Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping.

Identifying associations between phenotype and genotype is the fundamental basis of genetic analyses. Inspired by frequentist probability and the work of R.A. Fisher, genome-wide association studies (GWAS) extract information using averages and variances from genotype-phenotype datasets. Averages and variances are legitimated upon creating distribution density functions obtained through the grouping of data into categories. However, as data from within a given category cannot be differentiated, the investigative power of such methodologies is limited. Genomic Informational Field Theory (GIFT) is a method specifically designed to circumvent this issue. The way GIFT proceeds is opposite to that of GWAS. Whilst GWAS determines the extent to which genes are involved in phenotype formation (bottom-up approach), GIFT determines the degree to which the phenotype can select microstates (genes) for its subsistence (top-down approach). Doing so requires dealing with new genetic concepts, a.k.a. genetic paths, upon which significance levels for genotype-phenotype associations can be determined. By using different datasets obtained in ovis aries related to bone growth (Dataset-1) and to a series of linked metabolic and epigenetic pathways (Dataset-2), we demonstrate that removing the informational barrier linked to categories enhances the investigative and discriminative powers of GIFT, namely that GIFT extracts more information than GWAS. We conclude by suggesting that GIFT is an adequate tool to study how phenotypic plasticity and genetic assimilation are linked.

The potential for use of haematological and anti-IgE humoral responses as phenotypic markers for tick resistance in cattle.

Approximately 80% of the global cattle population is at risk of infestation and infection by ticks and tick-borne diseases (TTBDs). The economic losses from animal mortality, reduced production, vector control costs and animal treatment are very substantial, hence there is an urgent need to develop and deploy alternative vector control strategies. Breeding for host tick resistance has the potential for sustainable large-scale TTBD control especially in cattle. The gold standard method for phenotyping tick resistance in cattle is by counting ticks on the body but is very laborious and subjective. Better methods for phenotyping tick resistance more objectively, faster and at scale, are essential for selecting host genetic resistance to ticks. This study investigated the correlation between haematological cellular profiles and immunological responses (immunoglobulin E, IgE) and full body tick counts in herds of Bos indicus and Bos taurus following artificial tick challenge with Rhipicephalus decoloratus larvae. Fifty-four Friesian and Ayrshire (Bos taurus) and 52 East African Zebu (Bos indicus) calves were each infested with ∼2500 larvae. Near-replete adult female ticks (≥ 4.5 mm) were counted daily from Day 20-25. Blood and serum samples were obtained from each animal on Days 0 and 23 for cellular blood and IgE titre analysis, respectively. The indicine cattle were refractory to R. decoloratus infestation in comparison with the taurine breed (P < 0.0001). Repeated measurements of blood components pre-infestation revealed a significant (P < 0.05) association with tick count in IgE and red blood cells, haematocrit, and haemoglobin post-infestation. There was also a strong positive correlation between the tick counts and red blood cell numbers, haemoglobin, haematocrit, and IgE concentration (P < 0.0001) following tick challenge. The application of this approach to phenotype host resistance needs to be assessed using higher cattle numbers and with different tick species or genera.

Exploring the value of genomic predictions to simultaneously improve production potential and resilience of farmed animals.

Sustainable livestock production requires that animals have a high production potential but are also highly resilient to environmental challenges. The first step to simultaneously improve these traits through genetic selection is to accurately predict their genetic merit. In this paper, we used simulations of sheep populations to assess the effect of genomic data, different genetic evaluation models and phenotyping strategies on prediction accuracies and bias for production potential and resilience. In addition, we also assessed the effect of different selection strategies on the improvement of these traits. Results show that estimation of both traits greatly benefits from taking repeated measurements and from using genomic information. However, the prediction accuracy for production potential is compromised, and resilience estimates tends to be upwards biased, when families are clustered in groups even when genomic information is used. The prediction accuracy was also found to be lower for both traits, resilience and production potential, when the environment challenge levels are unknown. Nevertheless, we observe that genetic gain in both traits can be achieved even in the case of unknown environmental challenge, when families are distributed across a large range of environments. Simultaneous genetic improvement in both traits however greatly benefits from the use of genomic evaluation, reaction norm models and phenotyping in a wide range of environments. Using models without the reaction norm in scenarios where there is a trade-off between resilience and production potential, and phenotypes are collected from a narrow range of environments may result in a loss for one trait. The study demonstrates that genomic selection coupled with reaction-norm models offers great opportunities to simultaneously improve productivity and resilience of farmed animals even in the case of a trade-off.

