scholarly journals Genome-wide analysis of growth-regulating factors (GRFs) in Triticum aestivum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10701
Author(s):  
Wendi Huang ◽  
Yiqin He ◽  
Lei Yang ◽  
Chen Lu ◽  
Yongxing Zhu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Stress Response ◽  
Pcr Analysis ◽  
Synteny Analysis ◽  
Wheat Growth ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Wheat Development ◽  
Motif Composition

The Growth-Regulating Factor (GRF) family encodes a type of plant-specific transcription factor (TF). GRF members play vital roles in plant development and stress response. Although GRF family genes have been investigated in a variety of plants, they remain largely unstudied in bread wheat (Triticum aestivum L.). The present study was conducted to comprehensively identify and characterize the T. aestivum GRF (TaGRF) gene family members. We identified 30 TaGRF genes, which were divided into four groups based on phylogenetic relationship. TaGRF members within the same subgroup shared similar motif composition and gene structure. Synteny analysis suggested that duplication was the dominant reason for family member expansion. Expression pattern profiling showed that most TaGRF genes were highly expressed in growing tissues, including shoot tip meristems, stigmas and ovaries, suggesting their key roles in wheat growth and development. Further qRT-PCR analysis revealed that all 14 tested TaGRFs were significantly differentially expressed in responding to drought or salt stresses, implying their additional involvement in stress tolerance of wheat. Our research lays a foundation for functional determination of TaGRFs, and will help to promote further scrutiny of their regulatory network in wheat development and stress response.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of CAMTA Family Genes in Cucumber (Cucumis sativus L.)

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1827
Author(s):  
Rong Gao ◽  
Yanyan Luo ◽  
Fahong Yun ◽  
Xuetong Wu ◽  
Peng Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Growth And Development ◽  
Chemical Properties ◽  
Pcr Analysis ◽  
Transcription Activator ◽  
Cucumis Sativus L ◽  
Expression Levels ◽  
Calmodulin Binding ◽  
Genome Wide ◽  
A Genome

The calmodulin-binding transcription activator (CAMTA), as one of the most distinctive families of transcription factors, plays an important role in plant growth and development and in the stress response. However, it is currently unknown whether CAMTA exists in cucumbers and what its function is. In this study, we first identified four CAMTA genes in the cucumber genome using a genome-wide search method. Subsequently, we analyzed their physical and chemical properties, gene structure, protein domains, and phylogenetic relationships. The results show that the structure of CsCAMTAs is similar to that of other plants, and a phylogenetic analysis divides them into three groups. The analysis of cis-acting elements shows that most CsCAMTAs contain a variety of hormones and stress-related elements. The RT-PCR analysis shows that CsCAMTAs have different expression levels in different tissues and can be induced by IAA, ABA, MeJA, NaCl, and PEG. Finally, we analyzed the expression pattern of CsCAMTAs’ alternative spliceosomes under salt and drought stress. The results show that the expression levels of the different spliceosomes are affected by the type of stress and the duration of stress. These data indicate that CsCAMTAs participate in growth and development and in the stress response in cucumbers, a finding which lays the foundation for future CsCAMTAs’ functional research.

scholarly journals Genome-wide identification, evolution, expression, and alternative splicing profiles of peroxiredoxin genes in cotton

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10685
Author(s):  
Yulong Feng ◽  
Renhui Wei ◽  
Aiying Liu ◽  
Senmiao Fan ◽  
JinCan Che ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Cytoplasmic Membrane ◽  
Redox Status ◽  
Pcr Analysis ◽  
Systematic Research ◽  
Oxygen Species ◽  
Cis Acting ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Starting Point

