Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection

Aboshady, Hadeer M.; Mandonnet, Nathalie; Johansson, Anna M.; Jonas, Elisabeth; Bambou, Jean-Christophe

doi:10.1371/journal.pone.0248405

Cited by 6 publications

(3 citation statements)

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“…Moreover, we recently identified genomic variants between resistant and susceptible goats to GIN, in 78% of genes controlling the T-cell receptor-signaling pathway (32). The T-cell receptor-signaling pathway would play a role in the development of host immunity against GIN infection.…”

Section: Discussionmentioning

confidence: 99%

Early Transcriptome Differences Between Pre-Infected and Naïve Kid Goats Infected With Haemonchus contortus

et al. 2022

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In small ruminant production, gastrointestinal nematode (GIN) infection is one of the major causes of economic losses. The aim of this study was to compare the abomasal mucosa transcriptome of naïve and pre-infected goats at early time points after Haemonchus contortus infection, in order to identify different pathways and upstream regulators involved in the host immune response. Naïve and pre-infected Creole kids were orally infected with 10,000 H. contortus infective larvae (L3), and abomasal mucosa was sampled at 0, 4, and 6 days post-infection (dpi). At 6 dpi, all the animals were slaughtered to perform parasite burden counts. The mean number of L4 recovered in naïve kids was more than twice as high as that recovered in the pre-infected ones (5,860 and 2,474 respectively, p < 0.001). RNA-seq analysis showed a number of differentially expressed genes (DEGs) very low for both naïve and pre-infected animals when comparing day 0 vs. day 4 post-infection. A total of 2,237 and 3,206 DEGs were identified comparing 0 vs. 6 dpi in naïve and pre-infected animals, respectively. Interestingly, only 18 DEGs were found for the comparison of pre-infected vs. naïve animals at 6 dpi. Ingenuity pathway analysis (IPA) showed that several immune responses were activated in pre-infected compared with naïve animals at 0 and 4 dpi such as Th2 and Th1 pathways, natural killer cell, B cell receptor, IL-2, and IL-15 signaling. On the other hand, both naïve and pre-infected animals showed activation for those pathways comparing 6 vs. 0 dpi, with no difference between them. A similar pattern was recorded for upstream regulator genes which were related to immunity like TNF, IL-1β, IL-2, IL-5, TGFβ1, IFNγ, TCR, IL-18, IL-6, and IL-4. Our results showed that at 0 and 4 dpi the immune response was activated toward Th1 and Th2 pathways in pre-infected kids compared to the naïve ones, however, the same immune response was developed in naïve kids as earlier as 6 dpi. We conclude that repeated H. contortus infection in kid goats induced a concomitant early activation of a Th1 and Th2 immune response resulting in the regulation of worm establishment.

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Section: Discussionmentioning

confidence: 99%

Early Transcriptome Differences Between Pre-Infected and Naïve Kid Goats Infected With Haemonchus contortus

et al. 2022

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“…In another study, the resistance or susceptibility of Creole goats to gastrointestinal nematodes was studied by RNAseq (Aboshady et al, 2021). Aboshady et al (2021) reported that the T-cell receptor signaling pathway was one of the top significant pathways that distinguish the resistant from the susceptible genotype, with 78% of the genes involved in this pathway showing genomic variants in Creole goats. This shows another important example of applying omics for selecting diseaseresistant animals.…”

Section: Transcriptomicsmentioning

confidence: 99%

Applications of Omics Technology for Livestock Selection and Improvement

et al. 2022

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Conventional animal selection and breeding methods were based on the phenotypic performance of the animals. These methods have limitations, particularly for sex-limited traits and traits expressed later in the life cycle (e.g., carcass traits). Consequently, the genetic gain has been slow with high generation intervals. With the advent of high-throughput omics techniques and the availability of multi-omics technologies and sophisticated analytic packages, several promising tools and methods have been developed to estimate the actual genetic potential of the animals. It has now become possible to collect and access large and complex datasets comprising different genomics, transcriptomics, proteomics, metabolomics, and phonemics data as well as animal-level data (such as longevity, behavior, adaptation, etc.,), which provides new opportunities to better understand the mechanisms regulating animals’ actual performance. The cost of omics technology and expertise of several fields like biology, bioinformatics, statistics, and computational biology make these technology impediments to its use in some cases. The population size and accurate phenotypic data recordings are other significant constraints for appropriate selection and breeding strategies. Nevertheless, omics technologies can estimate more accurate breeding values (BVs) and increase the genetic gain by assisting the section of genetically superior, disease-free animals at an early stage of life for enhancing animal productivity and profitability. This manuscript provides an overview of various omics technologies and their limitations for animal genetic selection and breeding decisions.