Investigating volatile semiochemical production from Bos taurus and Bos indicus as a novel phenotype for breeding host resistance to ixodid ticks.

Ticks and tick-borne diseases cause significant loss in livestock production with about 80% world's cattle at risk. The cost of chemical control is high and there is an ever-increasing tick resistance to chemical acaricides. Genetic selection as alternative long-term control strategy is constrained by laborious phenotyping using tick counts or scores. This study explored the use of host volatile semiochemicals that may be attractants or repellents to ticks as a phenotype for new tick resistance, with potential to be used as a proxy in selection programmes. Approximately 100 young cattle composed of Bos indicus and Bos taurus were artificially infested with 2,500 African blue tick, Rhipicephalus decoloratus larvae, with daily female tick (4.5 mm) counts taken from day 20 post-infestation. Volatile organic compounds were sampled from cattle before and after tick infestation by dynamic headspace collection, analysed by high-resolution gas chromatography (GC) and subjected to multivariate statistical analysis. Using 6-day repeated measure analysis, three pre-infestation GC peaks (BI938 - unknown, BI966 - 6-methyl-5-hepten-2-one and BI995 - hexyl acetate) and one post-infestation GC peak (AI933 - benzaldehyde / (E)-2-heptenal) were associated with tick resistance (P < 0.01 and P < 0.05 respectively). The high correlation coefficients (r = 0.66) between repeated records with all volatile compounds support the potential predictive value for volatile compounds in selective breeding programmes for tick resistance in cattle.

A locus conferring tolerance to Theileria infection in African cattle.

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Bos indicus (Boran) cattle demonstrating heritable tolerance to infection with T. parva (h2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on bovine chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained variant in a paralogue of the FAF1 gene in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa's most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva.

Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle.

Ticks cause substantial production losses for beef and dairy cattle. Cattle resistance to ticks is one of the most important factors affecting tick control, but largely neglected due to the challenge of phenotyping. In this study, we evaluate the pooling of tick resistance phenotyped reference populations from multi-country beef cattle breeds to assess the possibility of improving host resistance through multi-trait genomic selection. Data consisted of tick counts or scores assessing the number of female ticks at least 4.5 mm length and derived from seven populations, with breed, country, number of records and genotyped/phenotyped animals being respectively: Angus (AN), Brazil, 2,263, 921/1,156, Hereford (HH), Brazil, 6,615, 1,910/2,802, Brangus (BN), Brazil, 2,441, 851/851, Braford (BO), Brazil, 9,523, 3,062/4,095, Tropical Composite (TC), Australia, 229, 229/229, Brahman (BR), Australia, 675, 675/675, and Nguni (NG), South Africa, 490, 490/490. All populations were genotyped using medium density Illumina SNP BeadChips and imputed to a common high-density panel of 332,468 markers. The mean linkage disequilibrium (LD) between adjacent SNPs varied from 0.24 to 0.37 across populations and so was sufficient to allow genomic breeding values (GEBV) prediction. Correlations of LD phase between breeds were higher between composites and their founder breeds (0.81 to 0.95) and lower between NG and the other breeds (0.27 and 0.35). There was wide range of estimated heritability (0.05 and 0.42) and genetic correlation (-0.01 and 0.87) for tick resistance across the studied populations, with the largest genetic correlation observed between BN and BO. Predictive ability was improved under the old-young validation for three of the seven populations using a multi-trait approach compared to a single trait within-population prediction, while whole and partial data GEBV correlations increased in all cases, with relative improvements ranging from 3% for BO to 64% for TC. Moreover, the multi-trait analysis was useful to correct typical over-dispersion of the GEBV. Results from this study indicate that a joint genomic evaluation of AN, HH, BN, BO and BR can be readily implemented to improve tick resistance of these populations using selection on GEBV. For NG and TC additional phenotyping will be required to obtain accurate GEBV.