Peroxiredoxin (PRX) is a ubiquitous thioredoxin-dependent peroxidase that can eliminate excessive free radicals produced by stress and protect cells from oxidative damage. PRXs are also involved in reactive oxygen species (ROS)- and redox-dependent signaling by performing redox interactions with other proteins and modify their redox status. At present, PRX family identification, evolution and regulation research has been conducted in some plants; however, systematic research about this family is lacking in cotton. In this study, a total of 44 PRXs were identified in the cotton genome. Phylogenetic and conserved active site analyses showed that the PRXs were divided into six subfamilies according to the conserved site (PxxxTxxC…S…W/F) and conserved cysteinyl residues positions. Segmental duplication and polyploid events were the main methods for PRX family expansion, and the PRXs of diploid G. arboreum were the donors of PRXs in the D subgenomes of allotetraploid G. hirsutum and G. barbadense during the evolution of the PRX family. qRT-PCR analysis confirmed that cis-acting elements play important roles in regulating the expression of PRXs. Alternative splicing events occurred in GhPRX14-D that can increased the complexity of transcripts in G. hirsutum. Subcellular localization showed that most PRX members were located in chloroplasts, the cytoplasmic membrane and the nucleus. Our results provide systematic support for a better understanding of PRXs in cotton and a starting point for further studies of the specific functions of PRXs in cotton.

scholarly journals Genome-Wide Identification and Expression Profiles of Late Embryogenesis-Abundant (LEA) Genes during Grain Maturation in Wheat (Triticum aestivum L.)

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 696
Author(s):  
Datong Liu ◽  
Jing Sun ◽  
Dongmei Zhu ◽  
Guofeng Lyu ◽  
Chunmei Zhang ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Expression Profiles ◽  
Triticum Aestivum L ◽  
Late Embryogenesis Abundant ◽  
Wheat Breeding ◽  
Pcr Analysis ◽  
Lea Genes ◽  
Cellular Dehydration ◽  
Genome Wide ◽  
Late Embryogenesis

Late embryogenesis-abundant (LEA) genes play important roles in plant growth and development, especially the cellular dehydration tolerance during seed maturation. In order to comprehensively understand the roles of LEA family members in wheat, we carried out a series of analyses based on the latest genome sequence of the bread wheat Chinese Spring. 121 Triticum aestivum L. LEA (TaLEA) genes, classified as 8 groups, were identified and characterized. TaLEA genes are distributed in all chromosomes, most of them with a low number of introns (≤3). Expression profiles showed that most TaLEA genes expressed specifically in grains. By qRT-PCR analysis, we confirmed that 12 genes among them showed high expression levels during late stage grain maturation in two spring wheat cultivars, Yangmai16 and Yangmai15. For most genes, the peak of expression appeared earlier in Yangmai16. Statistical analysis indicated that expression level of 8 genes in Yangmai 16 were significantly higher than Yangmai 15 at 25 days after anthesis. Taken together, our results provide more knowledge for future functional analysis and potential utilization of TaLEA genes in wheat breeding.

scholarly journals Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8062 ◽  
Author(s):  
Wenqiang Jiang ◽  
Lei Yang ◽  
Yiqin He ◽  
Haotian Zhang ◽  
Wei Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Phylogenetic Analyses ◽  
Pcr Analysis ◽  
Response Patterns ◽  
Qrt Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Almost All ◽  
Location Mapping ◽  
Sod Gene Family

Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed. Twenty-six SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, six Fe-SODs, and three Mn-SODs. The chromosomal location mapping analysis indicated that these three types of SOD genes were only distributed on 2, 4, and 7 chromosomes, respectively. Phylogenetic analyses of wheat SODs and several other species revealed that these SOD proteins can be assigned to two major categories. SOD1 mainly comprises of Cu/Zn-SODs, and SOD2 mainly comprises of Fe-SODs and Mn-SODs. Gene structure and motif analyses indicated that most of the SOD genes showed a relatively conserved exon/intron arrangement and motif composition. Analyses of transcriptional data indicated that most of the wheat SOD genes were expressed in almost all of the examined tissues and had important functions in abiotic stress resistance. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to reveal the regulating roles of wheat SOD gene family in response to NaCl, mannitol, and polyethylene glycol stresses. qRT-PCR showed that eight randomly selected genes with relatively high expression levels responded to all three stresses based on released transcriptome data. However, their degree of response and response patterns were different. Interestingly, among these genes, TaSOD1.7, TaSOD1.9, TaSOD2.1, and TaSOD2.3 feature research value owing to their remarkable expression-fold change in leaves or roots under different stresses. Overall, our results provide a basis of further functional research on the SOD gene family in wheat and facilitate their potential use for applications in the genetic improvement on wheat in drought and salt stress environments.

