scholarly journals Genome-Wide Identification and Expression Profile of OSCA Gene Family Members in Triticum aestivum L.

2021 ◽  
Vol 23 (1) ◽  
pp. 469
Author(s):  
Kai Tong ◽  
Xinyang Wu ◽  
Long He ◽  
Shiyou Qiu ◽  
Shuang Liu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Expression Profiles ◽  
Stomatal Closure ◽  
Expression Patterns ◽  
Family Members ◽  
Triticum Aestivum L ◽  
Free Calcium ◽  
Cis Acting ◽  
Gene Structures

Hyperosmolality and various other stimuli can trigger an increase in cytoplasmic-free calcium concentration ([Ca2+]cyt). Members of the Arabidopsis thaliana (L.) reduced hyperosmolality-gated calcium-permeable channels (OSCA) gene family are reported to be involved in sensing extracellular changes to trigger hyperosmolality-induced [Ca2+]cyt increases and controlling stomatal closure during immune signaling. Wheat (Triticum aestivum L.) is a very important food crop, but there are few studies of its OSCA gene family members. In this study, 42 OSCA members were identified in the wheat genome, and phylogenetic analysis can divide them into four clades. The members of each clade have similar gene structures, conserved motifs, and domains. TaOSCA genes were predicted to be regulated by cis-acting elements such as STRE, MBS, DRE1, ABRE, etc. Quantitative PCR results showed that they have different expression patterns in different tissues. The expression profiles of 15 selected TaOSCAs were examined after PEG (polyethylene glycol), NaCl, and ABA (abscisic acid) treatment. All 15 TaOSCA members responded to PEG treatment, while TaOSCA12/-39 responded simultaneously to PEG and ABA. This study informs research into the biological function and evolution of TaOSCA and lays the foundation for the breeding and genetic improvement of wheat.

scholarly journals Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ying Li ◽  
Qilu Song ◽  
Yamin Zhang ◽  
Zheng Li ◽  
Jialin Guo ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Genome Wide ◽  
Related Development ◽  
Gene Structures

Abstract SQUAMOSA promoter-binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play roles in plant growth and development. The characteristics of SBP-box genes in rice (Oryza sativa) and Arabidopsis have been reported, but their potential roles in wheat (Triticum aestivum) are not fully understood. In this study, 48 SBP-box genes (TaSBPs) were identified; they were located in all wheat chromosomes except for 4B and 4D. Six TaSBPs were identified as tandem duplication genes that formed three tandem duplication pairs, while 22 were segmentally duplicated genes that formed 16 segmental duplication pairs. Subcellular localization prediction showed TaSBPs were located in nucleus. Among the 48 TaSBPs, 24 were predicted to be putative targets of TamiR156. Phylogenetic analysis showed that TaSBPs, AtSBPs, and OsSBPs that shared similar functions were clustered into the same subgroups. The phylogenetic relationships between the TaSBPs were supported by the identification of highly conserved motifs and gene structures. Four types of cis-elements––transcription-related, development-related, hormone-related, and abiotic stress-related elements––were found in the TaSBP promoters. Expression profiles indicated most TaSBPs participate in flower development and abiotic stress responses. This study establishes a foundation for further investigation of TaSBP genes and provides novel insights into their biological functions.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

scholarly journals Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1855
Author(s):  
Dan Luo ◽  
Ziqi Jia ◽  
Yong Cheng ◽  
Xiling Zou ◽  
Yan Lv
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chromosomal Distribution ◽  
Brassica Napus L ◽  
Oil Crops ◽  
Genome Wide ◽  
Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

scholarly journals Genome-Wide Identification of the NHX Gene Family in Punica granatum L. and Their Expressional Patterns under Salt Stress

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 264
Author(s):  
Jianmei Dong ◽  
Cuiyu Liu ◽  
Yuying Wang ◽  
Yujie Zhao ◽  
Dapeng Ge ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Tertiary Structure ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Punica Granatum ◽  
Conserved Motifs ◽  
Cis Acting ◽  
Gene Structures ◽  
Punica Granatum L