Integrating Genetic and Genomic Analyses of Combined Health Data Across Ecotypes to Improve Disease Resistance in Indigenous African Chickens.

Poultry play an important role in the agriculture of many African countries. The majority of chickens in sub-Saharan Africa are indigenous, raised in villages under semi-scavenging conditions. Vaccinations and biosecurity measures rarely apply, and infectious diseases remain a major cause of mortality and reduced productivity. Genomic selection for disease resistance offers a potentially sustainable solution but this requires sufficient numbers of individual birds with genomic and phenotypic data, which is often a challenge to collect in the small populations of indigenous chicken ecotypes. The use of information across-ecotypes presents an attractive possibility to increase the relevant numbers and the accuracy of genomic selection. In this study, we performed a joint analysis of two distinct Ethiopian indigenous chicken ecotypes to investigate the genomic architecture of important health and productivity traits and explore the feasibility of conducting genomic selection across-ecotype. Phenotypic traits considered were antibody response to Infectious Bursal Disease (IBDV), Marek's Disease (MDV), Fowl Cholera (PM) and Fowl Typhoid (SG), resistance to Eimeria and cestode parasitism, and productivity [body weight and body condition score (BCS)]. Combined data from the two chicken ecotypes, Horro (n = 384) and Jarso (n = 376), were jointly analyzed for genetic parameter estimation, genome-wide association studies (GWAS), genomic breeding value (GEBVs) calculation, genomic predictions, whole-genome sequencing (WGS), and pathways analyses. Estimates of across-ecotype heritability were significant and moderate in magnitude (0.22-0.47) for all traits except for SG and BCS. GWAS identified several significant genomic associations with health and productivity traits. The WGS analysis revealed putative candidate genes and mutations for IBDV (TOLLIP, ANGPTL5, BCL9, THEMIS2), MDV (GRM7), SG (MAP3K21), Eimeria (TOM1L1) and cestodes (TNFAIP1, ATG9A, NOS2) parasitism, which warrant further investigation. Reliability of GEBVs increased compared to within-ecotype calculations but accuracy of genomic prediction did not, probably because the genetic distance between the two ecotypes offset the benefit from increased sample size. However, for some traits genomic prediction was only feasible in across-ecotype analysis. Our results generally underpin the potential of genomic selection to enhance health and productivity across-ecotypes. Future studies should establish the required minimum sample size and genetic similarity between ecotypes to ensure accurate joint genomic selection.

Arginine to Glutamine Variant in Olfactomedin Like 3 (OLFML3) Is a Candidate for Severe Goniodysgenesis and Glaucoma in the Border Collie Dog Breed.

