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This paper reviews the evidence for host genetic variation in resistance to infectious diseases for a wide variety of diseases of economic importance in poultry, cattle, pig, sheep and Atlantic salmon. Further, it develops a method of ranking each disease in terms of its overall impact, and combines this ranking with published evidence for host gen...
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... to these advances, swine Salmonella is a good OG candidate pathogen. Table 3 shows a summary of the nine pig pathogens and diseases, ranked as previously described. The highest priority diseases or pathogens highlighted by this approach are E. coli, PRRS and Salmonella, broadly reflecting ongoing research efforts in Europe and North America. ...
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Marek’s disease (MD) is a lymphoproliferative disease of poultry induced by Marek’s disease virus (MDV), a highly oncogenic alphaherpesvirus. Identifying the underlying genes conferring MD genetic resistance is desired for more efficacious control measures including genomic selection, which requires accurately identified genetic markers throughout...
Farming practices have changed dramatically over the years. The industrialization of farming has provided parasites with an abundance of hosts and is thought to have influenced parasite evolution. For example, the parasite that causes the highly contagious poultry disease, Marek's disease, has evolved over the past 60 years into a highly virulent p...
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... The NRAMP gene in many previous studies was polymorphic and associated with pathogenic bacterial resistance traits. Infections by pathogenic bacteria have been reported as main factor of economic losses and lower productivity of livestock (Davies et al., 2009). Several diseases in cattle that are caused by pathogenic bacteria are Mastitis and Leptospirosis. ...
The pathogenic bacterial infection is the main cause of decreased cow productivity. This study aimed to investigate the relationship of Natural Resistance Associated Macrophage Protein 1 (NRAMP1) gene polymorphisms with pathogenic bacterial resistance traits in Indonesian cattle. A total of seventeen (17) animals of mixed-breed cattle comprising two categories healthy (7 heads) and infected with bacteria (10 heads) were used in this study. Forward sequencing analysis was performed to detect single nucleotide polymorphisms (SNPs) in the partial NRAMP1 gene (954 bp) using polymerase chain reaction (PCR). Results showed that a novel SNP of g.109Y (intron 5) and two common SNPs of g.221K (intron 5) and g.642R (intron 6) were detected in the NRAMP gene in Indonesian native cattle. In addition, these SNPs have a moderate polymorphic information content (PIC) value (0.30 - 0.50). Therefore, eight (8) haplotypes of the NRAMP1 gene were determined in the present study. Thus, the highest bacterial infection frequency was shown in the TT/GT/AG haplotype. In conclusion, three (3) nonsense SNP in the NRAMP1 gene have the potency as a genetic marker for bacterial resistance trait in Indonesian cattle
... Conventional genetic improvement programs combine phenotypic measurements with pedigree information. Phenotypic measurements involve measuring traits such as disease incidence, severity, or pathogen load in host populations [18]. A pedigree is a family tree that keeps records over multiple generations and is maintained through physical tagging methods, such as PIT tags for fish and visible elastomer tags for crustaceans or DNA markers. ...
Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease- and species-specific and contingent upon a multitude of factors. The field of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favourable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate to high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems, AI algorithms, and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.
... In order to improve disease resistance, a genetic strategy could be used in conjunction with current control methods [28]. The use of genomic selection in numerous nations and the discovery of genomic areas linked to disease resistance traits are the results of advancements in animal genome sequencing technologies [29]. This two-fold effect makes it easier to incorporate information about disease-resistant loci into animal breeding [30]. ...
The immune and antioxidant genetic factors that could converse with mastitis susceptibility in dromedary camels were looked at in this research. Of 120 female dromedary camels (60 healthy, and 60 with mastitis) were utilised. Each camel's jugular vein was pierced to obtain five millilitres of blood. The blood was placed within tubes containing sodium fluoride or EDTA anticoagulants to obtain whole blood and extract DNA and RNA. The immunological (OTUD3, TLR2, TLR4, STAB2, MBL2, TRAPPC9, and C4A) and antioxidant (CAT, SOD3, PRDX6, OXSR1, NDUFS6, SERP2, and ST1P1) genes' nucleotide sequence polymorphisms between healthy and mastitis affected she-camels were discovered using PCR-DNA sequencing. Fisher's exact test revealed that camel groups with and without mastitis had noticeably different odds of all major nucleotide alterations propagating (p < 0.01). Mastitic camels were significantly more likely to express the OTUD3, TLR2, TLR4, STAB2, MBL2, TRAPPC9, C4A, OXSR1, SERP2, and ST1P1 genes (p < 0.05). However, CAT, SOD3, PRDX6, and NDUFS6 genes elicited a different pattern. The results may be used to develop management strategies and support the significance of nucleotide differences and gene expression patterns in these markers as indicators of the incidence of mastitis.
