scholarly journals Transcriptome-based Analysis of Tomato Genotypes Resistant to Bacterial spot (Xanthomonas perforans) Race T4

2019 ◽  
Author(s):  
Rui Shi ◽  
Dilip R. Panthee
Keyword(s):  
Biotic Stress ◽  
Rna Seq ◽  
Resistant Line ◽  
Bacterial Spot ◽  
Resistance Qtls ◽  
Susceptible Line ◽  
Xanthomonas Perforans ◽  
Sequence Variations ◽  
Stress Pathway ◽  
Go Terms

AbstractBacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato caused by multiple species of Xanthomonas. We performed the RNA-Seq analysis of three tomato lines with different level of resistance to Xanthomonas perforans race T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations.Analysis between inoculated and control samples revealed that resistant line PI 270443 had more DEGs (834), followed by susceptible line NC 714 (373), and intermediate line NC 1CELBR (154). Gene functional analysis based on Gene Ontology (GO) terms revealed that more GO terms (51) were enriched for up-regulated DEGs in the resistant line PI 270443, and more down-regulated DEGs (67) were enriched in the susceptible line NC 714. The specific analysis for DEGs in biotic stress pathway using MapMan software showed more up-regulated biotic stress pathway DEGs (67) for PI 270443 compared to more down-regulated DEGs (125) for susceptible NC 714 line. One interesting feature was that resistant PI 270443 has three up-regulated DEGs for PR-protein, and susceptible line NC 714 has one down-regulated R gene, which is disease-related.Analysis of sequence variations called from RNA-Seq reads against the reference genome of susceptible Heinz 1706 showed that chr11 which has multiple reported resistance QTLs to BS race T4 is identical between two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR-resistance proteins with sequence variation between the resistant and susceptible tomato lines were identified near the known Rx4 resistance gene on chr11. These findings may be useful for further molecular breeding of tomato.

scholarly journals Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot (Xanthomonas perforans) Race T4

2020 ◽  
Vol 21 (11) ◽  
pp. 4070
Author(s):  
Rui Shi ◽  
Dilip R. Panthee
Keyword(s):  
Biotic Stress ◽  
Breeding Line ◽  
Rna Seq ◽  
Susceptible Genotype ◽  
Bacterial Spot ◽  
Resistant Genotype ◽  
Xanthomonas Perforans ◽  
Sequence Variations ◽  
Stress Pathway ◽  
Go Terms

Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato and is caused by multiple species of Xanthomonas. We performed the RNA sequencing (RNA-Seq) analysis of three tomato lines with different levels of resistance to Xanthomonas perforans race T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations. Analysis between inoculated and control samples revealed that resistant genotype Solanum pimpinellifolium accession PI 270443 had more DEGs (834), followed by susceptible genotype tomato (S. lycopersicum L) breeding line NC 714 (373), and intermediate genotype tomato breeding line NC 1CELBR (154). Gene ontology (GO) terms revealed that more GO terms (51) were enriched for upregulated DEGs in the resistant genotype PI 270443, and more downregulated DEGs (67) were enriched in the susceptible genotype NC 714. DEGs in the biotic stress pathway showed more upregulated biotic stress pathway DEGs (67) for PI 270443 compared to more downregulated DEGs (125) for the susceptible NC 714 genotype. Resistant genotype PI 270443 has three upregulated DEGs for pathogenesis-related (PR) proteins, and susceptible genotype NC 714 has one downregulated R gene. Sequence variations called from RNA-Seq reads against the reference genome of susceptible Heinz 1706 showed that chr11, which has multiple reported resistance quantitative trait loci (QTLs) to BS race T4, is identical between two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR resistance proteins with sequence variation between the resistant and susceptible tomato lines were near the known Rx4 resistance gene on chr11, and additional biotic stress associated DEGs near to the known Rx4 resistance gene were also identified from the susceptible NC 714 line.

scholarly journals Analysis of Sequenced Genomes of Xanthomonas perforans Identifies Candidate Targets for Resistance Breeding in Tomato

2016 ◽  
Vol 106 (10) ◽  
pp. 1097-1104 ◽  
Author(s):  
Sujan Timilsina ◽  
Peter Abrahamian ◽  
Neha Potnis ◽  
Gerald V. Minsavage ◽  
Frank F. White ◽  
...  
Keyword(s):  
Resistance Breeding ◽  
Effector Protein ◽  
Bacterial Disease ◽  
Bacterial Spot ◽  
Genome Sequences ◽  
Xanthomonas Perforans ◽  
Modern Agriculture ◽  
Rapid Changes ◽  
Pathogen Populations ◽  
Race 4

