scholarly journals Genome-wide analysis of maize OSCA family members and their involvement in drought stress

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6765 ◽  
Author(s):  
Shuangcheng Ding ◽  
Xin Feng ◽  
Hewei Du ◽  
Hongwei Wang
Keyword(s):  
Genetic Variation ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Gene Family ◽  
Association Analysis ◽  
Expression Profiles ◽  
Protein Domain ◽  
Maize Genome ◽  
Genome Wide ◽  
A Genome

Background Worldwide cultivation of maize is often impacted negatively by drought stress. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis. However, the involvement of members of the maize OSCA (ZmOSCA) gene family in response to drought stress is unknown. It is furthermore unclear which ZmOSCA gene plays a major role in genetic improvement of drought tolerance in Maize. Methods We predicted the protein domain structure and transmembrane regions by using the NCBI Conserved Domain Database database and TMHMM server separately. The phylogeny tree was built by Mega7. We used the mixed linear model in TASSEL to perform the family-based association analysis. Results In this report, 12 ZmOSCA genes were uncovered in the maize genome by a genome-wide survey and analyzed systematically to reveal their synteny and phylogenetic relationship with the genomes of rice, maize, and sorghum. These analyses indicated a relatively conserved evolutionary history of the ZmOSCA gene family. Protein domain and transmembrane analysis indicated that most of the 12 ZmOSCAs shared similar structures with their homologs. The result of differential expression analysis under drought at various stages, as well as the expression profiles in 15 tissues, revealed a functional divergence of ZmOSCA genes. Notably, the expression level of ZmOSCA4.1 being up-regulated in both seedlings and adult leaves. Notably, the association analysis between genetic variations in these genes and drought tolerance was detected. Significant associations between genetic variation in ZmOSCA4.1 and drought tolerance were found at the seedling stage. Our report provides a detailed analysis of the ZmOSCAs in the maize genome. These findings will contribute to future studies on the functional characterization of ZmOSCA proteins in response to water deficit stress, as well as understanding the mechanism of genetic variation in drought tolerance in maize.

scholarly journals Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 610
Author(s):  
Ding ◽  
He ◽  
Tang ◽  
Du ◽  
Wang
Keyword(s):  
Drought Stress ◽  
Active Sites ◽  
Expression Profiles ◽  
Maize Genome ◽  
Tblastn Search ◽  
Redox Active ◽  
Genome Wide ◽  
A Genome ◽  
Maize Cultivation ◽  
Conservative Domain

Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear. We performed a TBLASTN search to identify ZmGRXCCs in the maize genome and verified the identified sequences using the NCBI conservative domain database (CDD). We further established a phylogenetic tree using Mega7 and surveyed known cis-elements in the promoters of ZmGRXCCs using the PlantCARE database. We found twenty-one ZmGRXCCs in the maize genome by a genome-wide investigation and compared their phylogenetic relationships with rice, maize, and Arabidopsis. The analysis of their redox active sites showed that most of the 21 ZmGRXCCs share similar structures with their homologs. We assessed their expression at young seedlings and adult leaves under drought stress and their expression profiles in 15 tissues, and found that they were differentially expressed, indicating that different ZmGRXCC genes have different functions. Notably, ZmGRXCC14 is up-regulated at seedling, V12, V14, V16, and R1 stages. Importantly, significant associations between genetic variation in ZmGRXCC14 and drought tolerance are found at the seedling stage. These results will help to advance the study of the function of ZmGRXCCs genes under drought stress and understand the mechanism of drought resistance in maize.

scholarly journals Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10617
Author(s):  
Jie Li ◽  
Xinhao Liu ◽  
Qingmei Wang ◽  
Junyan Sun ◽  
Dexian He
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Seed Formation ◽  
Aphid Infestation ◽  
Genome Wide ◽  
A Genome ◽  
Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

scholarly journals Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yuzhu Huo ◽  
Wangdan Xiong ◽  
Kunlong Su ◽  
Yu Li ◽  
Yawen Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Panicum Virgatum ◽  
Expression Profiles ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

scholarly journals Response of Tibetan Wild Barley Genotypes to Drought Stress and Identification of Quantitative Trait Loci by Genome-Wide Association Analysis

