scholarly journals Transcriptomic profiling against Globodera pallida in resistant and susceptible potato roots

2020 ◽  
Vol 27 (1) ◽  
pp. 027-034
Author(s):  
Hans Carreño ◽  
Olga Ponce ◽  
Regina Casanova ◽  
Germán De la Cruz ◽  
Edgar Neyra
Keyword(s):  
Candidate Genes ◽  
Susceptible Variety ◽  
Fold Change ◽  
Globodera Pallida ◽  
Post Inoculation ◽  
White Potato ◽  
Illumina Hiseq ◽  
Potato Genome ◽  
The Andes ◽  
Lrr Protein

Globodera pallida is a white potato cyst nematode present in the Andes, which causes huge losses to Peruvian farmers. An RNA-seq analysis allowed the identification of candidate genes that could mediate resistance against this pathogen. Two varieties, “María Huanca” (Solanum andigena) clone resistant (CIP 279142.12) and “Chimbina Colorada” (Solanum chaucha) (CIP 701013) clone susceptible to G. pallida, were used to identify differentially expressed genes. Total RNA from roots was extracted 72 hours post inoculation with second stage juveniles. Sequencing was done using the Illumina Hiseq 2500 platform. Reads were screened for quality issues and then mapped to the reference potato genome (clone DM1-3516 R44 v4.03). Here, we report 27717 and 27750 genes expressed in the resistant and susceptible variety respectively. The comparative analysis of expression identified 100 candidate genes. 91 genes were associated with resistance to G. pallida with Fold Change ≥ 2 (p <0.05). The remaining 9 R genes had Fold Change ≤ 1. We show differences in the expression of an NBS-LRR protein similar to Gro1-8, genes linked to late blight and TMV virus resistance.

Globodera pallida (white potato cyst nematode).

2021 ◽  
Author(s):  
Janet Rowe
Keyword(s):  
Life Cycle ◽  
Host Plant ◽  
Related Species ◽  
Cyst Nematode ◽  
Globodera Pallida ◽  
Common Method ◽  
White Potato ◽  
Soil Particles ◽  
Flood Water ◽  
The Andes

Abstract G. pallida originates from the Andes and is known to be present in 55 countries. It is found predominantly in temperate regions as is the related species, Globodera rostochiensis. It is possibly more difficult to manage than G. rostochiensis because there is currently less resistance available in commercially-grown potato cultivars. Egg-laden cysts are the most environmentally resistant and easily transportable stage in the parasites life cycle, and are found in soil particles, on host roots, stolons or tubers. The microscopic size of the cyst makes it difficult to detect, and it can successfully establish new infestations when an appropriate climate and host plant are available. Machinery used on infested land followed by use in otherwise uninfested areas is a common method of spread, for example, fumigation equipment that has not been cleaned before use in another area. Disinfection of farming tools, transport and clothing helps to keep uninfested land free from G. pallida. Wind, rain and flood water are also capable of redistributing viable cysts to create new infestations.

An investigation of resistance to the white potato cyst-nematode

1982 ◽  
Vol 99 (2) ◽  
pp. 325-328 ◽  
Author(s):  
M. F. B. Dale ◽  
M. S. Phillips
Keyword(s):  
Solanum Tuberosum ◽  
Major Gene ◽  
Cyst Nematode ◽  
Potato Cyst Nematode ◽  
Globodera Pallida ◽  
Screening Methods ◽  
Inheritance Of Resistance ◽  
White Potato

SUMMARYThe inheritance of resistance to Globodera pallida was studied in seedling progenies derived from Solanum tuberosum ssp. andigena CPC 2802 (H3) and S. vernei and compared with resistance to G. rostochiensis derived from S. tuberosum ssp. andigena CPC 1673(H1). The resistance of CPC 2802 was originally thought to be due to a major gene (H3), but results presented here demonstrate that it and that derived from S. vernei are inherited in a similar manner quite distinct from the major gene inheritance from CPC 1673 (HI). It is concluded that the resistances derived from CPC 2802 and S. vernei are both polygenic in nature. These findings are discussed in relation to breeding policy and screening methods.

