Transcriptomic responses of common wheat segregating for Wsm2 locus to wheat streak mosaic virus (WSMV) and mock infection
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ABSTRACT:
ORGANISM(S): Triticum aestivum
PROVIDER: GSE190382 | GEO | 2022/04/27
REPOSITORIES: GEO
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Project description:Transcriptomic responses of common wheat segregating for Wsm2 locus to wheat streak mosaic virus (WSMV) and mock infection
| PRJNA786911 | ENA
Project description:Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are type members of Tritimovirus and Poacevirus genera, respectively, in the family Potyviridae, and are transmitted by wheat curl mites. Co-infection of these two viruses causes synergistic interaction with increased virus accumulation and disease severity in wheat. In this study, we examined the effects of synergistic interaction between WSMV and TriMV on endogenous small (s) RNAs and virus-specific small interfering RNAs (vsiRNAs) in susceptible (Arapahoe) and temperature-sensitive resistant (Mace) wheat cultivars at 27ºC and 18ºC. Single- and double-infections in wheat caused a shift in the profile of endogenous sRNAs from 24 nt being the most predominant in healthy plants to 21 nt in infected wheat. Additionally, we report high-resolution vsiRNA maps of WSMV and TriMV in singly- and doubly-infected wheat cultivars Arapahoe and Mace at 18ºC and 27ºC. Massive amounts of 21 and 22 nt vsiRNA reads were accumulated in Arapahoe at both temperatures and in Mace at 27ºC but not at 18ºC. The plus- and minus-sense vsiRNAs were distributed throughout the genomic RNAs in Arapahoe at both temperature regimens and in Mace at 27ºC, although some regions of genomic RNAs serve as hot-spots with an excessive number of vsiRNAs. The positions of vsiRNA peaks were conserved among wheat cultivars Arapahoe and Mace, suggesting that Dicer-like enzymes of susceptible and resistant wheat cultivars are similarly accessed the genomic RNAs of WSMV and TriMV. Additionally, several cold-spot regions were found in the genomes of TriMV and WSMV with no or a few vsiRNAs, indicating that certain regions of WSMV and TriMV genomes are not accessible to Dicer-like enzymes. The high-resolution map of endogenous and vsiRNAs from wheat cultivars synergistically infected with WSMV and TriMV at two temperature regimens form a foundation for understanding the virus-host interactions, effect of synergistic interactions on host defense mechanisms, and virus resistance mechanisms in wheat.
2014-12-01 | GSE54026 | GEO
Project description:Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are type members of Tritimovirus and Poacevirus genera, respectively, in the family Potyviridae, and are transmitted by wheat curl mites. Co-infection of these two viruses causes synergistic interaction with increased virus accumulation and disease severity in wheat. In this study, we examined the effects of synergistic interaction between WSMV and TriMV on endogenous small (s) RNAs and virus-specific small interfering RNAs (vsiRNAs) in susceptible (Arapahoe) and temperature-sensitive resistant (Mace) wheat cultivars at 27C and 18C. Single- and double-infections in wheat caused a shift in the profile of endogenous sRNAs from 24 nt being the most predominant in healthy plants to 21 nt in infected wheat. Additionally, we report high-resolution vsiRNA maps of WSMV and TriMV in singly- and doubly-infected wheat cultivars Arapahoe and Mace at 18C and 27C. Massive amounts of 21 and 22 nt vsiRNA reads were accumulated in Arapahoe at both temperatures and in Mace at 27C but not at 18C. The plus- and minus-sense vsiRNAs were distributed throughout the genomic RNAs in Arapahoe at both temperature regimens and in Mace at 27C, although some regions of genomic RNAs serve as hot-spots with an excessive number of vsiRNAs. The positions of vsiRNA peaks were conserved among wheat cultivars Arapahoe and Mace, suggesting that Dicer-like enzymes of susceptible and resistant wheat cultivars are similarly accessed the genomic RNAs of WSMV and TriMV. Additionally, several cold-spot regions were found in the genomes of TriMV and WSMV with no or a few vsiRNAs, indicating that certain regions of WSMV and TriMV genomes are not accessible to Dicer-like enzymes. The high-resolution map of endogenous and vsiRNAs from wheat cultivars synergistically infected with WSMV and TriMV at two temperature regimens form a foundation for understanding the virus-host interactions, effect of synergistic interactions on host defense mechanisms, and virus resistance mechanisms in wheat. Small RNA was sequenced from two wheat cultivars (Mace and Araphahoe), at two temperatures 18C and 27C, for healthy (control/uninfected), infected with wheat streak mosaic virus (WSMV), infected with Triticum mosaic virus (TriMV), and a double-infecttion of WSMV and TriMV.
