Association studies using random and "candidate" microsatellite loci in two infectious goat diseases

Prevalence and resistance to gastrointestinal parasites in goats: A review

Gastrointestinal parasitism, particularly nematode infection, is a major health issue affecting goats worldwide, resulting in clinical diseases and productivity loss. Prevalent gastrointestinal parasites (GIPs) affecting goats in South Africa are the Strongyloides papillosus, Eimeria spp., and Strongyles, especially the Haemonchus contortus and Trichostrongylus spp. According to the issues discussed in this paper and by other authors, the prevalence and intensity of various GIPs vary with an animal's location, breed, age, sex, and season. Because GIPs easily develop resistance to chemical treatment, selecting and breeding genetically GIP-resistant animals would be a relatively simple and inexpensive strategy for reducing or eliminating the current reliance on chemotherapy. Potential phenotypic indicators for selecting GIP-resistant goats include parasitological, immunological, and pathological phenotypic markers. Synergistic use of these indicators should be encouraged for a more accurate simplified genotype selection of resistant animals. Genes with Mendelian inheritance, particularly those involved in immunoregulatory mechanisms, have been identified in goats. Exploring this knowledge base to develop cost-effective molecular tools that facilitate enhanced genetic improvement programs is a current challenge. Future statistical and biological models should investigate genetic variations within genomic regions and different candidate genes involved in immunoregulatory mechanisms, as well as the identification of single nucleotide polymorphisms known to affect GIP infection levels.

Seroprevalence of Ehrlichia ruminantium antibodies and its associated risk factors in indigenous goats of South Africa

The present study investigated the seroprevalence of antibodies to Ehrlichia ruminantium and the associated risk factors in goats from five different farming provinces of South Africa. Sera collected from 686 goats of the commercial meat type (n=179), mohair type (n=9), non-descript indigenous goats from Eastern Cape (n=56), KwaZulu-Natal (n=209), Limpopo (n=111), North West (n=61) and Northern Cape (n=11) provinces and a feral Tankwa goat (n=50) were tested for the presence of immunoglobulin G (IgG) antibodies to antigens of E. ruminantium using the indirect fluorescent-antibody test (IFAT). Fifty two percent of these goats had ticks. The overall seroprevalence of antibodies to E. ruminantium was 64.87% (445/686) with the highest seroprevalence reported for Limpopo (95.50%) and lowest for Northern Cape (20.29%). Highest seroprevalence for antibodies to E. ruminantium was observed in goats from endemic regions (76.09%), and from smallholder production systems (89.54%). High seroprevalence was also observed in non-descript indigenous goats (85.04%), adult goat (69.62%), in does (67.46%) and goats infested with ticks (85.79%). The logistic model showed a gradient of increasing risk for commercial meat type Savanna (OR=3.681; CI=1.335-10.149) and non-descript indigenous (OR=3.466; CI=1.57-7.645) compared to Boer goats and for goats from the smallholder production system (OR=2.582; CI=1.182-5.639) and those with ticks (OR=3.587; CI=2.105-6.112). Results from this study showed that E. ruminantium infections were prevalent but were widely and unevenly distributed throughout South Africa. Findings from the study facilitate identification and mapping of risk areas for heartwater and its endeminicity in South Africa and should be taken into consideration for future disease control strategies and local goat improvement programs.

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.

Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach

Identifying the genes underlying phenotypic variation in natural populations can provide novel insight into the evolutionary process. The candidate gene approach has been applied to studies of a number of traits in various species, in an attempt to elucidate their genetic basis. Here, we test the application of the candidate gene approach to identify the loci involved in variation in gastrointestinal parasite burden, a complex trait likely to be controlled by many loci, in a wild population of Soay sheep. A comprehensive literature review, Gene Ontology databases, and comparative genomics resources between cattle and sheep were used to generate a list of candidate genes. In a pilot study, these candidates, along with 50 random genes, were then sequenced in two pools of Soay sheep; one with low gastrointestinal nematode burden and the other high, using a NimbleGen sequence capture experiment. Further candidates were identified from single nucleotide polymorphisms (SNPs) that were highly differentiated between high- and low-resistance sheep breeds. A panel of 192 candidate and control SNPs were then typed in 960 individual Soay sheep to examine whether they individually explained variation in parasite burden, as measured as faecal egg count, as well as two immune measures (Teladorsagia circumcincta-specific antibodies and antinuclear antibodies). The cumulative effect of the candidate and control SNPs were estimated by fitting genetic relationship matrices (GRMs) as random effects in animal models of the three traits. No more significant SNPs were identified in the pilot sequencing experiment and association study than expected by chance. Furthermore, no significant difference was found between the proportions of candidate or control SNPs that were found to be significantly associated with parasite burden/immune measures. No significant effect of the candidate or control gene GRMs was found. There is thus little support for the candidate gene approach to the identification of loci explaining variation in parasitological and immunological traits in this population. However, a number of SNPs explained significant variation in multiple traits and significant correlations were found between the proportions of variance explained by individual SNPs across multiple traits. The significant SNPs identified in this study may still, therefore, merit further investigation.