... The average flock size varies from small to medium (140 to 333 ewes/farm), and the average milk yield ranges from low to middle (170 to 500 L/ewe) [7], showing substantial space for improvement in relation to cows' milk [8]. Furthermore, sheep milk has higher protein, fat, lactose, total non-fat solids, and ash contents and a higher nutritional value than cows' and goats' milk [9], which makes it suitable for processing into various types of dairy products. Most sheep milk is sold to industries and then processed into traditional cheese products, most of which are made into Protected Denomination of Origin (PDO) cheeses for gourmets. ...
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In our research, candidate genes related to sheep-milk production were revealed by a genome-resequencing analysis and a genome-signal-selection analysis, and a RT-qPCR experiment was performed to prove the expression levels of these candidate genes, the results showed that the FCGR3A gene’s expression level had a significant negative relationship with sheep-milk production.
Abstract
Natural selection and domestication have shaped modern sheep populations into a vast range of phenotypically diverse breeds. Among these breeds, dairy sheep have a smaller population than meat sheep and wool sheep, and less research is performed on them, but the lactation mechanism in dairy sheep is critically important for improving animal-production methods. In this study, whole-genome sequences were generated from 10 sheep breeds, including 57 high-milk-yield sheep and 44 low-milk-yield sheep, to investigate the genetic signatures of milk production in dairy sheep, and 59,864,820 valid SNPs (Single Nucleotide Polymorphisms) were kept after quality control to perform population-genetic-structure analyses, gene-detection analyses, and gene-function-validation analyses. For the population-genetic-structure analyses, we carried out PCA (Principal Component Analysis), as well as neighbor-joining tree and structure analyses to classify different sheep populations. The sheep used in our study were well distributed in ten groups, with the high-milk-yield-group populations close to each other and the low-milk-yield-group populations showing similar classifications. To perform an exact signal-selection analysis, we used three different methods to find SNPs to perform gene-annotation analyses within the 995 common regions derived from the fixation index (FST), nucleotide diversity (Ɵπ), and heterozygosity rate (ZHp) results. In total, we found 553 genes that were located in these regions. These genes mainly participate in the protein-binding pathway and the nucleoplasm-interaction pathway, as revealed by the GO- and KEGG-function-enrichment analyses. After the gene selection and function analyses, we found that FCGR3A, CTSK, CTSS, ARNT, GHR, SLC29A4, ROR1, and TNRC18 were potentially related to sheep-milk-production traits. We chose the strongly selected genes, FCGR3A, CTSK, CTSS, and ARNT during the signal-selection analysis to perform a RT-qPCR (Reale time Quantitative Polymerase Chain Reaction) experiment to validate their expression-level relationship with milk production, and the results showed that FCGR3A has a significant negative relationship with sheep-milk production, while other three genes did not show any positive or negative relations. In this study, it was discovered and proven that the candidate gene FCGR3A potentially contributes to the milk production of dairy sheep and a basis was laid for the further study of the genetic mechanism underlying the strong milk-production traits of sheep.
... For this reason, animal breeders and farmers are searching for robust strains of animals, able to cope with environmental stresses and to resist epizootics. However, a measure of individual responses to diseases resistance that is accurate, cheap, heritable and easy to perform on farm is difficult to obtain (Davies et al., 2009;Bishop and Woolliams, 2014). In this study, we performed a selection experiment to improve the general resistance of animals to the various diseases they may encounter. ...
... Mastitis is still one of the major diseases affecting dairy cattle, with negative effects on milk production (Davies et al., 2009). Despite the wealth of research performed on the physiological and cellular processes taking place in the mammary gland in response to infection, knowledge of many of the defense mechanisms remains incomplete (Sordillo, 2005). ...