Bacterial disease management is a challenge for modern agriculture due to rapid changes in pathogen populations. Genome sequences for hosts and pathogens provide detailed information that facilitates effector-based breeding strategies. Tomato genotypes have gene-for-gene resistance to the bacterial spot pathogen Xanthomonas perforans. The bacterial spot populations in Florida shifted from tomato race 3 to 4, such that the corresponding tomato resistance gene no longer recognizes the effector protein AvrXv3. Genome sequencing showed variation in effector profiles among race 4 strains collected in 2006 and 2012 and compared with a race 3 strain collected in 1991. We examined variation in putative targets of resistance among Florida strains of X. perforans collected from 1991 to 2006. Consistent with race change, avrXv3 was present in race 3 strains but nonfunctional in race 4 strains due to multiple independent mutations. Effectors xopJ4 and avrBs2 were unchanged in all strains. The effector avrBsT was absent in race 3 strains collected in the 1990s but present in race 3 strains collected in 2006 and nearly all race 4 strains. These changes in effector profiles suggest that xopJ4 and avrBsT are currently the best targets for resistance breeding against bacterial spot in tomato.

scholarly journals First Report of Bacterial Spot of Tomato Caused by Xanthomonas perforans in Mississippi

Plant Disease ◽  
2019 ◽  
Vol 103 (1) ◽  
pp. 147-147
Author(s):  
P. Abrahamian ◽  
J. M. Klein ◽  
J. B. Jones ◽  
G. E. Vallad ◽  
R. A. Melanson
Keyword(s):  
Bacterial Spot ◽  
First Report ◽  
Xanthomonas Perforans

scholarly journals Characterization of Hypersensitive Resistance to Bacterial Spot Race T3 (Xanthomonas perforans) from Tomato Accession PI 128216

2009 ◽  
Vol 99 (9) ◽  
pp. 1037-1044 ◽  
Author(s):  
Matthew D. Robbins ◽  
Audrey Darrigues ◽  
Sung-Chur Sim ◽  
Mohammed Abu Taher Masud ◽  
David M. Francis
Keyword(s):  
Gene Dosage ◽  
Hypersensitive Reaction ◽  
Recurrent Parent ◽  
Chromosome 6 ◽  
Chromosome 11 ◽  
Bacterial Spot ◽  
Hypersensitive Resistance ◽  
Xanthomonas Perforans ◽  
Additive Gene ◽  
Candidate Loci

Bacterial spot of tomato is caused by four species of Xanthomonas. The accession PI 128216 (Solanum pimpinellifolium) displays a hypersensitive reaction (HR) to race T3 strains (predominately Xanthomonas perforans). We developed an inbred backcross (IBC) population (BC2S5, 178 families) derived from PI 128216 and OH88119 (S. lycopersicum) as the susceptible recurrent parent for simultaneous introgression and genetic analysis of the HR response. These IBC families were evaluated in the greenhouse for HR to race T3 strain Xcv761. The IBC population was genotyped with molecular markers distributed throughout the genome in order to identify candidate loci conferring resistance. We treated the IBC population as a hypothesis forming generation to guide validation in subsequent crosses. Nonparametric analysis identified an association between HR and markers clustered on chromosome 11 (P < 0.05 to 0.0001) and chromosome 6 (0.04 > P > 0.002). Further analysis of the IBC population suggested that markers on chromosome 6 and 11 failed to assort independently, a phenomenon known as gametic phase disequilibrium. Therefore, to validate marker-trait linkages, resistant IBC plants were crossed with OH88119 and BC3F2 progeny were evaluated for HR in the greenhouse. In these subsequent populations, the HR response was associated with the chromosome 11 markers (P < 0.0002) but not with the markers on chromosome 6 (P > 0.25). Independent F2 families were developed by crossing resistant IBC lines to OH8245, OH88119, and OH7530. These populations were genotyped, organized into classes based on chromosome 11 markers, and evaluated for resistance in the field. The PI 128216 locus on chromosome 11 provided resistance that was dependent on gene dosage and genetic background. These results define a single locus, Rx-4, from PI 128216, which provides resistance to bacterial spot race T3, has additive gene action, and is located on chromosome 11.