scholarly journals Environmentally Induced Variability in the Host Reaction of Barley to Net Blotch

1969 ◽  
Vol 22 (5) ◽  
pp. 1237 ◽  
Author(s):  
TN Khan ◽  
WJR Boyd
Keyword(s):  
Environmental Conditions ◽  
Susceptible Variety ◽  
Post Inoculation ◽  
Net Blotch ◽  
Host Reaction ◽  
Drechslera Teres ◽  
Resistant Varieties

The host reaction of two Ethiopian and four Manchurian resistant varieties, and one susceptible variety of barley to isolate 177 of Drechslera teres was studied under a range of environmental conditions. The effects were specific to the variety(ies) used, with the exception of the factor of post-inoculation temperature. High post-inoculation temperatures brought about the breakdown of resistance in all the varieties.

scholarly journals ANGI-07. NOVEL FUSION GENE PTPRZ1-MET PROMOTES GLIOMAS ANGIOGENESIS BY UP-REGULATING EXOCRINE PROTEIN IGF2BP3

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi31-vi31
Author(s):  
Yanwei Liu ◽  
Xiaoguang Qiu ◽  
Tao Jiang
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Kinase Inhibitor ◽  
Fusion Gene ◽  
Vascular Endothelial Cells ◽  
Negative Control ◽  
Fold Change ◽  
Prognostic Analysis ◽  
Stat3 Signaling ◽  
Worse Prognosis

Abstract We previously reported a novel fusion gene PTPRZ1-MET in 15% of secondary GBM (sGBM). Subsequent studies showed that ZM fusion indicates a significantly worse prognosis and promotes glioma progression by increasing MET activity. We have demonstrated hyper-activation of MAPK and STAT3 signaling and elevated angiogenesis activities in patients and subcutaneous tumors with ZM fusion. However, the angiogenesis mechanism regulated by ZM is still unclear. In this study, 66 up-regulated and 66 down-regulated genes were identified on 8 sGBMs with ZM fusion comparing gene expression with 135 negative sGBMs (fold-change >2.5 & p.value < 0.05). ZM-harboring U87 MG xenograft models were conducted and RNA sequencing was performed in 3 subcutaneous tumors with ZM-harboring U87 MG and 3 negative control. 384 up-regulated and 698 down-regulated genes were identified on 3 ZM-harboring samples comparing gene expression with 3 negative control samples (fold-change >2.5 & p.value < 0.05. Three subcutaneous tumors with ZM-harboring U87 MG were treated by a MET kinase inhibitor, PLB-1001. Finally, the expression of 13 up-regulated gene decreased and 10 down-regulated genes increased after treatment by PLB-1001. We overlapped the candidate genes between patient samples and subcutaneous tumors and 5 up-regulated and 4 down-regulated genes was appeared and most associated with ZM fusion. Prognostic analysis of 9 candidate genes on sGBM revealed that a higher expression of IGF2BP3 indicates a worse prognosis. In further study, we found that IGF2BP3 can be secreted out of the gliomas stem cells (GSCs) and promote proliferation of vascular endothelial cells and the expression of CD31. IGF2BP3 siRNA can block this pathway and inhibit the angiogenesis. Conclusion, our study demonstrated a new pathway promoting angiogenesis in gliomas. But the regulating mechanism between ZM fusion gene and IGF2BP3 deserves to do further research.

scholarly journals RNA-seq screening of the CPGs in Culex pipiens pallens among cypermethrin-resistant populations

2019 ◽  
Author(s):  
Qiqi Shi ◽  
Peng Cheng ◽  
Chongxing Zhang ◽  
Lijuan Liu ◽  
Xiao Song ◽  
...  
Keyword(s):  
Culex Pipiens ◽  
Noncoding Rna ◽  
Pyrethroid Resistance ◽  
Fold Change ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Culex Pipiens Pallens ◽  
Metabolic Resistance ◽  
Illumina Hiseq ◽  
Pipiens Pallens

