Gene mapping in the wild with SNPs: guidelines and future directions

Slate, Jon; Gratten, Jacob; Beraldi, Dario; Stapley, Jessica; Hale, Matt; Pemberton, Josephine M.

doi:10.1007/s10709-008-9317-z

Cited by 153 publications

(142 citation statements)

References 92 publications

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“…This will, for example, facilitate QTL mapping studies and will increase the quality of outlier-and structure analyses. Massively increasing the number of markers will enable researchers not only to get better precision in population genetic studies (Novembre et al, 2008), QTL and linkage disequilibrium (LD) mapping projects (Slate et al, 2009) and kinship assignments (Santure et al, 2010), but also to pursue topics such as historical demographic patterns, introgression and admixture (Jakobsson et al, 2008).…”

Section: Large-scale Identification and Development Of Molecular Markersmentioning

confidence: 99%

“…With the advent of NGS, the use of SNPs in molecular ecology studies is predicted to expand dramatically. Once identified these markers can be typed in a large number of individuals using a wide variety of platforms (reviewed in Slate et al, 2009). InDel (insertion-deletion) markers can be detected with similar software as the SNPs and they will probably become a popular kind of molecular marker in future population genetic studies, as they are easy and cheap to identify and score (Väli et al, 2008).…”

Section: Large-scale Identification and Development Of Molecular Markersmentioning

confidence: 99%

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Applications of next generation sequencing in molecular ecology of non-model organisms

2010

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As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.

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Section: Large-scale Identification and Development Of Molecular Markersmentioning

confidence: 99%

Section: Large-scale Identification and Development Of Molecular Markersmentioning

confidence: 99%

Applications of next generation sequencing in molecular ecology of non-model organisms

2010

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“…have been highlighted as a potential alternative (Anderson & Garza, 2006;Slate et al, 2009). Individually SNPs are less informative than microsatellites because they are less polymorphic (Glaubitz, Rhodes & Dewoody, 2003;Wang, 2006): most SNPs have just two alleles, and their allele frequencies tend to be skewed, resulting in low heterozygosity and information content (Marth et al, 2001).…”

Section: Error and Mutationmentioning

confidence: 99%

Molecular marker‐based pedigrees for animal conservation biologists

Jones

Wang

2010

Animal Conservation

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Pedigrees, depicting the genealogical relationships between individuals in a population, are of fundamental importance to several research areas including conservation biology. For example, they are useful for estimating inbreeding, heritability, selection, studying kin selection and for measuring gene flow between populations. Pedigrees constructed from direct observations of reproduction are usually unavailable for wild populations. Therefore, pedigrees for these populations are usually estimated using molecular marker data. Despite their obvious importance, and the fact that pedigrees are conceptually well understood, the methods, and limitations of marker-based pedigree inference are often less well understood. Here we introduce animal conservation biologists to molecular marker-based pedigrees. We briefly describe the history of pedigree inference research, before explaining the underlying theory and basic mechanics of pedigree construction using standard methods. We explain the assumptions and limitations that accompany many of these methods, before going on to explain methods that relax several of these assumptions. Finally, we look to future and discuss some recent exciting advances such as the use of single-nucleotide polymorphisms, inference of multigenerational pedigrees and incorporation of non-genetic data such as field observations into the calculations. We also provide some guidelines on efficient marker selection in order to maximize accuracy and power. Throughout we use examples from the field of animal conservation and refer readers to appropriate software where possible. It is our hope that this review will help animal conservation biologists to understand, choose, and use the methods and tools of this fast-moving field.

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“…Slate et al 2009). Tools developed for genetic conservation of livestock species generally require knowledge of genetic relations (e.g.…”

Section: Relevance Of Genomics For Conserving Genetic Variation In Wimentioning

confidence: 99%

Perspectives of genomics for genetic conservation of livestock

Windig

Engelsma

2009

Conserv Genet

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Genomics provides new opportunities for conservation genetics. Conservation genetics in livestock is based on estimating diversity by pedigree relatedness and managing diversity by choosing those animals that maximize genetic diversity. Animals can be chosen as parents for the next generation, as donors of material to a gene bank, or as breeds for targeting conservation efforts. Genomics provides opportunities to estimate diversity for specific parts of the genome, such as neutral and adaptive diversity and genetic diversity underlying specific traits. This enables us to choose candidates for conservation based on specific genetic diversity (e.g. diversity of traits or adaptive diversity) or to monitor the loss of diversity without conservation. In wild animals direct genetic management, by choosing candidates for conservation as in livestock, is generally not practiced. With dense marker maps opportunities exist for monitoring relatedness and genetic diversity in wild populations, thus enabling a more active management of diversity.

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Gene mapping in the wild with SNPs: guidelines and future directions

Cited by 153 publications

References 92 publications

Applications of next generation sequencing in molecular ecology of non-model organisms

Applications of next generation sequencing in molecular ecology of non-model organisms

Molecular marker‐based pedigrees for animal conservation biologists

Perspectives of genomics for genetic conservation of livestock

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