scholarly journals Genome-Wide Expression Profiling of Genes Associated with the Lr47-Mediated Wheat Resistance to Leaf Rust (Puccinia triticina)

2019 ◽  
Vol 20 (18) ◽  
pp. 4498 ◽  
Author(s):  
Jiaojiao Wu ◽  
Jing Gao ◽  
Weishuai Bi ◽  
Jiaojie Zhao ◽  
Xiumei Yu ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Fungal Pathogens ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Puccinia Triticina ◽  
Gene Families ◽  
Aegilops Speltoides ◽  
Post Inoculation ◽  
Q Value ◽  
Pr Genes

Puccinia triticina (Pt), the causal agent of wheat leaf rust, is one of the most destructive fungal pathogens threatening global wheat cultivations. The rational utilization of leaf rust resistance (Lr) genes is still the most efficient method for the control of such diseases. The Lr47 gene introgressed from chromosome 7S of Aegilops speltoides still showed high resistance to the majority of Pt races collected in China. However, the Lr47 gene has not been cloned yet, and the regulatory network of the Lr47-mediated resistance has not been explored. In the present investigation, transcriptome analysis was applied on RNA samples from three different wheat lines (“Yecora Rojo”, “UC1037”, and “White Yecora”) carrying the Lr47 gene three days post-inoculation with the epidemic Pt race THTT. A comparison between Pt-inoculated and water-inoculated “Lr47-Yecora Rojo” lines revealed a total number of 863 upregulated (q-value < 0.05 and log2foldchange > 1) and 418 downregulated (q-value < 0.05 and log2foldchange < −1) genes. Specifically, differentially expressed genes (DEGs) located on chromosomes 7AS, 7BS, and 7DS were identified, ten of which encoded receptor-like kinases (RLKs). The expression patterns of these RLK genes were further determined by a time-scale qRT-PCR assay. Moreover, heatmaps for the expression profiles of pathogenesis-related (PR) genes and several transcription factor gene families were generated. Using a transcriptomic approach, we initially profiled the transcriptional changes associated with the Lr47-mediated resistance. The identified DEGs, particularly those genes encoding RLKs, might serve as valuable genetic resources for the improvement of wheat resistance to Pt.

scholarly journals Transcriptomic Profiling of Populus Roots Challenged with Fusarium Reveals Differential Responsive Patterns of Invertase and Invertase Inhibitor-Like Families within Carbohydrate Metabolism

2021 ◽  
Vol 7 (2) ◽  
pp. 89
Author(s):  
Tao Su ◽  
Biyao Zhou ◽  
Dan Cao ◽  
Yuting Pan ◽  
Mei Hu ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Plant Pathogen ◽  
Fungal Pathogens ◽  
Time Course ◽  
Expression Patterns ◽  
Gene Families ◽  
Transcript Abundance ◽  
Post Inoculation ◽  
Transcriptomic Profiling ◽  
Invertase Inhibitor

Fusarium solani (Fs) is one of the notorious necrotrophic fungal pathogens that cause root rot and vascular wilt, accounting for the severe loss of Populus production worldwide. The plant–pathogen interactions have a strong molecular basis. As yet, the genomic information and transcriptomic profiling on the attempted infection of Fs remain unavailable in a woody model species, Populus trichocarpa. We used a full RNA-seq transcriptome to investigate the molecular interactions in the roots with a time-course infection at 0, 24, 48, and 72 h post-inoculation (hpi) of Fs. Concomitantly, the invertase and invertase inhibitor-like gene families were further analyzed, followed by the experimental evaluation of their expression patterns using quantitative PCR (qPCR) and enzyme assay. The magnitude profiles of the differentially expressed genes (DEGs) were observed at 72 hpi inoculation. Approximately 839 genes evidenced a reception and transduction of pathogen signals, a large transcriptional reprogramming, induction of hormone signaling, activation of pathogenesis-related genes, and secondary and carbohydrate metabolism changes. Among these, a total of 63 critical genes that consistently appear during the entire interactions of plant–pathogen had substantially altered transcript abundance and potentially constituted suitable candidates as resistant genes in genetic engineering. These data provide essential clues in the developing new strategies of broadening resistance to Fs through transcriptional or translational modifications of the critical responsive genes within various analyzed categories (e.g., carbohydrate metabolism) in Populus.

scholarly journals Cytogenetic analysis and mapping of leaf rust resistance in Aegilops speltoides Tausch derived bread wheat line Selection2427 carrying putative gametocidal gene(s)

