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

Obexer-Ruff, Gabriela; Sattler, Ursula; Martinez, Dominique; Maillard, Jean‐Charles; Chartier, Christophe; Saitbekova, N; Glowatzki, Marie-Louise; Gaillard, C.

doi:10.1186/1297-9686-35-s1-s113

Cited by 15 publications

(8 citation statements)

References 11 publications

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“…associated with genes of known function), transcript-associated microsatellites also represent ideal markers for studying the genetic basis of phenotypic trait variation [13]. However, despite several studies having developed panels of candidate-gene targeted microsatellites from the complete genome sequences of humans and their companion species [41]–[43], cDNA has not yet been widely exploited for this purpose, particularly in non-model organisms. Our study highlights the eminent feasibility of such an approach, although the numbers of markers obtainable will clearly depend on the relative abundance of various classes of transcript.…”

Section: Discussionmentioning

confidence: 99%

A Novel Approach for Mining Polymorphic Microsatellite Markers In Silico

Hoffman

Nichols

2011

PLoS ONE

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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.

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Section: Discussionmentioning

confidence: 99%

A Novel Approach for Mining Polymorphic Microsatellite Markers In Silico

Hoffman

Nichols

2011

PLoS ONE

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“…Moreover, at linked microsatellites there are allelic correlations to disease resistance in both sheep (Coltman et al . 2001) and goats (Obexer‐Ruff et al . 2003).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2006

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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.

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“…However, novel microsatellites often have to be isolated before they can be utilized for each species, which generally demands considerable time and high cost. Recently many studies have demonstrated cross-species amplification of Bovidae microsatellites in the Caprinae, allowing possible population studies on species for which microsatellites are not yet developed (Li et al 2002;Obexer et al 2003;Saitbekova et al 1999). This approach is advantageous to the study of endangered species, which might have reduced genetic variation (Maudet et al 2001).…”

mentioning

confidence: 99%

Cross-Species Amplification of Bovidae Microsatellites and Low Diversity of the Endangered Korean Goral

Kim

Min

et al. 2004

Journal of Heredity

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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.

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

Cited by 15 publications

References 11 publications

A Novel Approach for Mining Polymorphic Microsatellite Markers In Silico

A Novel Approach for Mining Polymorphic Microsatellite Markers In Silico

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

Cross-Species Amplification of Bovidae Microsatellites and Low Diversity of the Endangered Korean Goral

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