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“…Aboshady identified variants in the GIN-sensitive or GIN-resistant creole goat genome by RNA seq, and the T-cell receptor signaling pathway was one of the most important pathways to distinguish the resistant from the susceptible genotypes, with 78% of the genes in this pathway showing a genomic variation. These genomic variants are expected to provide a useful resource for the molecular breeding of GIN resistance in goats [ 10 ]. Liu performed a comprehensive transcriptome and proteome analysis of goat skin at 45, 108 and 365 days of age, and found that the KRT and collagen α family proteins may play an important role in the development of the goat hair follicle and wool bending, providing a theoretical basis for revealing the molecular mechanism of goat wool bending [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

Combined Transcriptomic and Proteomic of Corynebacterium pseudotuberculosis Infection in the Spleen of Dairy Goats

Cheng

et al. 2022

Animals

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Corynebacterium pseudotuberculosis (C. pseudotuberculosis) is a zoonotic chronic infectious disease. It mainly occurs in dairy goats reared in herds, and once it invades the dairy goats, it is difficult to completely remove it, causing great harm to the development of the sheep industry. This study mainly was based on TMT-based quantitative proteomics and RNA-seq methods to measure the spleen samples of infected dairy goats at different time periods. Nine four-month-old dairy goats were divided into three groups, with three goats in each group. The dairy goats in the first group (NC group) were inoculated with 1.0 mL of sterilized normal saline subcutaneously, and the second (72 h group) and third groups (144 h group) were inoculated with 1.0 mL of 1 × 107 cfu/mL bacterial solution subcutaneously in the neck. Significant changes in the protein and mRNA expression were observed in different infection and control groups. In the 72 h group, 85 genes with differential genes and proteins were up-regulated and 91 genes were down-regulated in this study. In the 144 h group, 38 genes with differential genes and proteins were up-regulated and 51 genes were down-regulated. It was found that 21 differentially expressed genes and proteins were co-up-regulated in the two groups. There were 20 differentially expressed genes and proteins which were co-down-regulated in both groups. The 72 h group were mainly enriched in protein processing in the endoplasmic reticulum, lysosome, amino sugar and nucleotide sugar metabolism and the estrogen signaling pathway. In the 144 h group, they were protein processing in the endoplasmic reticulum pathway which was enriched by mRNA–proteins pairs co-upregulated by the five pairs. The combined transcriptomic and proteomic analyses were performed to provide insights into the effects of C. pseudotuberculosis through several regulatory features and pathways. We found that in the early stage of infection (72 h), the co-upregulated gene–protein pairs were enriched in multiple pathways, which jointly defended against a bacterial invasion. However, in the later stages of infection (144 h), when the disease stabilizes, a few co-upregulated gene–protein pairs played a role in protein processing in the endoplasmic reticulum pathway. In addition, the mRNA and protein expressions of dairy goats infected with the bacteria at different periods of time indicated the adaptability of dairy goats to the bacteria. At the same time, it guides us to carry out a corresponding treatment and feeding management for dairy goats according to different periods of time.

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Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection

Cited by 6 publications

References 45 publications

Early Transcriptome Differences Between Pre-Infected and Naïve Kid Goats Infected With Haemonchus contortus

Early Transcriptome Differences Between Pre-Infected and Naïve Kid Goats Infected With Haemonchus contortus

Applications of Omics Technology for Livestock Selection and Improvement

Combined Transcriptomic and Proteomic of Corynebacterium pseudotuberculosis Infection in the Spleen of Dairy Goats

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