Goniodysgenesis is a developmental abnormality of the anterior chamber of the eye. It is generally considered to be congenital in dogs (Canis lupus familiaris), and has been associated with glaucoma and blindness. Goniodysgenesis and early-onset glaucoma initially emerged in Border Collies in Australia in the late 1990s and have subsequently been found in this breed in Europe and the USA. The objective of the present study was to determine the genetic basis of goniodysgenesis in Border Collies. Clinical diagnosis was based on results of examinations by veterinary ophthalmologists of affected and unaffected dogs from eleven different countries. Genotyping using the Illumina high density canine single nucleotide variant genotyping chip was used to identify a candidate genetic region. There was a highly significant peak of association over chromosome 17, with a p-value of 2 × 10-13 Expression profiles and evolutionary conservation of candidate genes were assessed using public databases. Whole genome sequences of three dogs with glaucoma, three severely affected by goniodysgenesis and three unaffected dogs identified a missense variant in the olfactomedin like 3 (OLFML3) gene in all six affected animals. This was homozygous for the risk allele in all nine cases with glaucoma and 12 of 14 other severely affected animals. Of 67 reportedly unaffected animals, only one was homozygous for this variant (offspring of parents both with goniodysgenesis who were also homozygous for the variant). Analysis of pedigree information was consistent with an autosomal recessive mode of inheritance for severe goniodysgenesis (potentially leading to glaucoma) in this breed. The identification of a candidate genetic region and putative causative variant will aid breeders to reduce the frequency of goniodysgenesis and the risk of glaucoma in the Border Collie population.

Balancing selection at a premature stop mutation in the myostatin gene underlies a recessive leg weakness syndrome in pigs.

Balancing selection provides a plausible explanation for the maintenance of deleterious alleles at moderate frequency in livestock, including lethal recessives exhibiting heterozygous advantage in carriers. In the current study, a leg weakness syndrome causing mortality of piglets in a commercial line showed monogenic recessive inheritance, and a region on chromosome 15 associated with the syndrome was identified by homozygosity mapping. Whole genome resequencing of cases and controls identified a mutation causing a premature stop codon within exon 3 of the porcine Myostatin (MSTN) gene, similar to those causing a double-muscling phenotype observed in several mammalian species. The MSTN mutation was in Hardy-Weinberg equilibrium in the population at birth, but significantly distorted amongst animals still in the herd at 110 kg, due to an absence of homozygous mutant genotypes. In heterozygous form, the MSTN mutation was associated with a major increase in muscle depth and decrease in fat depth, suggesting that the deleterious allele was maintained at moderate frequency due to heterozygous advantage (allele frequency, q = 0.22). Knockout of the porcine MSTN by gene editing has previously been linked to problems of low piglet survival and lameness. This MSTN mutation is an example of putative balancing selection in livestock, providing a plausible explanation for the lack of disrupting MSTN mutations in pigs despite many generations of selection for lean growth.

The Genomic Architecture of Fowl Typhoid Resistance in Commercial Layers.

Salmonella enterica serovar Gallinarum causes devastating outbreaks of fowl typhoid across the globe, especially in developing countries. With the use of antimicrobial agents being reduced due to legislation and the absence of licensed vaccines in some parts of the world, an attractive complementary control strategy is to breed chickens for increased resistance to Salmonella. The potential for genetic control of salmonellosis has been demonstrated by experimental challenge of inbred populations. Quantitative trait loci (QTL) associated with resistance have been identified in many genomic regions. A major QTL associated with systemic salmonellosis has been identified in a region termed SAL1. In the present study, two outbreaks of fowl typhoid in 2007 and 2012 in the United Kingdom were used to investigate the genetic architecture of Salmonella resistance in commercial laying hens. In the first outbreak 100 resistant and 150 susceptible layers were genotyped using 11 single nucleotide polymorphism (SNP) and 3 microsatellite markers located in the previously identified SAL1 region on chromosome 5. From the second outbreak 100 resistant and 200 susceptible layers, belonging to a different line, were genotyped with a high-density (600 K) genome-wide SNP array. Substantial heritability estimates were obtained in both populations (h 2 = 0.22 and 0.26, for the layers in the first and second outbreak, respectively). Significant associations with three markers on chromosome 5 located close to AKT1 and SIVA1 genes, coding for RAC-alpha serine/threonine protein kinase, and the CD27-binding protein SIVA1, respectively, were identified in the first outbreak. From analysis of the second outbreak, eight genome-wide significant associations with Salmonella resistance were identified on chromosomes 1, 6, 7, 11, 23, 24, 26, 28 and several others with suggestive genome-wide significance were found. Pathway and network analysis revealed the presence of many innate immune pathways related to Salmonella resistance. Although, significant associations with SNPs located in the SAL1 locus were not identified by the genome-wide scan for layers from the second outbreak, pathway analysis revealed P13K/AKT signaling as the most significant pathway. In summary, resistance to fowl typhoid is a heritable polygenic trait that could possibly be enhanced through selective breeding.