Genome ◽  
2017 ◽  
Vol 60 (12) ◽  
pp. 1076-1085 ◽  
Author(s):  
M. Niranjana ◽  
Vinod ◽  
J.B. Sharma ◽  
Niharika Mallick ◽  
S.M.S. Tomar ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Bread Wheat ◽  
Rust Resistance ◽  
Dominant Gene ◽  
Puccinia Triticina ◽  
Leaf Rust Resistance ◽  
Aegilops Speltoides ◽  
Lr Genes ◽  
Gametocidal Gene ◽  
Chromosome 3B

Leaf rust (Puccinia triticina) is a major biotic stress affecting wheat yields worldwide. Host-plant resistance is the best method for controlling leaf rust. Aegilops speltoides is a good source of resistance against wheat rusts. To date, five Lr genes, Lr28, Lr35, Lr36, Lr47, and Lr51, have been transferred from Ae. speltoides to bread wheat. In Selection2427, a bread wheat introgresed line with Ae. speltoides as the donor parent, a dominant gene for leaf rust resistance was mapped to the long arm of chromosome 3B (LrS2427). None of the Lr genes introgressed from Ae. speltoides have been mapped to chromosome 3B. Since none of the designated seedling leaf rust resistance genes have been located on chromosome 3B, LrS2427 seems to be a novel gene. Selection2427 showed a unique property typical of gametocidal genes, that when crossed to other bread wheat cultivars, the F1 showed partial pollen sterility and poor seed setting, whilst Selection2427 showed reasonable male and female fertility. Accidental co-transfer of gametocidal genes with LrS2427 may have occurred in Selection2427. Though LrS2427 did not show any segregation distortion and assorted independently of putative gametocidal gene(s), its utilization will be difficult due to the selfish behavior of gametocidal genes.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

Genome-wide analysis of NAAT, DMAS, TOM, and ENA gene families in maize reveals their roles in regulating iron homeostasis

2020 ◽  
Author(s):  
Xin Zhang ◽  
Xiaojin Zhou ◽  
Suzhen Li ◽  
Jiaxing Huang ◽  
Sen Pang ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Iron Homeostasis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Mining ◽  
Gene Families ◽  
Pcr Analysis ◽  
Efflux Transporter ◽  
Iron Starvation ◽  
Maize Varieties

Abstract Background: Nicotianamine (NA) serves as not only the major chelator for iron transport but also the intermediate for synthesizing mugineic acid family phytosiderophores (MAs) which are secreted by graminaceous plants for Fe uptake. Therefore, the production and secretion of MAs are key steps for maintaining iron homeostasis in plants. Nicotianamine aminotransferase (NAAT), 2’-deoxymugineic acid synthase (DMAS), MAs efflux transporter (TOM), and efflux transporter of NA (ENA) were identified to be involved in these processes in rice and barley, whereas little systematic study has been performed in maize (Zea mays.L). Results: Here, we identified five ZmNAAT, nine ZmDMAS, eleven ZmTOM, and two ZmENA genes in maize by genome mining. RNA-sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) analysis revealed that the expression of these genes exhibited diverse tissue specificity and different responses to environmental iron conditions. Moreover, the expression patterns were related to their evolution relationships. In particular, the ZmNAAT family can be classified into two subgroups, with one group showed inhibited expression in root under iron excess status and another subclass were repressed in shoot under both iron deficiency and excess. Likewise, the expression of ZmDMAS1 was stimulated under iron deficiency, while the remaining genes fell into two sub-clades with different expression patterns. Significant up-regulation of ZmTOM1, ZmTOM3 and ZmENA1 were observed under iron starvation, while ZmTOM2 was induced under both iron-excess and deficiency. These results reflect changing demands for the synthesis and secretion of NA/MAs to balance iron homeostasis under fluctuating conditions. All the examined ZmNAAT and ZmDMAS proteins localized in cytoplasm, while plasma and tonoplast membrane, endomembrane, and vesicle localization were observed for ZmTOM and ZmENA proteins. These results indicate that ZmTOM and ZmENA proteins may contribute to not only intercellular export but also intracellular sequestration of NA and MAs to facilitate iron homeostasis. Conclusions: Our results suggest that different gene expression profiles and subcellular localization of ZmNAAT, ZmDMAS, ZmTOM, and ZmENA members may enable dedicate regulation of NA and phytosiderophores (PS) metabolism, shedding light on the understanding of iron-homeostasis in maize. Additionally, we also provided candidate genes for breeding iron-rich maize varieties.