Genetic variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers

The present study aimed at analyzing the genetic variability of indigenous goat breeds (Capra hircus) using the MHC-associated microsatellite markers BF1, BM1818, BM1258, DYMS1, and SMHCC1. The following breeds were included: Chinese Xuhuai, Indian Changthangi and Pashmina, Kenyan Small East African (SEA) and Galla, and Albanian Vendi. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from nine in the Galla to 14.5 in the Vendi breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.483 in the Vendi to 0.577 in the Galla breed, and from 0.767 in the SEA to 0.879 in the Vendi breed, respectively. Significant loss of heterozygosity (p < 0.01) indicated that these loci were not in Hardy-Weinberg equilibrium. The mean F(IS) values ranged from 0.3299 in the SEA to 0.4605 in the Vendi breed with a mean value of 0.3623 in all breeds (p < 0.001). Analysis of molecular variance indicated that 7.14% and 4.74% genetic variation existed among the different breeds and geographic groups, whereas 92.86% and 95.26% existed in the breeds and the geographic groups, respectively (p < 0.001). The microsatellite marker analysis disclosed a high degree of genetic polymorphism. Loss of heterozygosity could be due to genetic drift and endogamy. The genetic variation among populations and geographic groups does not indicate a correlation of genetic differences with geographic distance.

A novel approach for mining polymorphic microsatellite markers in silico

An important emerging application of high-throughput 454 sequencing is the isolation of molecular markers such as microsatellites from genomic DNA. However, few studies have developed microsatellites from cDNA despite the added potential for targeting candidate genes. Moreover, to develop microsatellites usually requires the evaluation of numerous primer pairs for polymorphism in the focal species. This can be time-consuming and wasteful, particularly for taxa with low genetic diversity where the majority of primers often yield monomorphic polymerase chain reaction (PCR) products. Transcriptome assemblies provide a convenient solution, functional annotation of transcripts allowing markers to be targeted towards candidate genes, while high sequence coverage in principle permits the assessment of variability in silico. Consequently, we evaluated fifty primer pairs designed to amplify microsatellites, primarily residing within transcripts related to immunity and growth, identified from an Antarctic fur seal (Arctocephalus gazella) transcriptome assembly. In silico visualization was used to classify each microsatellite as being either polymorphic or monomorphic and to quantify the number of distinct length variants, each taken to represent a different allele. The majority of loci (n = 36, 76.0%) yielded interpretable PCR products, 23 of which were polymorphic in a sample of 24 fur seal individuals. Loci that appeared variable in silico were significantly more likely to yield polymorphic PCR products, even after controlling for microsatellite length measured in silico. We also found a significant positive relationship between inferred and observed allele number. This study not only demonstrates the feasibility of generating modest panels of microsatellites targeted towards specific classes of gene, but also suggests that in silico microsatellite variability may provide a useful proxy for PCR product polymorphism.

Naturally occurring variability in some phenotypic markers and correlates of haemonchotolerance in West African Dwarf goats in a subhumid zone of Nigeria