Dissecting the Genomic Architecture of Resistance to Eimeria maxima Parasitism in the Chicken.

Coccidiosis in poultry, caused by protozoan parasites of the genus Eimeria, is an intestinal disease with substantial economic impact. With the use of anticoccidial drugs under public and political pressure, and the comparatively higher cost of live-attenuated vaccines, an attractive complementary strategy for control is to breed chickens with increased resistance to Eimeria parasitism. Prior infection with Eimeria maxima leads to complete immunity against challenge with homologous strains, but only partial resistance to challenge with antigenically diverse heterologous strains. We investigate the genetic architecture of avian resistance to E. maxima primary infection and heterologous strain secondary challenge using White Leghorn populations of derived inbred lines, C.B12 and 15I, known to differ in susceptibility to the parasite. An intercross population was infected with E. maxima Houghton (H) strain, followed 3 weeks later by E. maxima Weybridge (W) strain challenge, while a backcross population received a single E. maxima W infection. The phenotypes measured were parasite replication (counting fecal oocyst output or qPCR for parasite numbers in intestinal tissue), intestinal lesion score (gross pathology, scale 0-4), and for the backcross only, serum interleukin-10 (IL-10) levels. Birds were genotyped using a high density genome-wide DNA array (600K, Affymetrix). Genome-wide association study located associations on chromosomes 1, 2, 3, and 5 following primary infection in the backcross population, and a suggestive association on chromosome 1 following heterologous E. maxima W challenge in the intercross population. This mapped several megabases away from the quantitative trait locus (QTL) linked to the backcross primary W strain infection, suggesting different underlying mechanisms for the primary- and heterologous secondary- responses. Underlying pathways for those genes located in the respective QTL for resistance to primary infection and protection against heterologous challenge were related mainly to immune response, with IL-10 signaling in the backcross primary infection being the most significant. Additionally, the identified markers associated with IL-10 levels exhibited significant additive genetic variance. We suggest this is a phenotype of interest to the outcome of challenge, being scalable in live birds and negating the requirement for single-bird cages, fecal oocyst counts, or slaughter for sampling (qPCR).

Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction.

Pacific oysters are a key aquaculture species globally, and genetic improvement via selective breeding is a major target. Genomic selection has the potential to expedite genetic gain for key target traits of a breeding program, but has not yet been evaluated in oyster. The recent development of SNP arrays for Pacific oyster (Crassostrea gigas) raises the opportunity to test genomic selection strategies for polygenic traits. In this study, a population of 820 oysters (comprising 23 full-sibling families) were genotyped using a medium density SNP array (23 K informative SNPs), and the genetic architecture of growth-related traits [shell height (SH), shell length (SL), and wet weight (WW)] was evaluated. Heritability was estimated to be moderate for the three traits (0.26 ± 0.06 for SH, 0.23 ± 0.06 for SL and 0.35 ± 0.05 for WW), and results of a GWAS indicated that the underlying genetic architecture was polygenic. Genomic prediction approaches were used to estimate breeding values for growth, and compared to pedigree based approaches. The accuracy of the genomic prediction models (GBLUP) outperformed the traditional pedigree approach (PBLUP) by ∼25% for SL and WW, and ∼30% for SH. Further, reduction in SNP marker density had little impact on prediction accuracy, even when density was reduced to a few hundred SNPs. These results suggest that the use of genomic selection in oyster breeding could offer benefits for the selection of breeding candidates to improve complex economic traits at relatively modest cost.

Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus infection.