scholarly journals Genome-Wide SNPs Identification and Determination of Proteins Associated with Stress Response in Sorghum (<i>Sorghum bicolor</i> L. Monech) Accessions

2017 ◽  
Vol 08 (07) ◽  
pp. 1624-1631
Author(s):  
Hind Emad Fadoul ◽  
Marmar A. El Siddig ◽  
Abdel Wahab H. Abdalla ◽  
Adil A. El Hussein
Keyword(s):  
Stress Response ◽  
Sorghum Bicolor ◽  
Genome Wide

scholarly journals Study of transgene expression in Triticum aestivum L. after Agrobacterium-mediated in planta transformation

2019 ◽  
Vol 16 (2) ◽  
pp. 159-165
Author(s):  
N. A. Zhalii ◽  
M. O. Bannikova ◽  
M. O. Plugatar ◽  
L. H. Velikozhon ◽  
A. M. Taranenko ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Winter Wheat ◽  
Genetically Modified Organisms ◽  
Triticum Aestivum L ◽  
Pcr Analysis ◽  
Test Results ◽  
In Planta ◽  
Genetic Construct ◽  
Pcr Method

Aim. Detection of sequences of target transgenes nptII and bar in the genome of probable transformants of bread winter wheat Triticum aestivum L. cultivars Zymoiarka and Podolianka obtained as a result of Agrobacterium-mediated transformation in planta and determination of their expression level. Methods. Polymerase chain reaction (PCR) method was used independently and in combination with reverse transcription (RT-PCR), electrophoresis of DNA in agarose gel. Tolerance to the herbicide was evaluated in the physiological test. Results Through PCR analysis, the sequence of nptII transgene was detected in 30 samples of 145 analyzed, the frequency of transformation was 20.7 %. The sequence of the gene bar was observed in 85 experimental plants, and the frequency of transformation was 15.6 %. mRNAs of both transgenes were detected, indicating their transcriptional activity and stable expression. Conclusions PCR analysis allowed to detect nptII transgenic signal in 20.7 % of plants, while the presence of the bar gene was detected in 15.6 % of cases, indicating a higher efficiency of this genetic construct. The transcription is shown in all the specimens studied for both transgene. According to the results of the physiological test, 25 % of plants containing the gene bar showed resistance to the Basta® herbicide.Keywords: genetically modified organisms, transgenic plants, biotechnological cultures, bread winter wheat, genetic engineering.

scholarly journals Genome-Wide Identification, Characterization and Evolution of BBX Gene Family in Cotton

2020 ◽  
Author(s):  
Jun-Shan Gao ◽  
Pei-pei Wang ◽  
Na Sun ◽  
Jessica-Maguy ◽  
MIENANDI NKODIA ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Cotton Fibers ◽  
Pcr Analysis ◽  
Conserved Domains ◽  
Qrt Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Phylogenetic Evolution ◽  
Genome Wide Survey

Abstract Background: The B-BOX (BBX) proteins have important functions in the regulation of photomorphogenesis. The BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in cotton. Results: In our present study, 63 GhBBX genes were identified in cotton. The analyses of phylogenetic evolution and gene structure showed that the GhBBX genes were divided into five subfamilies, and contained B-box conserved domains. qRT-PCR analysis releaved that both GhBBX27 and GhBBX33 had potential roles in proanthocyanidin synthesis of brown cotton fibers.Conclusions: This study provides a genome-wide survey of the BBX gene family in cotton and highlights its role in proanthocyanidin synthesis. This result will help us to further understand the complexity of the BBX gene family and the functional characteristics of its members.

Sign in / Sign up

Export Citation Format

Share Document