scholarly journals Transcriptome Sequencing and Comparative Analysis of Amphoteric ESCs and PGCs in Chicken (Gallus gallus)

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2228
Author(s):  
Kai Jin ◽  
Jing Zhou ◽  
Qisheng Zuo ◽  
Jiuzhou Song ◽  
Yani Zhang ◽  
...  
Keyword(s):  
Primordial Germ Cells ◽  
Embryonic Stem ◽  
Gallus Gallus ◽  
Future Research ◽  
Biological Processes ◽  
Rna Seq ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
The Difference ◽  
Go Terms

Chicken (Gallus gallus) pluripotent embryonic stem cells (ESCs) and primordial germ cells (PGCs) can be broadly applied in the research of developmental and embryonic biology, but the difference between amphoteric ESCs and PGCs is still elusive. This study determined the sex of collected samples by identifying specific sex markers via polymerase chain reaction (PCR) and fluorescence activated cell sorter (FACS). RNA-seq was utilized to investigate the transcriptomic profile of amphoteric ESCs and PGCs in chicken. The results showed no significant differentially expressed genes (DEGs) in amphoteric ESCs and 227 DEGs exhibited in amphoteric PGCs. Moreover, those 227 DEGs were mainly enriched in 17 gene ontology (GO) terms and 27 pathways according to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Furthermore, qRT-PCR was performed to verify RNA-seq results, and the results demonstrated that Notch1 was highly expressed in male PGCs. In summary, our results provided a knowledge base of chicken amphoteric ESCs and PGCs, which is helpful for future research in relevant biological processes.

scholarly journals Identifying differential isoform abundance with RATs: a universal tool and a warning

2017 ◽  
Author(s):  
Kimon Froussios ◽  
Kira Mourão ◽  
Gordon G. Simpson ◽  
Geoffrey J. Barton ◽  
Nick J. Schurch
Keyword(s):  
Transcript Abundance ◽  
Pcr Primers ◽  
R Package ◽  
Original Study ◽  
Transcript Expression ◽  
Rna Seq ◽  
Qrt Pcr ◽  
False Discovery ◽  
Alignment Free ◽  
Go Terms

AbstractMotivationThe biological importance of changes in gene and transcript expression is well recognised and is reflected by the wide variety of tools available to characterise these changes. Regulation via Differential Transcript Usage (DTU) is emerging as an important phenomenon. Several tools exist for the detection of DTU from read alignment or assembly data, but options for detection of DTU from alignment-free quantifications are limited.ResultsWe present an R package named RATs – (Relative Abundance of Transcripts) – that identifies DTU transcriptome-wide directly from transcript abundance estimations. RATs is agnostic to quantification methods and exploits bootstrapped quantifications, if available, to inform the significance of detected DTU events. RATs contextualises the DTU results and shows good False Discovery performance (median FDR ≤0.05) at all replication levels. We applied RATs to a human RNA-seq dataset associated with idiopathic pulmonary fibrosis with three DTU events validated by qRT-PCR. RATs found all three genes exhibited statistically significant changes in isoform proportions based on Ensembl v60 annotations, but the DTU for two were not reliably reproduced across bootstrapped quantifications. RATs also identified 500 novel DTU events that are enriched for eleven GO terms related to regulation of the response to stimulus, regulation of immune system processes, and symbiosis/parasitism. Repeating this analysis with the Ensembl v87 annotation showed the isoform abundance profiles of two of the three validated DTU genes changed radically. RATs identified 414 novel DTU events that are enriched for five GO terms, none of which are in common with those previously identified. Only 141 of the DTU evens are common between the two analyses, and only 8 are among the 248 reported by the original study. Furthermore, the original qRT-PCR probes no longer match uniquely to their original transcripts, calling into question the interpretation of these data. We suggest parallel full-length isoform sequencing, annotation pre-filtering and sequencing of the transcripts captured by qRT-PCR primers as possible ways to improve the validation of RNA-seq results in future experiments.AvailabilityThe package is available through Github at https://github.com/bartongroup/Rats.

scholarly journals The Metabolic Reprogramming of Frem2 Mutant Mice Embryos in Cryptophthalmos Development