Abstract Background Long-lasting overdependence on insecticides has led to the rapid spread of pyrethroid resistance in mosquito vectors, which is of great concern to the general public. There are many studies on metabolic resistance and target resistance, but fewer studies have been conducted on cuticle resistance and behaviour resistance. The cuticle of mosquitoes has been hypothesized to play a role in insecticide resistance by reducing penetration or sequestering insecticides. Methods We used RNA sequencing (RNA-seq) to analyse the transcriptome of cypermethrin-resistant and cypermethrin-susceptible strains of Culex pipiens pallens . Sequenced 6 samples using an Illumina HiSeq platform, and generated approximately 6.66 Gb bases from each sample on average. Mapping the sequenced reads to a reference genome and reconstructing the transcripts, through gene expression analysis, we detected differentially expressed genes (DEGs) among the samples. Followed Gene Ontology (GO) classification and functional enrichment. Finally, we screened the genes of cuticle proteins associated with drug resistance throughout the genome, selected the significant DEGs with a log2 fold change>3.0 and Padj<0.05, and applied real-time fluorescence quantitative PCR to verify the DEGs. Results We obtained 13,517 novel transcripts, of which 8,653 were previously unknown splicing events for known genes, 665 were novel coding transcripts without any known features, and 4,199 were long noncoding RNA. A total of 1035, 944, and 657 genes were upregulated in comparisons between samples, and 2680, 1215, and 975 genes were downregulated in comparisons between samples. Finally, among all samples, 167 genes upregulated, and 145 genes downregulated. The GO classification and functional enrichment of DEGs as follows: molecular function, 224 genes; cellular component, 149 genes; and biological process, 272 genes. The expression of XM_001863852 and XM_001845881 in resistant strains of Culex pipiens pallens was lower than that in the laboratory sensitive strain, with fold changes in expression of 0.177 and 0.548, respectively; the expression of the XM_001845883.1 in the resistant strain was higher than that in the susceptible strain, and a 2.281-fold change in expression. Conclusions The results provide a reference for resistance mechanisms through the mosquito cuticle, furthermore, could provide a new perspective for disease vector control.

scholarly journals Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

2019 ◽  
Author(s):  
María I. Cádiz ◽  
María E. López ◽  
Diego Díaz-Domínguez ◽  
Giovanna Cáceres ◽  
Grazyella M. Yoshida ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Illumina Hiseq ◽  
Extended Haplotype ◽  
Commercial Interest ◽  
Snp Data ◽  
Improvement Programs ◽  
Signatures Of Selection ◽  
Log Ratio

AbstractNile tilapia (Oreochromis niloticus Linnaeus, 1758) belong to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs in this species began in the late 1980s to enhance some traits of commercial interest. The resulting domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, using two complementary methods based in extended haplotype homozygosity (EHH)._Whole-genome sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia from two countries (Brazil and Costa Rica) was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control pipelines, a total of ~1.3M high-quality SNPs were inferred and used as input for the Integrated Haplotype Score (|iHS|) and standardized log-ratio of integrated EHH between pairs of populations (Rsb) methods. We detected 16, 174 and 96 candidate genes subjected to selection in strain A, B, and C, respectively. These candidate genes represent putative genomic landmarks that could contain functions of biological and commercial interest.

scholarly journals Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Yujie Chang ◽  
Feifei Sun ◽  
Suli Sun ◽  
Lanfen Wang ◽  
Jing Wu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fusarium Wilt ◽  
Transcriptome Analysis ◽  
Stress Responses ◽  
Mung Bean ◽  
Differential Expression Analysis ◽  
Differentially Expressed ◽  
Post Inoculation ◽  
Wilt Resistance ◽  
Fusarium Wilt Resistance