2014-12-01 | E-GEOD-54026 | biostudies-arrayexpress
Project description:Common wheat is one of the most widely cultivated staple crops worldwide. Elucidating the gene regulatory network will provide essential information for mechanism studies and targeted manipulation of gene activity for breeding. However, detecting cis-regulatory elements and transcription factor (TF) bindings in the extremely large intergenic regions of the wheat genome is challenging. Linking cis-regulatory elements and TF binding to target genes is even more difficult given that enhancers can function irrespective of the strand and distance from target genes. Combining genome-wide TF binding profiles, epigenomic patterns, and transcriptome analysis is a compelling approach to detect the hierarchical regulatory network. We generated and collected 189 TF binding profiles, 90 epigenomic datasets, and 2,356 transcriptomic datasets in common wheat, which were further integrated using machine learning approach to infer direct target genes and the hierarchical regulatory network. We developed a web-based platform, Wheat-RegNet, that provides four major functions: (i) to identify regulatory elements regulating input gene(s), and to infer the tissue and environmental response specificity; (ii) to identify the TFs responsible for regulating input gene(s) or locus/loci; (iii) to construct the hierarchical regulatory network regulating input gene(s); and (iv) to browse hundreds of TF binding, epigenomic, and transcriptomic profiles of an input region or gene(s). Well-organized results and multiple tools for interactive visualization are available through a user-friendly web interface, making Wheat-RegNet a highly useful resource for exploring gene regulatory information for hypothesis-driven studies and for targeted manipulation for breeding research in common wheat. Wheat-RegNet is freely available at http://bioinfo.sibs.ac.cn/Wheat-RegNet
2024-07-08 | GSE207939 | GEO
Project description:Wheat streak mosaic virus (WSMV) is an economically important viral pathogen that threatens global wheat production, particularly in the Great Plains of the United States. The Wsm2 locus confers resistance to WSMV and has been widely deployed in common wheat varieties adapted to this region. Characterizing the underlying causative genetic variant would contribute to our understanding of viral resistance mechanisms in wheat and aid the development of perfect markers for breeding. In this study, linkage mapping in a doubled-haploid (DH) mapping population confirmed Wsm2 as a major locus conferring WSMV resistance in wheat. The Wsm2 flanking markers were mapped to a 4.0 Mbp region at the distal end of chromosome 3BS containing 142 candidate genes. Eight haplotypes were identified from seventeen wheat genotypes collected from different agroecological zones, indicating that Wsm2 lies in a dynamic region of the genome with extensive structural variation and that it is likely a rare allele in most available genome assemblies of common wheat varieties. Exome sequencing of the variety "Snowmass", which carries Wsm2, revealed several loss-of-function mutations and copy number variants in the 142 candidate genes within the Wsm2 interval. Six of these genes are differentially expressed in "Snowmass" compared to "Antero," a variety lacking Wsm2, including a gene that encodes a nucleotide-binding site leucine-rich repeat (NBS-LRR) type protein with homology to RPM1. A de novo assembly of unmapped RNA-seq reads identified nine transcripts expressed only in "Snowmass," three of which are also induced in response to WSMV inoculation. This study sheds light on the variation underlying Wsm2 and provides a list of candidate genes for subsequent validation.
| S-EPMC9285007 | biostudies-literature
Project description:Aim:To characterise a recently discovered stem rust resistance locus on wheat chromosome 7AL. Transcriptome analysis by RNA-sequencing, in association with microscopic observations, was used to compare responses to the Puccinia graminis f. sp. tritici pathogen of the susceptible line Columbus, and two independent backcrossed resistant lines containing the locus, Columbus-NS765 and Columbus-NS766. Results: Microscopic observations of infected leaves revealed that the resistance conferred by the 7AL resistance locus was initiated by two days post-inoculation, upon the entry of the stem rust fungus into the plant through the stoma. Death of guard and epidermal cells adjacent to the fungal points of entry was observed to be clearly more frequent in resistant lines than in the susceptible genotype, suggesting that the resistance response is similar in all genotypes, but enhanced in the resistant lines. Transcriptomic analysis, combined with assignment of genes to wheat chromosomes, revealed a disporportionately high number of differentially expressed genes were located on chromosomes 7AL and 6A. A number of genes annotated as cysteine-rich receptor-like kinases were located on chromosome 7AL. Closer investigation indicated that the encoded proteins were in fact putative receptor-like cytoplasmic kinases (RLCKs). One of the putative RLCK genes contained a SNP marker previously shown to co-segregate with the 7AL resistance locus. The large number of differentially expressed genes on chromosome 6A indicated the presence of a large introgression on this chromosome that co-segregated with stem rust resistance in the two independent resistant lines, but its role in the resistance response is currently unclear. Conclusions: This study represents the first transcriptome analysis of responses to stem rust in wheat, and the first investigation of the resistance conferred by the newly-discovered wheat 7AL stem rust resistance locus. Microscopy showed the resistance response was associated with pre-haustorial cell death. Results of the RNA-seq, which has the resolution to discriminate between homeologous wheat genes, along with assignment of differentially expressed genes to wheat chromosomes, suggested putative receptor-like cytoplasmic kinases linked to the 7AL locus as candidate resistance genes for further investigation.