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiayin Zhang ◽  
Ruixin Wang ◽  
Ting Wang ◽  
Xulin Zhang ◽  
Meimei Dongye ◽  
...  
Keyword(s):  
Metabolic Reprogramming ◽  
Mutant Mice ◽  
Compound Heterozygous ◽  
Rna Seq ◽  
Targeted Metabolomics ◽  
Expression Of Genes ◽  
Fetal Mice ◽  
Genes Encoding ◽  
Go Terms ◽  
Increased Susceptibility

BackgroundCryptophthalmos is characterized by congenital ocular dysplasia with eyelid malformation. The pathogenicity of mutations in genes encoding components of the FRAS1/FREM protein complex is well established, but the underlying pathomechanisms of this disease are still unclear. In the previous study, we generated mice carrying Frem2R725X/R2156W compound heterozygous mutations using CRISPR/Cas9 and showed that these mice recapitulated the human cryptophthalmos phenotype.MethodsIn this study, we tracked changes in the metabolic profile of embryos and expression of metabolism-related genes in Frem2 mutant mice on E13.5 compared with wild-type mice. RNA sequencing (RNA-seq) was utilized to decipher the differentiated expression of genes associated with metabolism. Untargeted metabolomics and targeted metabolomics analyses were performed to detect and verify the shifts in the composition of the embryonic metabolome.ResultsDifferentially expressed genes participating in amino acid metabolism and energy metabolism were observed by RNA-seq. Transcriptomic analysis suggests that 821 (39.89%) up-regulated genes and 320 (32.99%) down-regulated genes were involved in the metabolic process in the enriched GO terms. A total of 92 significantly different metabolites were identified including creatine, guanosine 5′-monophosphate, cytosine, cytidine 5′-monophosphate, adenine, and L-serine. Interestingly, major shifts related to ATP binding cassette transporters (ABC transporters) and the biosynthesis of amino acids in the composition of the embryonic metabolome were observed by KEGG metabolic analysis, indicating that these pathways could also be involved in the pathogenesis of cryptophthalmos.ConclusionWe demonstrate that Frem2 mutant fetal mice have increased susceptibility to the disruption of eye morphogenesis in association with distinct transcriptomic and metabolomic signatures. Our findings suggest that the metabolomic signature established before birth may play a role in mediating cryptophthalmos in Frem2 mutant mice, which may have important implications for the pathogenesis of cryptophthalmos.

Glucosinolate profile and Myrosinase gene expression are modulated upon Plasmodiophora brassicae infection in cabbage

2021 ◽  
Vol 48 (1) ◽  
pp. 103
Author(s):  
Md. Abdul Kayum ◽  
Ujjal Kumar Nath ◽  
Jong-In Park ◽  
Mohammad Rashed Hossain ◽  
Hoy-Taek Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Principal Component ◽  
Resistant Line ◽  
Clubroot Disease ◽  
Disease Symptoms ◽  
Susceptible Line ◽  
Glucosinolate Profile ◽  
In Silico Analyses

Clubroot is a devastating disease of Brassicaceae caused by the biotrophic protist Plasmodiophora brassicae. The progression of clubroot disease is modulated by the glucosinolate (GSL) profile of the host plant. GSL is hydrolysed by the enzyme myrosinase upon cell disruption and gives rise to metabolites like isothiocyanate, nitriles, thiocyanates, epithionitriles and oxazolidines. Some of these metabolites play important roles in the plant’s defence mechanism. We identified 13 Myrosinase (Myro) and 28 Myrosinase-Binding Protein-like (MBP) genes from Brassica oleracea L. using a comparative genomics approach and characterised them through in silico analyses. We compared the expression patterns of these genes in a clubroot-susceptible line and a resistant line following inoculation with P. brassicae. Two BolMyro and 12 BolMBP genes were highly expressed in the susceptible line, whereas only one BolMyro and five BolMBP genes were highly expressed in the resistant line. Principal component analysis confirmed that specific GSL profiles and gene expression were modulated due to pathogen infection. Plants with higher levels of neoglucobrassicin, glucobrassicin and methooxyglucobrassicin produced disease symptoms and formed galls, whereas, plants with higher levels of sinigrin, hydroxyglucobrassicin and progoitrin produced less symptoms with almost no galls. Our results provide insights into the roles of Myro and MBP genes in GSL hydrolysis during P. brassicae infection, which will help for developing clubroot resistant cabbage lines.

Sign in / Sign up

Export Citation Format

Share Document