Wheat TaLr35PR2 gene is required for Lr35-mediated adult plant resistance against leaf rust fungus

2020 ◽  
Vol 47 (1) ◽  
pp. 26
Author(s):  
Fang Liang ◽  
Xiong Du ◽  
Jiarui Zhang ◽  
Xiaoying Li ◽  
Fei Wang ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Fungal Pathogens ◽  
Developmental Stages ◽  
Rust Fungus ◽  
Expression Patterns ◽  
Plant Defence ◽  
Adult Plant ◽  
Isogenic Line ◽  
Critical Function ◽  
Pathogenesis Related Protein

In this study we analysed the expression patterns of TaLr35PR2 and confirmed its role in Lr35-mediated adult resistance to leaf rust fungus. β-1,3-glucanase, a pathogenesis-related protein, has a critical function in plant defence response against fungal pathogens. We previously described the full-length gene TaLr35PR2, which encodes a protein exhibiting amino acid and structural similarity to β-1,3-glucanase, in the wheat near-isogenic line TcLr35 (GenBank accession number DQ294235.1). This work aimed to further assess TaLr35PR2 expression patterns and function in Lr35-mediated adult resistance to Puccinia triticina. Immunoblot was performed to demonstrate that TaLr35PR2 expression was triggered early by P. triticina, with expression levels markedly elevated in incompatible interaction compared with those in compatible one. Additionally, TaLr35PR2 accumulation steadily increased and overtly peaked after challenge with P. triticina through the various developmental stages of TcLr35 wheat, and remaining at similar levels after mock inoculation. Furthermore, TaLr35PR2 expression was significantly reduced in barley stripe mosaic virus (BSMV)-induced gene knockdown plants, in which pathological assessment revealed that TaLr35PR2-silenced plants was obviously susceptible to leaf rust fungus compared with wild-type TcLr35, indicating that Lr35-mediated resistance to leaf rust was diminished. These findings strongly suggest that TaLr35PR2 is involved in Lr35-mediated wheat defence against the leaf rust pathogen.

scholarly journals Temporal Gene Expression Profiling of the Wheat Leaf Rust Pathosystem Using cDNA Microarray Reveals Differences in Compatible and Incompatible Defence Pathways

2007 ◽  
Vol 2007 ◽  
pp. 1-13 ◽  
Author(s):  
Bourlaye Fofana ◽  
Travis W. Banks ◽  
Brent McCallum ◽  
Stephen E. Strelkov ◽  
Sylvie Cloutier
Keyword(s):  
Leaf Rust ◽  
Metabolic Pathways ◽  
Fungal Pathogens ◽  
Puccinia Triticina ◽  
Phenylpropanoid Pathway ◽  
Altered Expression ◽  
Temporal Gene Expression ◽  
Wheat Leaf ◽  
Mock Treatment ◽  
Host Genes

In this study, we detail the construction of a custom cDNA spotted microarray containing 7728 wheat ESTs and the use of the array to identify host genes that are differentially expressed upon challenges with leaf rust fungal pathogens. Wheat cultivar RL6003 (Thatcher Lr1) was inoculated with Puccinia triticina virulence phenotypes BBB (incompatible) or TJB (7-2) (compatible) and sampled at four different time points (3, 6, 12, and 24 hours) after inoculation. Transcript expression levels relative to a mock treatment were measured. One hundred ninety two genes were found to have significantly altered expression between the compatible and incompatible reactions. Among those were genes involved in photosynthesis, the production of reactive oxygen species, ubiquitination, signal transduction, as well as in the shikimate/phenylpropanoid pathway. These data indicate that various metabolic pathways are affected, some of which might be used by RL6003 to mount a coordinated defense against an incompatible fungal pathogen.

scholarly journals Transcriptomic Analysis of Starch Biosynthesis in the Developing Grain of Hexaploid Wheat

2009 ◽  
Vol 2009 ◽  
pp. 1-23 ◽  
Author(s):  
Boryana S. Stamova ◽  
Debbie Laudencia-Chingcuanco ◽  
Diane M. Beckles
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Soluble Sugars ◽  
Starch Synthesis ◽  
Gene Families ◽  
Starch Accumulation ◽  
Protein Accumulation ◽  
High Accumulation

The expression of genes involved in starch synthesis in wheat was analyzed together with the accumulation profiles of soluble sugars, starch, protein, and starch granule distribution in developing caryopses obtained from the same biological materials used for profiling of gene expression using DNA microarrays. Multiple expression patterns were detected for the different starch biosynthetic gene isoforms, suggesting their relative importance through caryopsis development. Members of the ADP-glucose pyrophosphorylase, starch synthase, starch branching enzyme, and sucrose synthase gene families showed different expression profiles; expression of some members of these gene families coincided with a period of high accumulation of starch while others did not. A biphasic pattern was observed in the rates of starch and protein accumulation which paralleled changes in global gene expression. Metabolic and regulatory genes that show a pattern of expression similar to starch accumulation and granule size distribution were identified, suggesting their coinvolvement in these biological processes.