2017-02-22 | GSE83149 | GEO
Project description:Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are important viral pathogens of wheat in the Great Plains. These viruses individually or in mixed infections with High Plains wheat mosaic virus cause a devastating wheat streak mosaic (WSM) disease. Although seed transmission of WSMV has been studied, no information is currently available on that of TriMV. Furthermore, no study has explored the implications of mixed infections of WSMV and TriMV on seed transmission of one or both viruses. To study both aspects, seeds from differentially resistant field-grown wheat plants (cv. TAM 304 (susceptible), Joe (WSMV resistant, Wsm2 gene), and Breakthrough (BT) (WSMV and TriMV resistant, Wsm1 gene)) showing characteristic WSM symptoms were collected and analyzed to quantify both viruses using qRT-PCR. The percentage of seeds tested positive for WSMV or TriMV individually and in mixed infection varied with cultivar and virus combinations; 13% of TAM 304 seeds tested positive for WSMV, followed by 8% of BT and 4% of Joe seeds. Similarly, TriMV was detected in 12% of BT seeds, followed by 11% of TAM 304 and 8% of Joe seeds. Lastly, mixed infection was detected in 7% of TAM 304 seeds, followed by 4% in BT, and 2% in Joe. Dissection of field-collected seeds into three parts, embryo, endosperm, and seed coat, revealed both WSMV and TriMV accumulated only in the seed coat. Consistent with seeds, percent infection of WSMV or TriMV in the plants that emerged from infected seeds in each treatment varied with cultivar and virus combinations (WSMV: BT 3%; Joe 2%; TAM 304 9%; TriMV: BT 7%; Joe 8%; and TAM 304 10%). Plants infected with mixed viruses showed more pronounced WSM symptoms compared to individual infections. However, both viruses were present only in a few plants (BT: 2%, Joe: 1%, and TAM 304: 4%). Taken together, this study showed that TriMV was transmitted vertically at a higher frequency than WSMV in resistant cultivars, and the seed transmission of TriMV with WSMV increased the virulence of both pathogens (measured via WSM symptom severity) in the emerged plants. Furthermore, Wsm1 and Wsm2 genes considerably reduced WSMV transmission via infected seeds. However, no such effects were observed on TriMV, especially in progeny plants. These results reiterated the importance of planting clean seeds and highlighted the immediate need to identify/develop new sources of TriMV resistance to effectively manage the recurring WSM epidemic.
| S-EPMC10459636 | biostudies-literature
Project description:Key messageThe resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect. Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to control the virus since no treatment is available. This paper reports studies of the inheritance of WSSMV resistance using two related durum wheat populations obtained by crossing two elite cultivars with a WSSMV-resistant emmer cultivar. In 2012 and 2015, 354 recombinant inbred lines (RIL) were phenotyped using visual notations, ELISA and qPCR and genotyped using locus targeted capture and sequencing. This allowed us to build a consensus genetic map of 8568 markers and identify three chromosomal regions involved in WSSMV resistance. Two major regions (located on chromosomes 7A and 7B) jointly explain, on the basis of epistatic interactions, up to 43% of the phenotypic variation. Flanking sequences of our genetic markers are provided to facilitate future marker-assisted selection of WSSMV-resistant cultivars.
| S-EPMC5487696 | biostudies-literature
Project description:Barley contains a much higher content of bioactive substances than wheat. In order to investigate the effect of genome interaction between barley and wheat on phytosterol content, we used a series of barley chromosome addition lines of common wheat. The wheat 38k-microarray was utilized for screening of genes with expression levels specifically increased by an additive effect or synergistic action between wheat and barley chromosomes. We determined the overall expression pattern of genes related to phytosterol biosynthesis in wheat and in each addition line. Together with determining the phytosterol levels of wheat, barley and each addition line, we assess the critical genes in the phytosterol pathway that can be expressed to promote phytosterol levels.
2011-12-08 | GSE28023 | GEO
Project description:Chinese wheat mosaic virus Genome sequencing
| PRJNA324141 | ENA