BACKGROUND: High resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are resilient to infections. For Porcine Reproductive and Respiratory Syndrome (PRRS), one of the most devastating swine diseases worldwide, studies have identified substantial genetic variation in resistance of pigs, but evidence for genetic variation in tolerance has so far been inconclusive. Resistance and tolerance are usually considered as static traits. In this study, we used longitudinal viremia measurements of PRRS virus infected pigs to define discrete stages of infection based on viremia profile characteristics. These were used to investigate host genetic effects on viral load (VL) and growth at different stages of infection, to quantify genetic variation in tolerance at these stages and throughout the entire 42-day observation period, and to assess whether the single nucleotide polymorphism (SNP) WUR10000125 (WUR) with known large effects on resistance confers significant differences in tolerance. RESULTS: Genetic correlations between resistance and growth changed considerably over time. Individuals that expressed high genetic resistance early in infection tended to grow slower during that time-period, but were more likely to experience lower VL and recovery in growth by the later stage. The WUR genotype was most strongly associated with VL at early- to mid-stages of infection, and with growth at mid- to late-stages of infection. Both, single-stage and repeated measurements random regression models identified significant genetic variation in tolerance. The WUR SNP was significantly associated only with the overall tolerance slope fitted through all stages of infection, with the genetically more resistant AB pigs for the WUR SNP being also more tolerant to PRRS. CONCLUSIONS: The results suggest that genetic selection for improved tolerance of pigs to PRRS is possible in principle, but may be feasible only with genomic selection, requiring intense recording schemes that involve repeated measurements to reliably estimate genetic effects. In the absence of such records, consideration of the WUR genotype in current selection schemes appears to be a promising strategy to improve simultaneously resistance and tolerance of growing pigs to PRRS.

A Genome-Wide Association Study for Host Resistance to Ostreid Herpesvirus in Pacific Oysters (Crassostrea gigas).

Ostreid herpesvirus (OsHV) can cause mass mortality events in Pacific oyster aquaculture. While various factors impact on the severity of outbreaks, it is clear that genetic resistance of the host is an important determinant of mortality levels. This raises the possibility of selective breeding strategies to improve the genetic resistance of farmed oyster stocks, thereby contributing to disease control. Traditional selective breeding can be augmented by use of genetic markers, either via marker-assisted or genomic selection. The aim of the current study was to investigate the genetic architecture of resistance to OsHV in Pacific oyster, to identify genomic regions containing putative resistance genes, and to inform the use of genomics to enhance efforts to breed for resistance. To achieve this, a population of ∼1,000 juvenile oysters were experimentally challenged with a virulent form of OsHV, with samples taken from mortalities and survivors for genotyping and qPCR measurement of viral load. The samples were genotyped using a recently-developed SNP array, and the genotype data were used to reconstruct the pedigree. Using these pedigree and genotype data, the first high density linkage map was constructed for Pacific oyster, containing 20,353 SNPs mapped to the ten pairs of chromosomes. Genetic parameters for resistance to OsHV were estimated, indicating a significant but low heritability for the binary trait of survival and also for viral load measures (h2 0.12 - 0.25). A genome-wide association study highlighted a region of linkage group 6 containing a significant QTL affecting host resistance. These results are an important step toward identification of genes underlying resistance to OsHV in oyster, and a step toward applying genomic data to enhance selective breeding for disease resistance in oyster aquaculture.

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

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.

A candidate gene approach to study nematode resistance traits in naturally infected sheep.