Fusarium wilt is a destructive soil-borne disease that threatens the production of mung bean. Mung bean lines Zheng8-4 and Zheng8-20 show high resistance and high susceptibility to Fusarium wilt, respectively. Transcriptome analysis was carried out to identify candidate genes involved in Fusarium wilt resistance using Zheng8-4 and Zheng8-20 at 0, 0.5, 1, 2, and 4 days post inoculation (dpi). Differential expression analysis showed that 3,254 genes responded to pathogen infection and were differentially expressed in the resistant and susceptible lines. Weighted gene co-expression network analysis (WGCNA) was also performed to identify five modules highly correlated with Fusarium wilt resistance, in which 453 differentially expressed genes (DEGs) were considered likely to be involved in Fusarium wilt resistance. Among these DEGs, we found 24 genes encoding resistance (R) proteins, 22 encoding protein kinases, 20 belonging to transcription factor families, 34 encoding proteins with oxidoreductase activity, 17 involved in stimulation/stress responses, and 54 annotated to pathogen resistance-related pathways. Finally, 27 annotated genes were further selected as candidate genes of Fusarium wilt resistance in mung bean. This study identifies novel potential resistance-related genes against Fusarium wilt and provides a theoretical basis for further investigation of Fusarium wilt resistance in mung bean breeding.

scholarly journals Signatures of Environmental Adaptation During Range Expansion of Wild Common Bean (Phaseolus vulgaris)

2019 ◽  
Author(s):  
Andrea Ariani ◽  
Paul Gepts
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Candidate Genes ◽  
Outlier Detection ◽  
Long Range ◽  
Range Expansion ◽  
Environmental Adaptation ◽  
Landscape Genomics ◽  
Wild Bean ◽  
The Andes

AbstractLandscape genomics integrates population genetics with landscape ecology, allowing the identification of putative molecular determinants involved in environmental adaptation across the natural geographic and ecological range of populations. Wild Phaseolus vulgaris, the progenitor of common bean (P. vulgaris), has a remarkably extended distribution over 10,000 km from northern Mexico to northwestern Argentina. Earlier research has shown that this distribution represents a range expansion from Mesoamerica to the southern Andes through several discrete migration events and that the species colonized areas with different temperature and rainfall compared to its core area of origin. Thus, this species provides an opportunity to examine to what extent adaptation of a species can be broadened or, conversely, ecological or geographical distribution can be limited by inherent adaptedness. In the current study, we applied a landscape genomics approach to a collection of 246 wild common bean accessions representative of its broad geographical and climatic distribution and genotyped for ∼20K SNPs. We applied two different but complementary approaches for identifying loci putatively involved in environmental adaptation: i) an outlier-detection method that identifies loci showing strong differentiation between sub-populations; ii) an association method based on the identification of loci associated with bio-climatic variables. This integrated approach allowed the identification of several genes showing signature of selection across the different natural sub-populations of this species, as well as genes associated with specific bio-climatic variables related to temperature and precipitation. The current study demonstrates the feasibility of landscape genomics approach for a preliminary identification of specific populations and novel candidate genes involved in environmental adaptation in P. vulgaris. As a resource for broadening the genetic diversity of the domesticated gene pool of this species, the genes identified constitute potential molecular markers and introgression targets for the breeding improvement of domesticated common bean.Author SummaryThe ancestral form of common bean has an unusually large distribution in the Americas, extending over 10,000 km from ∼35° N. Lat. to ∼35° S. Lat. This wide distribution results from discrete long-range dissemination events to the Andes region from the original environments in Mesoamerica. It also suggests adaptation to new environments that are distinct from those encountered in Mesoamerica. In this research, we identified genes that may be involved in adaptation to climate variables in these new environments using two methods. A first method – outlier detection – was used to identify genome regions that differentiated the wild bean groups in the Andes resulting from discrete dissemination events among themselves and the different groups in Mesoamerica. The second method – genome-wide association – was used to identify candidate genome regions correlated with these same variables across the entire distribution from Mesoamerica to the southern Andes. The two methods identified two sets of candidate genes, several of which were related to the water status of plants, and illustrate how the genetic architecture of adaptation following long-range dissemination. This study provides sets of candidate genes as well as candidate wild bean populations that need to be corroborated for their use in increasing the water use efficiency of domesticated beans.

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