2019 ◽  
Vol 20 (3) ◽  
pp. 791
Author(s):  
Mian Zhang ◽  
Man-Man Fu ◽  
Cheng-Wei Qiu ◽  
Fangbin Cao ◽  
Zhong-Hua Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Quantitative Trait ◽  
Wild Barley ◽  
Genome Wide Association ◽  
Dart Markers ◽  
Tibetan Wild Barley ◽  
Genome Wide ◽  
Barley Genotypes

Tibetan wild barley has been identified to show large genetic variation and stress tolerance. A genome-wide association (GWA) analysis was performed to detect quantitative trait loci (QTLs) for drought tolerance using 777 Diversity Array Technology (DArT) markers and morphological and physiological traits of 166 Tibetan wild barley accessions in both hydroponic and pot experiments. Large genotypic variation for these traits was found; and population structure and kinship analysis identified three subpopulations among these barley genotypes. The average LD (linkage disequilibrium) decay distance was 5.16 cM, with the minimum on 6H (0.03 cM) and the maximum on 4H (23.48 cM). A total of 91 DArT markers were identified to be associated with drought tolerance-related traits, with 33, 26, 16, 1, 3, and 12 associations for morphological traits, H+K+-ATPase activity, antioxidant enzyme activities, malondialdehyde (MDA) content, soluble protein content, and potassium concentration, respectively. Furthermore, 7 and 24 putative candidate genes were identified based on the reference Meta-QTL map and by searching the Barleymap. The present study implicated that Tibetan annual wild barley from Qinghai–Tibet Plateau is rich in genetic variation for drought stress. The QTLs detected by genome-wide association analysis could be used in marker-assisting breeding for drought-tolerant barley genotypes and provide useful information for discovery and functional analysis of key genes in the future.

scholarly journals Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

2020 ◽  
Vol 21 (18) ◽  
pp. 6594
Author(s):  
Shuting Zhang ◽  
Qin Zhou ◽  
Feng Chen ◽  
Lan Wu ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Leaf Morphogenesis ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

scholarly journals Genome-wide identification and functional characterization of the Camelina sativa WRKY gene family in response to abiotic stress

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanan Song ◽  
Hongli Cui ◽  
Ying Shi ◽  
Jinai Xue ◽  
Chunli Ji ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Stress Resistance ◽  
Segmental Duplication ◽  
Expression Profiles ◽  
High Stress ◽  
Camelina Sativa ◽  
Genome Wide ◽  
A Genome

Abstract Background WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas. Results A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress. Conclusions The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in 12 tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.

scholarly journals Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

2018 ◽  
Vol 19 (9) ◽  
pp. 2478 ◽  
Author(s):  
Qinglong Dong ◽  
Dingyue Duan ◽  
Shuang Zhao ◽  
Bingyao Xu ◽  
Jiawei Luo ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Gene Family ◽  
Transgenic Arabidopsis ◽  
Abiotic Stress Tolerance ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Sequence Alignments ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

scholarly journals Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

2020 ◽  
Author(s):  
Muhammad Zulfiqar Ahmad ◽  
Xiangsheng Zeng ◽  
Qiang Dong ◽  
Sehrish Manan ◽  
Huanan Jin ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Expression Profiles ◽  
Plant Defence ◽  
Constitutive Expression ◽  
Gene Families ◽  
Strong Positive Selection ◽  
Genome Wide ◽  
A Genome ◽  
Bahd Acyltransferase

Abstract Background: Members of the BAHD acyltransferase (ACT) family play important roles in plant defence against biotic and abiotic stresses. Previous genome-wide studies explored different acyltransferase gene families, but not a single study was found so far on the overall genome-wide or positive selection analyses of the BAHD family genes in Glycine max . A better understanding of the functions that specific members of this family play in stress defence can lead to better breeding strategies for stress tolerance. Results: A total of 103 genes of the BAHD family (GmACT genes) were mined from the soybean genome, which could be grouped into four phylogenetic clades (I- IV). Clade III was further divided into two sub-clades (IIIA and IIIB). In each clade, the constituent part of the gene structures and motifs were relatively conserved. These 103 genes were distributed unequally on all 20 chromosomes, and 16 paralogous pairs were found within the family. Positive selection analysis revealed important amino acids under strong positive selection, which suggests that the evolution of this gene family modulated soybean domestication. Most of the expression of ACT genes in soybean was repressed with Al 3+ and fungal elicitor exposure, except for GmACT84 , which expression increased in these conditions 2- and 3-fold, respectively. The promoter region of GmACT84 contains the maximum number of stress-responsive elements among all GmACT genes and is especially enriched in MYB-related elements. Some GmACT genes showed expression specific under specific conditions, while others showed constitutive expression in all soybean tissues or conditions analysed. Conclusions: This study provided a genome-wide analysis of the BAHD gene family and assessed their expression profiles. We found evidence of a strong positive selection of GmACT genes. Our findings will help efforts of functional characterisation of ACT genes in soybean in order to discover their involvement in growth, development, and defence mechanisms.

