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 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.

Differential responses of resistant and susceptible groundnut genotypes at cellular level to Ditylenchus africanus

Nematology ◽  
2011 ◽  
Vol 13 (2) ◽  
pp. 177-183
Author(s):  
Sonia Steenkamp ◽  
Anine Jordaan ◽  
Alexander Mc Donald ◽  
Dirk Waele
Keyword(s):  
Light Microscopy ◽  
Cellular Level ◽  
Breeding Line ◽  
Susceptible Genotype ◽  
Resistant Genotype ◽  
Mechanism Of Resistance ◽  
Differential Responses

Abstract Ditylenchus africanus causes cellular breakdown in pod tissue of susceptible groundnut cultivars. The histopathology of this nematode on a resistant genotype was studied using light microscopy and compared with the histopathology of D. africanus on a susceptible genotype. Plants of breeding line PC254K1 and cv. Sellie were propagated in a glasshouse, inoculated with D. africanus at inoculum levels of 2000, 5000 and 7000 nematodes per plant and the pods were collected at 90, 120 and 150 days after planting. In contrast to the susceptible genotype, only a small number of nematodes were observed in restricted areas of the pod tissue of the resistant genotype. Furthermore, the resistant genotype showed neither external symptoms nor cellular breakdown in reaction to D. africanus. According to results of this study, the mechanism of resistance involved may be the inhibition of proper development, migration and reproduction of this nematode, thus preventing it building up to damaging population levels.

scholarly journals Inheritance of Resistance to Bacterial Spot Race T4 from Three Tomato Breeding Lines with Differing Resistance Backgrounds

2010 ◽  
Vol 135 (2) ◽  
pp. 150-158 ◽  
Author(s):  
Samuel F. Hutton ◽  
Jay W. Scott ◽  
Jeffrey B. Jones
Keyword(s):  
Transgressive Segregation ◽  
Breeding Line ◽  
Bacterial Spot ◽  
Breeding Lines ◽  
Epistatic Effects ◽  
Xanthomonas Perforans ◽  
Generation Means ◽  
Generation Means Analysis ◽  
Main Effect ◽  
Tomato Breeding

Resistance of tomato (Solanum lycopersicum) to bacterial spot race T4 (Xanthomonas perforans) was characterized by generation means analysis (GMA) in three advanced breeding lines: Fla. 8326, Fla. 8233, and Fla. 8517. GMA of Fla. 8326 for two of three seasons (Fall 2006 and Summer 2007) indicated that resistance is mostly dominant with significant additive and epistatic effects. GMA of Fla. 8233 in Spring 2007 and of Fla. 8517 in Summer 2007 also showed dominance to be the main effect in addition to additive and epistatic effects. Duplicate dominance or recessive suppressor type epistasis was indicated in each breeding line. Transgressive segregation was not clearly observed in F2 populations of crosses between resistant parents, suggesting that these lines have quantitative trait loci in common.

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 NRAMP1 3′ Untranslated Region Polymorphisms Are Not Associated with Natural Resistance to Brucella abortus in Cattle

2007 ◽  
Vol 75 (5) ◽  
pp. 2493-2499 ◽  
Author(s):  
Tatiane A. Paixão ◽  
Fernando P. Poester ◽  
Alcina V. Carvalho Neta ◽  
Álan M. Borges ◽  
Andrey P. Lage ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Intracellular Survival ◽  
Natural Resistance ◽  
Susceptible Genotype ◽  
Bovine Brucellosis ◽  
Resistant Genotype ◽  
Naturally Occurring ◽  
High Prevalence ◽  
Resistant Genotypes ◽  
Very High

ABSTRACT The NRAMP1 gene encodes a divalent cation transporter, located in the phagolysosomal membrane of macrophages, that has been associated with resistance to intracellular pathogens. In cattle, natural resistance against brucellosis has been associated with polymorphisms at the 3′ untranslated region (3′UTR) of the NRAMP1 gene, which are detectable by single-strand conformational analysis (SSCA). This study aimed to evaluate the association between NRAMP1 3′UTR polymorphisms and resistance against bovine brucellosis in experimental and natural infections. In experimentally infected pregnant cows, abortion occurred in 42.1% of cows with a resistant genotype (SSCAr; n = 19) and in 43.1% of those with a susceptible genotype (SSCAs; n = 23). Furthermore, no association between intensity of pathological changes and genotype was detected. In a farm with a very high prevalence of bovine brucellosis, the percentages of strains of the SSCAr genotype were 86 and 84% in serologically positive (n = 64) and negative (n = 36) cows, respectively. Therefore, no association was found between the NRAMP1-resistant allele and the resistant phenotype in either experimental or naturally occurring brucellosis. To further support these results, bacterial intracellular survival was assessed in bovine monocyte-derived macrophages from cattle with either the resistant or susceptible genotype. In agreement with our previous results, no difference was observed in the rates of intracellular survival of B. abortus within macrophages from cattle with susceptible or resistant genotypes. Taken together, these results indicate that these polymorphisms at the NRAMP1 3′UTR do not affect resistance against B. abortus in cattle and that they are therefore not suitable markers of natural resistance against bovine brucellosis.

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.

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