The aim of this study was to evaluate the association between gene polymorphisms (SNPs) and mastitis indicators and their relationship with milk production profitability in dairy herd.A functional analysis was also performed of five genes containing the studied SNPs and those located close by. DNA was isolated from the hair bulb of 320 dairy cows kept in three herds and SNP-microarray analysis was performed. The data on 299 cows was subjected to final statistical analysis using AI-REML method with one-trait repeatability test-day animal model and pedigree information using the DMU4 package. Five from 35 SNPs significantly associated with mastitis indicators or production traits and located within a gene or no more than 500,000 nucleotides from the gene were selected for the functional and economic analysis. A questionnaire was also developed to collect associated economic data of 219 cows from three herds, such as the value of milk production and direct costs incurred over three years; this allowed the gross margin, direct profitability index and direct costs incurred to produce one liter of milk to be determined, among others. None of the five studied SNPs were related to protein content. The rs110785912(T/A), found near CXCR4 , and rs136813430(T/C), located in the TLR4 gene exon, were associated with lnSCC, while rs110455063(C/G), located near IGFI , was associated with milk yield, fat and total solid contents. rs109421300(T/C), associated with fat/protein content ratio, as well as fat and total solid content, is located in the DGAT1 gene intron. rs41587003(A/C), located in the DLG2 gene intron, was associated with lactose content. The economic analysis revealed differences between the variants of the three tested SNPs. The T/C variant of the rs136813430(T/C) SNP was characterized by the highest gross margin, the highest direct profitability index and the lowest costs incurred to produce 1 liter of milk. The T/A variant of rs110785912(T/A) was related to low lnSCC and was characterized by the highest direct profitability index. In turn, the C/C variant of the rs41587003(T/C) was related to the lowest level of lactose and the highest costs of milk production. It appears that rs136813430(T/C) may be the most promising of the tested SNPs for increasing the profitability of milk production. To our knowledge, it is the first effort to assess directly a correlation between the DNA polymorphism and economic output of a dairy enterprise.
... Infectious diseases have steadily increased morbidity and mortality in multiplication and production herds of the pig industry, which causes a significant loss of productivity. Moreover, infectious diseases also threaten food safety, animal welfare, and cause international trade restrictions to the industry (Davies et al. 2009;Tomley and Shirley 2009). The constant threats of infection have resulted in significant economic losses to the pig industry, which in some instances (e.g. ...
... The results will depend on the level of disease challenge in the different farms as well as the different pathogens present. As there is genetic variation in resistance (an animal's ability to maintain health or restrict the proliferation of pathogens and reduce within-host pathogen burden) to almost all pig pathogens, there is the potential to dissect and select for genetic resistance to infectious diseases (Davies et al. 2009;Plastow 2016). Indeed, PIC used simultaneous collection of purebred and crossbred records from nucleus sires to improve disease robustness as measured by grow-finish mortality (Newman et al. 2010). ...
... PIC is currently exploring the use of gene edited pigs to deliver resistance to PRRSV (Burkhard et al. 2017;PIC 2021). However, as there are many different pathogens impacting pig health and performance it may be an endless task to take this approach, although it may play a role for the major diseases such as PRRS and E. coli associated scours that were strongly justified as targets for genomic studies (Davies et al. 2009), and potentially for diseases such as ASF in the future. Alternatively, disease resilience, defined as an animal's ability to maintain high production levels despite disease and potentially applicable to multiple pathogens, has been identified as a desirable breeding goal and trait for pig breeding programs (Albers et al. 1987;Harlizius et al. 2020;Mulder and Rashidi 2017). ...
Disease resilience, defined as an animal’s ability to maintain productive performance in the face of infection, provides opportunities to manage the polymicrobial challenge common in pig production. Disease resilience can deliver a number of benefits, including more sustainable production as well as improved animal health and the potential for reduced antimicrobial use. However, little progress has been made to date in the application of disease resilience in breeding programs due to a number of factors, including (1) confusion around definitions of disease resilience and its component traits disease resistance and tolerance, and (2) the difficulty in characterizing such a complex trait consisting of multiple biological functions and dynamic elements of rates of response and recovery from infection. Accordingly, this review refines the definitions of disease resistance, tolerance, and resilience based on previous studies to help improve the understanding and application of these breeding goals and traits under different scenarios. We also describe and summarize results from a “natural disease challenge model” designed to provide inputs for selection of disease resilience. The next steps for managing polymicrobial challenges faced by the pig industry will include the development of large-scale multi-omics data, new phenotyping technologies, and mathematical and statistical methods adapted to these data. Genome editing to produce pigs resistant to major diseases may complement selection for disease resilience along with continued efforts in the more traditional areas of biosecurity, vaccination and treatment. Altogether genomic approaches provide exciting opportunities for the pig industry to overcome the challenges provided by hard-to-manage diseases as well as new environmental challenges associated with climate change.
... This is motivated by the need to obtain chemical and drug-free animal products, to avoid antibiotics, anthelmintics and acaricides resistance, and to minimize the impact on animal welfare [4][5][6][7]. Therefore, there is a need for complementary control strategies, such as the selection and breeding of animals with increased resistance to infection and disease [3,8]. ...
