Genome-Wide Association and Genomic Selection for Resistance to Amoebic Gill Disease in Atlantic Salmon

Abstract Amoebic gill disease (AGD) is one of the largest threats to salmon aquaculture, causing serious economic and animal welfare burden. Treatments can be expensive and environmentally damaging, hence the need for alternative strategies. Breeding for disease resistance can contribute to prevention and control of AGD, providing long-term cumulative benefits in selected stocks. The use of genomic selection can expedite selection for disease resistance due to improved accuracy compared to pedigree-based approaches. The aim of this work was to quantify and characterize genetic variation in AGD resistance in salmon, the genetic architecture of the trait, and the potential of genomic selection to contribute to disease control. An AGD challenge was performed in ∼1,500 Atlantic salmon, using gill damage and amoebic load as indicator traits for host resistance. Both traits are heritable (h2 ∼0.25-0.30) and show high positive correlation, indicating they may be good measurements of host resistance to AGD. While the genetic architecture of resistance appeared to be largely polygenic in nature, two regions on chromosome 18 showed suggestive association with both AGD resistance traits. Using a cross-validation approach, genomic prediction accuracy was up to 18% higher than that obtained using pedigree, and a reduction in marker density to ∼2,000 SNPs was sufficient to obtain accuracies similar to those obtained using the whole dataset. This study indicates that resistance to AGD is a suitable trait for genomic selection, and the addition of this trait to Atlantic salmon breeding programs can lead to more resistant stocks.</jats:p

Prevalence and tick loads in Nguni cattle reared in different environmental conditions across four provinces of South Africa

BACKGROUND AND AIM: In tropical and subtropical countries, ixodid ticks are among livestock’s most economically important ectoparasites. Although Nguni cattle from South Africa have adapted to harsh environments, it is unknown whether they will be resistant to ticks, and the diseases carried by ticks under various climatic conditions. Therefore, this study aimed to compare tick load and estimate the prevalence of different tick species among Nguni cattle under different environmental conditions. MATERIALS AND METHODS: Tick counts were conducted monthly under natural challenges over 2 years on 586 Nguni cattle located at ARC-Roodeplaat and Loskop farms (warmer climate), Mukhuthali Nguni Community and the University of Fort Hare farms (cooler climate). The generalized linear model procedure of the Statistical Analysis System was used to analyze the data. It fitted the location (farm), sex, year, month or season, and animal age as covariates. RESULTS: The tick species (relative prevalence) observed were as follows: Amblyomma hebraeum (42%), Rhipicephalus evertsi (22%), Rhipicephalus (Boophilus) spp. (16%), Rhipicephalus appendiculatus (11%), Hyalomma marginatum (5%), and Rhipicephalus simus (4%). Tick infestation was significantly affected by location, season, year, month of the tick counting and age of the animal. Loskop farm had the highest tick count (m = 30.69) and showed the largest variation in tick count. Compared to the other seasons, higher tick counts were seen during the hot-dry (September–November) and hot-wet (December–February) seasons. A. hebraeum was the dominant tick species across all four farms, followed by R. evertsi. The perianal region (under the tail head), the perineum and the belly body locations were the most preferred tick attachment sites. CONCLUSION: These results provide useful information for developing appropriate control strategies for ticks and tick-borne diseases in these provinces of South Africa. Further work must investigate the feasibility of genetic improvement for tick resistance

Genetic Analysis of Reproductive Traits and Antibody Response in PRRS Infected Sows

The genetic components of reproductive performance and antibody response of 641 commercial sows were assessed in a commercial herd that faced a PRRS outbreak. Antibody response after the PRRS outbreak was highly heritable and had high genetic correlations with reproductive traits. Many genomic regions were associated with antibody response in this study. These results indicate that there is a significant genomic component associated with PRRS antibody response and its high genetic correlations with reproductive traits during PRRS suggest that this trait could be used as an indicator trait to reduce the impact of PRRS on reproductive performance

Genomic Regions Underlying Susceptibility to Bovine Tuberculosis in Holstein-Friesian Cattle

BACKGROUND: The significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle susceptibility to bTB provides an opportunity to select for resistant animals and further understand the genetic mechanisms underlying disease dynamics. METHODS: The present study identified genomic regions associated with susceptibility to bTB using genome-wide association (GWA), regional heritability mapping (RHM) and chromosome association approaches. Phenotypes comprised de-regressed estimated breeding values of 804 Holstein-Friesian sires and pertained to three bTB indicator traits: i) positive reactors to the skin test with positive post-mortem examination results (phenotype 1); ii) positive reactors to the skin test regardless of post-mortem examination results (phenotype 2) and iii) as in (ii) plus non-reactors and inconclusive reactors to the skin tests with positive post-mortem examination results (phenotype 3). Genotypes based on the 50 K SNP DNA array were available and a total of 34,874 SNPs remained per animal after quality control. RESULTS: The estimated polygenic heritability for susceptibility to bTB was 0.26, 0.37 and 0.34 for phenotypes 1, 2 and 3, respectively. GWA analysis identified a putative SNP on Bos taurus autosomes (BTA) 2 associated with phenotype 1, and another on BTA 23 associated with phenotype 2. Genomic regions encompassing these SNPs were found to harbour potentially relevant annotated genes. RHM confirmed the effect of these genomic regions and identified new regions on BTA 18 for phenotype 1 and BTA 3 for phenotypes 2 and 3. Heritabilities of the genomic regions ranged between 0.05 and 0.08 across the three phenotypes. Chromosome association analysis indicated a major role of BTA 23 on susceptibility to bTB. CONCLUSION: Genomic regions and candidate genes identified in the present study provide an opportunity to further understand pathways critical to cattle susceptibility to bTB and enhance genetic improvement programmes aiming at controlling and eradicating the disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-017-0493-7) contains supplementary material, which is available to authorized users

Prevalence and risk factors of gastrointestinal parasitic infections in goats in low-input low-output farming systems in Zimbabwe

AbstractA longitudinal study was conducted in low-input low-output farming systems to determine the prevalence of gastrointestinal parasitic infections in different age groups, sex and associated risk factors in goats. A total of 580 indigenous goats were randomly selected in areas representing the five agro-ecological regions of Zimbabwe in the dry and wet seasons. Blood and faecal samples were collected from each animal and egg/oocyst per gram of faeces (epg/opg), larval culture, and packed cell volumes (PCV) were determined. Factors affecting parasitic infections were evaluated. Highest prevalence was determined for Eimeria oocysts (43%), strongyles (31%) and lower levels in trematodes and cestodes. Parasites identified were Haemonchus, Strongyloides and Oesophagostomum. Area, season, sex and age significantly influenced patterns of gastrointestinal infections (P<0.05). Cannonical correlations indicated that parasite species composition varied by area and impacts of risk factors also differed. Risk of infection was very high for goats sampled in Natural regions (NR) I, II, III (OR=6.6–8.2; P<0.05) as compared to those in NR IV and V. Highest helminths and Eimeria infections were observed in the wet vs. dry season (P<0.05). Young animals were more susceptible to parasitic infections (P<0.05). Prevalence was higher in males than females, with odds of infection for males being almost three times to that for females (P<0.0001). Knowledge concerning gastrointestinal helminth biology and epidemiological infection patterns caused by these parasites is essential in the development of appropriate control strategies and this has a potential to reduce production losses