Sheep naturally acquire a degree of resistant immunity to parasitic worm infection through repeated exposure. However, the immune response and clinical outcome vary greatly between animals. Genetic polymorphisms in genes integral to differential T helper cell polarization may contribute to variation in host response and disease outcome. A total of twelve single nucleotide polymorphisms (SNPs) were sequenced in IL23R, RORC2 and TBX21 from genomic DNA of Scottish Blackface lambs. Of the twelve SNPs, six were non-synonymous (missense), four were within the 3' UTRs and two were intronic. The association between nine of these SNPs and the traits of body weight, faecal egg count (FEC) and relative T. circumcincta L3-specific IgA antibody levels was assessed in a population of domestic Scottish Blackface ewe lambs and a population of free-living Soay ewe lambs both naturally infected with a mixture of nematodes. There were no significant associations identified between any of the SNPs and phenotypes recorded in either of the populations after adjustment for multiple testing (Bonferroni corrected P value≤0.002). In the Blackface lambs, there was a nominally significant association (P=0.007) between IL23R p.V324M and weight at 20 weeks. This association may be worthy of further investigation in a larger sample of sheep.

Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon.

Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programs, alongside high-resolution association mapping of the genetic basis of complex traits. However, in sibling testing schemes typical of salmon breeding programs, trait records are available on many thousands of fish with close relationships to the selection candidates. Therefore, routine high density SNP genotyping may be prohibitively expensive. One means to reducing genotyping cost is the use of genotype imputation, where selected key animals (e.g., breeding program parents) are genotyped at high density, and the majority of individuals (e.g., performance tested fish and selection candidates) are genotyped at much lower density, followed by imputation to high density. The main objectives of the current study were to assess the feasibility and accuracy of genotype imputation in the context of a salmon breeding program. The specific aims were: (i) to measure the accuracy of genotype imputation using medium (25 K) and high (78 K) density mapped SNP panels, by masking varying proportions of the genotypes and assessing the correlation between the imputed genotypes and the true genotypes; and (ii) to assess the efficacy of imputed genotype data in genomic prediction of key performance traits (sea lice resistance and body weight). Imputation accuracies of up to 0.90 were observed using the simple two-generation pedigree dataset, and moderately high accuracy (0.83) was possible even with very low density SNP data (∼250 SNPs). The performance of genomic prediction using imputed genotype data was comparable to using true genotype data, and both were superior to pedigree-based prediction. These results demonstrate that the genotype imputation approach used in this study can provide a cost-effective method for generating robust genome-wide SNP data for genomic prediction in Atlantic salmon. Genotype imputation approaches are likely to form a critical component of cost-efficient genomic selection programs to improve economically important traits in aquaculture.

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.

Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes.

BACKGROUND: The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. Although they are generally resilient to disease challenge, routine vaccination and biosecurity measures are rarely applied and infectious diseases remain a major cause of mortality and reduced productivity. Management and genetic improvement programmes are hampered by lack of routine data recording. Selective breeding based on genomic technologies may provide the means to enhance sustainability. In this study, we investigated the genetic architecture of antibody response to four major infectious diseases [infectious bursal disease (IBDV), Marek's disease (MDV), fowl typhoid (SG), fowl cholera (PM)] and resistance to Eimeria and cestode parasitism, along with two production traits [body weight and body condition score (BCS)] in two distinct indigenous Ethiopian chicken ecotypes. We conducted variance component analyses, genome-wide association studies, and pathway and selective sweep analyses. RESULTS: The large majority of birds was found to have antibody titres for all pathogens and were infected with both parasites, suggesting almost universal exposure. We derived significant moderate to high heritabilities for IBDV, MDV and PM antibody titres, cestodes infestation, body weight and BCS. We identified single nucleotide polymorphisms (SNPs) with genome-wide significance for each trait. Based on these associations, we identified for each trait, pathways, networks and functional gene clusters that include plausible candidate genes. Selective sweep analyses revealed a locus on chromosome 18 associated with viral antibody titres and resistance to Eimeria parasitism that is within a positive selection signal. We found no significant genetic correlations between production, immune and disease traits, implying that selection for altered antibody response and/or disease resistance will not affect production. CONCLUSIONS: We confirmed the presence of genetic variability and identified SNPs significantly associated with immune, disease and production traits in indigenous village chickens. Results underpin the feasibility of concomitant genetic improvement for enhanced antibody response, resistance to parasitism and productivity within and across indigenous chicken ecotypes.