Diseases caused by ticks have a high impact on the health, welfare, and productivity of livestock species. They are also an important cause of economic losses in farms worldwide. An example of such diseases is theileriosis, which can be controlled by drugs or vaccines, although these are not fully efficient. Therefore, there is a need to develop alternative and more sustainable and efficient complementary strategies. These may involve the identification and selection of animals more resistant to the disease. Several previous studies have identified significant differences in resistance between different breeds, with resistant breeds typically identified as those native to the region where they are being studied, and susceptible as those from exotic breeds. These studies have indicated that resistance traits are intrinsically related to the modulation of the immune response to infection. This review aims to systematize the general knowledge about theileriosis, emphasize resistance to this disease as a sustainable control strategy, and identify which traits of resistance to the disease are already known in cattle.
... Similarly, Pathak et al. [9], on using RNA-Seq approach, reported an enriched and better immune response in crossbred piglets after CSF vaccination as compared to indigenous (desi) pigs. Considerable variations in individuals' response against diseased states and vaccination can be partially ascribed to genetic causes [10]. In order to further explore the host-pathogen interactions and to identify the biomolecules involved in host tolerance mechanisms, comprehensive and accurate identification of cellular genes that exhibit altered expression during infection is crucial [11]. ...
The present study was undertaken to characterize the distinct immune response in indigenous Ghurrah and exotic Landrace pigs by challenging monocyte-derived macrophages (MDMs) with CSF virus under in-vitro conditions and assessing the variations in the transcriptome profile at 48 h post-infection (hpi). RNA-sequencing was carried out in infected and non-infected MDMs of Ghurrah (n = 3) and Landrace (n = 3) piglets prior- as well as post-stimulation. MDMs of Ghurrah showed greater immune regulation in response to CSF infection with 518 significantly differentially expressed genes (DEG) in infected versus non-infected MDMs, as compared to only 31 DEGs in Landrace MDMs. In Landrace, the principal regulators of inflammation (IL1α, IL1β and TNF) were upregulated in infected cells while in Ghurrah, these were downregulated. Overall, macrophages from indigenous Ghurrah showed more immunological dysregulation in response to virulent CSF virus infection as compared to the exotic Landrace pigs.
... Resilience traits in the present study focus primarily on traits associated with disease resistance, and especially on mastitis, gastrointestinal parasitism and footrot as these are the main infectious diseases of sheep and goats with respect to industry and public concern, economic impact, zoonotic potential and animal welfare (Davies et al., 2009). In meat sheep, lamb survival and longevity were included as additional resilience traits. ...
Genetic selection focused purely on production traits has proven very successful in improving the productive performance of livestock. However, heightened environmental and infectious disease challenges have raised the need to also improve the resilience of animals to such external stressors, as well as their efficiency in utilising available resources. A better understanding of the relationship between efficiency and production and health traits is needed to properly account for it in breeding programmes and to produce animals that can maintain high production performance in a range of environmental conditions with minimal environmental footprint. The aim of this study was to perform a meta-analysis of genetic parameters for production, efficiency and health traits in sheep and goats. The dataset comprised 963 estimates of heritability and 572 genetic correlations collated from 162 published studies. A threelevel meta-analysis model was fitted. Pooled heritability estimates for milk production traits ranged between 0.27 ± 0.03 and 0.48 ± 0.13 in dairy goats and between 0.21 ± 0.06 and 0.33 ± 0.07 in dairy sheep. In meat sheep, the heritability of efficiency traits ranged from 0.09 ± 0.02 (prolificacy) up to 0.32 ± 0.14 (residual feed intake). For health traits, pooled heritability was 0.07 ± 0.01 (faecal egg count) and 0.21 ± 0.01 (somatic cell score) in dairy goats and 0.14 ± 0.04 (faecal egg count) and 0.13 ± 0.02 (somatic cell score) in dairy sheep. In meat sheep, the heritability of disease resistance and survival traits ranged between 0.07 ± 0.02 (mastitis) and 0.50 ± 0.10 (breech strike). Pooled estimates of genetic correlations between resilience and efficiency traits in dairy goats were not significantly different from zero with the exception of somatic cell score and fat content (−0.19 ± 0.01). In dairy sheep, only the unfavourable genetic correlation between somatic cell score and protein content (0.12 ± 0.03) was statistically significant. In meat sheep only, the correlations between growth and faecal egg count (−0.28 ± 0.11) as well as between growth and dagginess (−0.33 ± 0.13) were statistically significant and favourable. Results of this meta-analysis provide evidence of genetic antagonism between production and health in dairy sheep and goats. This was not observed in meat sheep where most of the pooled estimates had high standard errors and were non-significant. Based on the obtained results, it seems feasible to simultaneously improve efficiency and health in addition to production by including the different types of traits in the breeding goal. However, a better understanding of potential trade-offs between these traits would be beneficial. Particularly, more studies focused on reproduction and resilience traits linked to the animal’s multi-trait response to challenges are required.