scholarly journals Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuxia Li ◽  
Lei Zhang ◽  
Panpan Zhu ◽  
Qinghe Cao ◽  
Jian Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Sweet Potato ◽  
Gene Structure ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Functional Evaluation ◽  
Ipomoea Trifida ◽  
Wild Ancestor ◽  
Genome Wide ◽  
A Genome

Abstract Background WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried out a genome-wide analysis of WRKYs in Ipomoea trifida (H.B.K.) G. Don., the wild ancestor of sweet potato. Results A total of 83 WRKY genes encoding 96 proteins were identified in I. trifida, and their gene distribution, duplication, structure, phylogeny and expression patterns were studied. ItfWRKYs were distributed on 15 chromosomes of I. trifida. Gene duplication analysis showed that segmental duplication played an important role in the WRKY gene family expansion in I. trifida. Gene structure analysis showed that the intron-exon model of the ItfWRKY gene was highly conserved. Meanwhile, the ItfWRKYs were divided into five groups (I, IIa + IIb, IIc, IId + IIe and III) on the basis of the phylogenetic analysis on I. trifida and Arabidopsis thaliana WRKY proteins. In addition, gene expression profiles confirmed by quantitative polymerase chain reaction showed that ItfWRKYs were highly up-regulated or down-regulated under salt, drought, cold and heat stress conditions, implying that these genes play important roles in response and adaptation to abiotic stresses. Conclusions In summary, genome-wide identification, gene structure, phylogeny and expression analysis of WRKY gene in I. trifida provide basic information for further functional studies of ItfWRKYs and for the molecular breeding of sweet potato.

scholarly journals Genome-Wide Analysis of TCP Family Genes in Zea mays L. Identified a Role for ZmTCP42 in Drought Tolerance

2019 ◽  
Vol 20 (11) ◽  
pp. 2762 ◽  
Author(s):  
Shuangcheng Ding ◽  
Zhenzhen Cai ◽  
Hewei Du ◽  
Hongwei Wang
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Zea Mays L ◽  
Maize Genome ◽  
Positive Role ◽  
Maize Production ◽  
Major Constraint ◽  
Genome Wide ◽  
Genes Expression ◽  
Maize Response

The Teosinte-branched 1/Cycloidea/Proliferating (TCP) plant-specific transcription factors (TFs) have been demonstrated to play a fundamental role in plant development and organ patterning. However, it remains unknown whether or not the TCP gene family plays a role in conferring a tolerance to drought stress in maize, which is a major constraint to maize production. In this study, we identified 46 ZmTCP genes in the maize genome and systematically analyzed their phylogenetic relationships and synteny with rice, sorghum, and Arabidopsis TCP genes. Expression analysis of the 46 ZmTCP genes in different tissues and under drought conditions, suggests their involvement in maize response to drought stress. Importantly, genetic variations in ZmTCP32 and ZmTCP42 are significantly associated with drought tolerance at the seedling stage. RT-qPCR results suggest that ZmTCP32 and ZmTCP42 RNA levels are both induced by ABA, drought, and polyethylene glycol treatments. Based on the significant association between the genetic variation of ZmTCP42 and drought tolerance, and the inducible expression of ZmTCP42 by drought stress, we selected ZmTCP42, to investigate its function in drought response. We found that overexpression of ZmTCP42 in Arabidopsis led to a hypersensitivity to ABA in seed germination and enhanced drought tolerance, validating its function in drought tolerance. These results suggested that ZmTCP42 functions as an important TCP TF in maize, which plays a positive role in drought tolerance.

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