Most cultivated lands are suffering from soil salinization, which is a global problem affecting agricultural development and economy. High NaCl concentrations in the soil result in the accumulation of toxic Cl− and Na+ in plants. Na+/H+ antiporter (NHX) can regulate Na+ compartmentalization or efflux to reduce Na+ toxicity. This study aims to identify the NHX genes in pomegranate (Punica granatum L.) from the genome sequences and investigate their expression patterns under different concentrations of NaCl stress. In this study, we used the sequences of PgNHXs to analyze the physicochemical properties, phylogenetic evolution, conserved motifs, gene structures, cis-acting elements, protein tertiary structure and expression pattern. A total of 10 PgNHX genes were identified, and divided into three clades. Conserved motifs and gene structures showed that most of them had an amiloride-binding site (FFI/LY/FLLPPI), except for the members of clade III. There were multiple cis-acting elements involved in abiotic stress in PgNHX genes. Additionally, protein-protein interaction network analysis suggested that PgNHXs might play crucial roles in keeping a balance of Na+ in cells. The qRT-PCR analysis suggested that PgNHXs had tissue-specific expressional patterns under salt stress. Overall, our findings indicated that the PgNHXs could play significant roles in response to salt stress. The theoretical foundation was established in the present study for the further functional characterization of the NHX gene family in pomegranate.

scholarly journals Analysis of high pI α-Amy-1 gene family members expressed in late maturity α-amylase in wheat (Triticum aestivum L.)

2013 ◽  
Vol 33 (3) ◽  
pp. 519-529 ◽  
Author(s):  
Cong-Rong Cheng ◽  
Klaus Oldach ◽  
Kolumbina Mrva ◽  
Daryl Mares
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Family Members ◽  
Triticum Aestivum L ◽  
Late Maturity

scholarly journals Comprehensive genome-wide identification, characterization, and expression analysis of CCHC zinc finger gene family in wheat (Triticum aestivum L.)

2021 ◽  
Author(s):  
Aolong Sun ◽  
Yongliang Li ◽  
Xiaoxiao Zou ◽  
Fenglin Chen ◽  
Ruqiong Cai ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Abiotic Stress ◽  
Zinc Finger ◽  
Metal Ion ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Nucleic Acid Binding ◽  
Metal Ion Binding ◽  
Gene Structures ◽  
Cchc Zinc Finger

Abstract Background: The CCHC zinc finger proteins (CCHC-ZFPs) are transcription factors that play versatile roles in plant growth, development, and responses to biotic/abiotic stress. However, little is known about the CCHC-ZF genes in bread wheat (Triticum aestivum), an important food crop. Results: In this study, 50 TaCCHC-ZF genes were identified and distributed unevenly on 21 wheat chromosomes. According to the phylogenetic features, the 50 TaCCHC-ZF genes were classified into eight groups with specific motifs and gene structures. 43 TaCCHC-ZF genes were identified as segmentally duplicated genes that formed 36 segmental duplication gene pairs. Additionally, the collinearity analyses between wheat and eight other representative plant species showed that wheat had closer phylogenetic relationships with monocots compared to dicots. A total of 636 cis-elements related to environmental stress and phytohormone responsiveness were identified in the promoter of TaCCHC-ZF genes. Moreover, GO enrichment results revealed that all 50 TaCCHC-ZF genes were annotated under metal ion binding and nucleic acid binding. 91 miRNA binding sites within the 34 TaCCHC-ZF genes were identified by miRNA targets analyses, indicating that the expression of TaCCHC-ZF genes could be regulated by the miRNAs. Based on published transcriptome data, 38 TaCCHC-ZF genes were identified as DEGs, and 15 TaCCHC-ZF genes among them were verified by qRT-PCR assays, which showed response to drought, heat, or simultaneous response of them. Conclusions: This study systematically explored the gene structures, evolutionary characteristics, and potential roles during environmental responses of TaCCHC-ZF genes, providing a foundation for further investigation and application of TaCCHC-ZF genes in the molecular breeding of T. aestivum. Keywords: Wheat, CCHC-ZFP genes, Structural analysis, Evolution, Abiotic stress, Expression patterns

scholarly journals B-box Proteins in Arachis duranensis: Genome-Wide Characterization and Expression Profiles Analysis

Agronomy ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 23 ◽  
Author(s):  
Hanqi Jin ◽  
Mengge Xing ◽  
Chunmei Cai ◽  
Shuai Li
Keyword(s):  
Developmental Regulation ◽  
Expression Profiles ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Promoter Regions ◽  
Essential Information ◽  
Cis Acting ◽  
Arachis Duranensis ◽  
Gene Structures ◽  
Wild Peanut