scholarly journals Wall-associated Receptor Kinase and The Expression Profiles in Wheat Responding to Fungal Stress

2021 ◽  
Author(s):  
Hong Zhang ◽  
Hanping Li ◽  
Xiangyu Zhang ◽  
Wenqian Yan ◽  
Pingchuan Deng ◽  
...  
Keyword(s):  
Puccinia Striiformis ◽  
Fungal Infections ◽  
Expression Profiles ◽  
Puccinia Triticina ◽  
Gene Families ◽  
Triticum Aestivum L ◽  
Pcr Analysis ◽  
Homologous Genes ◽  
Conserved Gene ◽  
Encoding Genes

Cell wall-associated kinases (WAKs), which are encoded by conserved gene families in plants, are crucial for development and responses to diverse stresses. However, the wheat (Triticum aestivum L.) WAKs have not been systematically classified, especially those involved in protecting plants from disease. Here, we classified 129 WAK proteins (encoded by 232 genes) and 75 WAK-Like proteins (WAKLs; encoded by 109 genes) into four groups, via a phylogenetic analysis. An examination of protein sequence alignment revealed diversity in the GUB-domain of WAKs structural organization, but it was usually characterized by a PYPFG motif followed by CxGxGCC motifs, while the EGF-domain was usually initiated with a YAC motif, and eight cysteine residues were spliced by GNPY motif. The expression profiles of WAK-encoding homologous genes varied in response to Blumeria graminis f. sp. tritici (Bgt), Puccinia striiformis f. sp. tritici (Pst) and Puccinia triticina (Pt) stress. A quantitative real-time polymerase chain reaction (qRT-PCR) analysis proved that TaWAK75 and TaWAK76b were involved in wheat resistance to Bgt. This study revealed the structure of the WAK-encoding genes in wheat, which may be useful for future functional elucidation of wheat WAKs responses to fungal infections.

scholarly journals Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

2020 ◽  
Author(s):  
Chong Yang ◽  
Juanjuan Li ◽  
Faisal Islam ◽  
Luyang Hu ◽  
Jiansu Wang ◽  
...  
Keyword(s):  
Helianthus Annuus ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Gene Families ◽  
Biotic And Abiotic Stresses

Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes and will be beneficial to crop improvement.

scholarly journals Genome-wide sequence and expression analysis of the NAC transcription factor family in polyploid wheat

2017 ◽  
Author(s):  
Philippa Borrill ◽  
Sophie A. Harrington ◽  
Cristobal Uauy
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Phylogenetic Groups ◽  
Future Studies ◽  
Nac Transcription Factors ◽  
Wide Range ◽  
Nac Family

ARTICLE SUMMARYTranscription factors are vital in plants to regulate gene expression in response to environmental stimuli and to control developmental processes. In this study, we annotated and classified transcription factors in polyploid bread wheat into gene families and explored the NAC family in detail. We combined phylogenetic analysis and transcriptome analysis, using publicly available RNA-seq data, to characterize the NAC gene family and provide hypotheses for putative functions of many NAC transcription factors. This study lays the groundwork for future studies on transcription factors in wheat which may be of great agronomic relevance.ABSTRACTMany important genes in agriculture correspond to transcription factors which regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. In this study, we identified 5,776 transcription factors in hexaploid wheat (Triticum aestivum) and classified them into gene families. We further investigated the NAC family exploring the phylogeny, C-terminal domain conservation and expression profiles across 308 RNA-seq samples. Phylogenetic trees of NAC domains indicated that wheat NACs divided into eight groups similar to rice (Oryza sativa) and barley (Hordeum vulgare). C-terminal domain motifs were frequently conserved between wheat, rice and barley within phylogenetic groups, however this conservation was not maintained across phylogenetic groups. We explored gene expression patterns across a wide range of developmental stages, tissues, and abiotic stresses. We found that more phylogenetically related NACs shared more similar expression patterns compared to more distant NACs. However, within each phylogenetic group there were clades with diverse expression profiles. We carried out a co-expression analysis on all wheat genes and identified 37 modules of co-expressed genes of which 23 contained NACs. Using GO term enrichment we obtained putative functions for NACs within co-expressed modules including responses to heat and abiotic stress and responses to water: these NACs may represent targets for breeding or biotechnological applications. This study provides a framework and data for hypothesis generation for future studies on NAC transcription factors in wheat.

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