West African Dwarf (WAD) goats of the Nigerian subhumid zone generally show strong resistance and resilience to Haemonchus contortus in laboratory experiments, although a relatively small proportion are susceptible to infection. Little is known about these extremes of response phenotype in nature. Therefore, a survey was carried out of gastrointestinal nematode infections in WAD goats, with emphasis on abomasal worms, at three goat markets in Southern Nigeria during the rainy season. Faecal samples (n=1070) were collected weekly from goats between April and September, and 352 abomasa and small intestines from local abattoirs were examined. Total strongyle (prevalence=65.0%) and H. contortus (prevalence=64.3%) faecal egg counts (FEC) varied between the three markets, being highest throughout at Opi. FEC increased from April to peak in August. Based on raw FEC, 76.1% of goats had FEC of <100, and 4.7%>500. Adjustment of these figures for monthly and between-market differences, gave figures of 78.8 and 3.4%, respectively. H. contortus worm burdens (WB) showed a similar pattern with 67.9% of goats harbouring <200 worms and 8.2% >1000, and after adjustment 69.6 and 6.0%, respectively. Fecundity, based on eggs in the uterus, did not vary between markets or monthly, but fell with increasing WB. Trichostrongylus colubriformis was less frequent (prevalence=42.4%) but goats from Opi also carried higher WB, and worms were similarly highly aggregated in hosts. When the between-market and monthly differences for both species were controlled, a highly significant positive correlation between the species emerged. Therefore, although a small subset of goats, highly susceptible to H. contortus, exists in this breed, the majority show resistance under field conditions and the resistant phenotype is also resistant to T. colubriformis. Both species are highly aggregated in the susceptible subset of the population. While, we cannot yet exclude alternative explanations, our data are compatible with a strong genetic basis for this phenomenon.

Associations between blood parasite infection and a microsatellite DNA allele in an Australian scincid lizard (Egernia stokesii)

We used blood samples from 175 individuals of the Australian lizard Egernia stokesii to determine infection status of three apicomplexan blood parasites from the genera Hemolivia, Schellackia, and Plasmodium and to determine genotypes at 12 microsatellite DNA loci. We found one significant association between genotype and infection status. For locus Est4, individuals carrying allele 159 had lower prevalence of infection with Hemolivia (14.3% of 28 lizards) than individuals that did not carry the allele (58.4% of 89 lizards). We interpret this as a linkage to a functional gene associated with parasite resistance. We found no evidence among seven lizard populations that the frequency of allele 159 was related to the population prevalence of Hemolivia infection and discuss several explanations of that pattern.

Detecting the signature of selection on immune genes in highly structured populations of wild sheep (Ovis dalli)

The confounding effects of population structure complicate efforts to identify regions of the genome under the influence of selection in natural populations. Here we test for evidence of selection in three genes involved in vertebrate immune function - the major histocompatibility complex (MHC), interferon gamma (IFNG) and natural resistance associated macrophage polymorphism (NRAMP) - in highly structured populations of wild thinhorn sheep (Ovis dalli). We examined patterns of variation at microsatellite loci linked to these gene regions and at the DNA sequence level. Simple Watterson's tests indicated balancing selection at all three gene regions. However, evidence for selection was confounded by population structure, as the Watterson's test statistics from linked markers were not outside of the range of values from unlinked and presumably neutral microsatellites. The translated coding sequences of thinhorn IFNG and NRAMP are fixed and identical to those of domestic sheep (Ovis aries). In contrast, the thinhorn MHC DRB locus shows significant evidence of overdominance through both an excess of nonsynonymous substitution and trans-species polymorphism. The failure to detect balancing selection at microsatellite loci linked to the MHC is likely the result of recombination between the markers and expressed gene regions.

Cross-species amplification of Bovidae microsatellites and low diversity of the endangered Korean goral

The Korean goral (Nemorhaedus caudatus) is an endangered species of wild goat. The conservation and management of this species could benefit from a better understanding of its genetic diversity and structure. Cross-species amplification of 34 Bovidae microsatellite loci was tested on a panel of 6 Korean gorals and 10 domestic goats. After polymerase chain reaction (PCR) optimization, 29 (85.3%) microsatellite loci amplified successfully for the Korean gorals and 27 (79.4%) for the domestic goats. Of the amplified products, 16 (55.2%) were polymorphic in the Korean goral and 22 (81.5%) in domestic goats. Nei's unbiased mean heterozygosity and mean allele number per locus were, respectively, 0.356 and 2.6 in the Korean goral and 0.636 and 4.8 in domestic goats. Low genetic diversity in the Korean gorals observed in this preliminary microsatellite survey suggests an urgent need for further detailed study of genetic diversity in Korean goral populations and a population management strategy based on these studies. Current results of cross-species amplification of domestic Bovidae microsatellites could be employed for the necessary population genetic studies on the Korean goral and other endangered Caprinae species.