China, foxtail millet has the characteristics of drought resistance, making it a valuable resource for anti-stress gene exploitation and utilization. In this study, SiSAP4 gene was cloned from foxtail millet variety Yugu 1. Analysis showed that SiSAP4 gene was expressed in roots, stems and leaves at seedling stage, and the highest expression level was detected in leaves. Expression patterns under different stress conditions showed that expression level of SiSAP4 gene was significantly up-regulated under drought stress, suggesting it may be involved in drought stress response. Subcellular localization indicated that SiSAP4 was present in the nucleus and cytoplasm. It was revealed that SiSAP4 had no function in transcriptional activation in the yeast system. Overexpression of SiSAP4 in transgenic Arabidopsis resulted in enhanced tolerance to drought stress, which was simultaneously demonstrated by increased expression of a broad range of stress response genes. Based on those results, SiSAP4 has the potential to be used in transgenic breeding to improve drought stress tolerance in other crops. © 2021 Friends Science Publishers

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Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit ripening in black raspberry (Rubus occidentalis L.)

Journal of Berry Research ◽

10.3233/jbr-200679 ◽

2021 ◽

pp. 1-15

Author(s):

Yaqiong Wu ◽

Chunhong Zhang ◽

Wenlong Wu ◽

Weilin Li ◽

Lianfei Lyu

Keyword(s):

Gene Family ◽

Fruit Ripening ◽

Fruit Development ◽

Expression Patterns ◽

Type I ◽

Black Raspberry ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide ◽

Mads Box Gene

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

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Identification, Expression, and Functions of the Somatostatin Gene Family in Spotted Scat (Scatophagus argus)

Genes ◽

10.3390/genes11020194 ◽

2020 ◽

Vol 11 (2) ◽

pp. 194

Author(s):

Peizhe Feng ◽

Changxu Tian ◽

Xinghua Lin ◽

Dongneng Jiang ◽

Hongjuan Shi ◽

...

Keyword(s):

Gene Family ◽

Growth Regulation ◽

Expression Patterns ◽

Open Reading Frames ◽

Pcr Analysis ◽

Sequence Alignments ◽

Scatophagus Argus ◽

Gene Structure And Expression ◽

Liver Fragments

Somatostatins (SSTs) are a family of proteins consisting of structurally diverse polypeptides that play important roles in the growth regulation in vertebrates. In the present study, four somatostatin genes (SST1, SST3, SST5, and SST6) were identified and characterized in the spotted scat (Scatophagus argus). The open reading frames (ORFs) of SST1, SST3, SST5, and SST6 cDNA consist of 372, 384, 321, and 333 bp, respectively, and encode proteins of 123, 127, 106, and 110 amino acids, respectively. Amino acid sequence alignments indicated that all SST genes contained conserved somatostatin signature motifs. Real-time PCR analysis showed that the SST genes were expressed in a tissue specific manner. When liver fragments were cultured in vitro with synthetic peptides (SST1, SST2, or SST6 at 1 μM or 10 μM) for 3 h or 6 h, the expression of insulin-like growth factor 1 and 2 (Igf-1 and Igf-2) in the liver decreased significantly. Treatment with SST5 had no significant effect on Igf-1 and Igf-2 gene expression. This study provides an enhanced understanding of the gene structure and expression patterns of the SST gene family in S. argus. Furthermore, this study provides a foundation for future exploration into the role of SST genes in growth and development.

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Genome-Wide Identification and Expression Profiling Analysis of the Galactinol Synthase Gene Family in Cassava (Manihot esculenta Crantz)

Agronomy ◽

10.3390/agronomy8110250 ◽

2018 ◽

Vol 8 (11) ◽

pp. 250 ◽

Cited By ~ 4

Author(s):

Ruimei Li ◽

Shuai Yuan ◽

Yingdui He ◽

Jie Fan ◽

Yangjiao Zhou ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Manihot Esculenta ◽

Expression Patterns ◽

Pcr Analysis ◽

Systematic Research ◽

Raffinose Family Oligosaccharides ◽

Manihot Esculenta Crantz ◽

Galactinol Synthase ◽

Genome Wide

Galactinol synthases (GolSs) are the key enzymes that participate in raffinose family oligosaccharides (RFO) biosynthesis, which perform a big role in modulating plant growth and response to biotic or abiotic stresses. To date, no systematic study of this gene family has been conducted in cassava (Manihot esculenta Crantz). Here, eight MeGolS genes are isolated from the cassava genome. Based on phylogenetic background, the MeGolSs are clustered into four groups. Through predicting the cis-elements in their promoters, it was discovered that all MeGolS members act as hormone-, stress-, and tissue-specific related elements to different degrees. MeGolS genes exhibit incongruous expression patterns in various tissues, indicating that different MeGolS proteins might have diverse functions. MeGolS1 and MeGolS3–6 are highly expressed in leaves and midveins. MeGolS3–6 are highly expressed in fibrous roots. Quantitative real-time Polymerase Chain Reaction (qRT-PCR) analysis indicates that several MeGolSs, including MeGolS1, 2, 5, 6, and 7, are induced by abiotic stresses. microRNA prediction analysis indicates that several abiotic stress-related miRNAs target the MeGolS genes, such as mes-miR156, 159, and 169, which also respond to abiotic stresses. The current study is the first systematic research of GolS genes in cassava, and the results of this study provide a basis for further exploration the functional mechanism of GolS genes in cassava.

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