B-box (BBX) proteins are important factors involved in plant growth and developmental regulation, and they have been identified in many species. However, information on the characteristics and transcription patterns of BBX genes in wild peanut are limited. In this study, we identified and characterized 24 BBX genes from a wild peanut, Arachis duranensis. Many characteristics were analyzed, including chromosomal locations, phylogenetic relationships, and gene structures. Arachis duranensis B-box (AdBBX) proteins were grouped into five classes based on the diversity of their conserved domains: I (3 genes), II (4 genes), III (4 genes), IV (9 genes), and V (4 genes). Fifteen distinct motifs were found in the 24 AdBBX proteins. Duplication analysis revealed the presence of two interchromosomal duplicated gene pairs, from group II and IV. In addition, 95 kinds of cis-acting elements were found in the genes’ promoter regions, 53 of which received putative functional predictions. The numbers and types of cis-acting elements varied among different AdBBX promoters, and, as a result, AdBBX genes exhibited distinct expression patterns in different tissues. Transcriptional profiling combined with synteny analysis suggests that AdBBX8 may be a key factor involved in flowering time regulation. Our study will provide essential information for further functional investigation of AdBBX genes.

scholarly journals Genome Wide Identification, Characterization, and Expression Analysis of YABBY-Gene Family in WHEAT (Triticum aestivum L.)

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1189
Author(s):  
Zeeshan Ali Buttar ◽  
Yuan Yang ◽  
Rahat Sharif ◽  
Sheng Nan Wu ◽  
Yanzhou Xie ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Phosphorus Deficiency ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Septoria Tritici ◽  
Genome Database ◽  
Yabby Gene

The small YABBY plant-specific transcription factor has a prominent role in regulating plant growth and developmental activities. However, little information is available about YABBY gene family in Triticum aestivum L. Herein, we identified 21 TaYABBY genes in the Wheat genome database. Then, we performed the conserved motif and domain analysis of TaYABBY proteins. The phylogeny of the TaYABBY was further sub-divided into 6 subfamilies (YABBY1/YABBY3, YABB2, YABBY5, CRC and INO) based on the structural similarities and functional diversities. The GO (Gene ontology) analysis of TaYABBY proteins showed that they are involved in numerous developmental processes and showed response against environmental stresses. The analysis of all identified genes in RNA-seq data showed that they are expressed in different tissues of wheat. Differential expression patterns were observed in not only control samples but also in stressed samples such as biotic stress (i.e., Fusarium graminearum (F.g), septoria tritici (STB), Stripe rust (Sr) and Powdery mildew (Pm), and abiotic stress (i.e., drought, heat, combined drought and heat and phosphorus deficiency), especially at different grain development stages. All identified TaYABBY-genes were localized in the nucleus which implies their participation in the regulatory mechanisms of various biological and cellular processes. In light of the above-mentioned outcomes, it has been deduced that TaYABBY-genes in the wheat genome play an important role in mediating various development, growth, and resistance mechanism, which could provide significant clues for future functional studies.

scholarly journals Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Muhammad Waheed Riaz ◽  
Jie Lu ◽  
Liaqat Shah ◽  
Liu Yang ◽  
Can Chen ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Triticum Aestivum L ◽  
Vital Role ◽  
Systematic Analysis ◽  
Wheat Seedlings ◽  
A Genome ◽  
Duplication Events

The AP2/ERF is a large protein family of transcription factors, playing an important role in signal transduction, plant growth, development, and response to various stresses. AP2/ERF super-family is identified and functionalized in a different plant but no comprehensive and systematic analysis in wheat (Triticum aestivum L.) has been reported. However, a genome-wide and functional analysis was performed and identified 322 TaAP2/ERF putative genes from the wheat genome. According to the phylogenetic and structural analysis, TaAP2/ERF genes were divided into 12 subfamilies (Ia, Ib, Ic, IIa, IIb, IIc, IIIa, IIIb, IIIc, IVa, IVb, and IVc). Furthermore, conserved motifs and introns/exons analysis revealed may lead to functional divergence within clades. Cis-Acting analysis indicated that many elements were involved in stress-related and plant development. Chromosomal location showed that 320 AP2/ERF genes were distributed among 21 chromosomes and 2 genes were present in a scaffold. Interspecies microsynteny analysis revealed that maximum orthologous between Arabidopsis, rice followed by wheat. Segment duplication events have contributed to the expansion of the AP2/ERF family and made this family larger than rice and Arabidopsis. Additionally, AP2/ERF genes were differentially expressed in wheat seedlings under the stress treatments of heat, salt, and drought, and expression profiles were verified by qRT-PCR. Remarkably, the RNA-seq data exposed that AP2/ERF gene family might play a vital role in stress-related. Taken together, our findings provided useful and helpful information to understand the molecular mechanism and evolution of the AP2/ERF gene family in wheat.

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