Determination of the minimum number of microsatellite markers for individual genotyping in wild boar (Sus scrofa) using a test with close relatives

Kołodziej, Karolina; Theissinger, Kathrin; Brün, Jörg; Schulz, H. K.; Schulz, Ralf

doi:10.1007/s10344-011-0588-9

Cited by 20 publications

(9 citation statements)

References 42 publications

(43 reference statements)

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“…The instability microsatellite markers, which is easily produce error genotypes, may result in mistakes in the individual identification, paternity test, population structure and genetic diversity analysis for the different species [ 47 ]. Especially for the DNA samples with poor quality, it may produce more error genotypes when using these instability loci.…”

Section: Discussionmentioning

confidence: 99%

“…In most other studies on wildlife forensics, six to ten microsatellite markers are commonly used [ 50 - 52 ]. In any case, the sufficient discriminating power must be contained in the minimum subset of microsatellite loci needed for accurate individual identification [ 31 , 47 ]. Following Waits et al [ 33 ], the value of PIDsib was used as a bound to estimate the minimum number of loci necessary to distinguish between individuals.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system

Huang

et al. 2015

BMC Genomics

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BackgroundThe giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda.ResultsBy screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What’s more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system.ConclusionThe microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual identification method and the genetic diversity analysis method in this study provided adequate material for the future study of giant panda.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1268-z) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system

Huang

et al. 2015

BMC Genomics

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“…Several studies were conducted to optimize genotyping on such noninvasive samples and assure it maximum reliability. As an example, Kolodziej et al (2012) recommended for feces a specific four-loci combination for a reliable individual identification and population size estimation in the wild boar population they tested. Fresh samples are best for analysis and DNA sampling requires the means and materials to preserve the samples in the field.…”

Section: Dna Genotypingmentioning

confidence: 99%

Monitoring wild pig populations: a review of methods

Engeman¹,

Massei

Sage³

et al. 2013

Environ Sci Pollut Res

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Wild pigs (Sus scrofa) are widespread across many landscapes throughout the world and are considered to be an invasive pest to agriculture and the environment, or conversely a native or desired game species and resource for hunting. Wild pig population monitoring is often required for a variety of management or research objectives, and many methods and analyses for monitoring abundance are available. Here, we describe monitoring methods that have proven or potential applications to wild pig management. We describe the advantages and disadvantages of methods so that potential users can efficiently consider and identify the option(s) best suited to their combination of objectives, circumstances, and resources. This paper offers guidance to wildlife managers, researchers, and stakeholders considering population monitoring of wild pigs and will help ensure that they can fulfill their monitoring objectives while optimizing their use of resources.

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“…Genotypic analyses of fecal samples were used to develop a CMR estimator of the actual population density (Ebert et al, 2012;Ebert, Knauer, Storch, & Hohmann, 2010;Kolodziej, Theissinger, Brün, Schulz, & Schulz, 2012) but require a considerable extra amount of money, work, and workforce.…”

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confidence: 99%

Population size estimates based on the frequency of genetically assigned parent–offspring pairs within a subsample

Müller

Mercker

Brün

2020

Ecology and Evolution

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Estimating population density as precise as possible is a key premise for managing wild animal species. This can be a challenging task if the species in question is elusive or, due to high quantities, hard to count. We present a new, mathematically derived estimator for population size, where the estimation is based solely on the frequency of genetically assigned parent–offspring pairs within a subsample of an ungulate population. By use of molecular markers like microsatellites, the number of these parent–offspring pairs can be determined. The study's aim was to clarify whether a classical capture–mark–recapture (CMR) method can be adapted or extended by this genetic element to a genetic‐based capture–mark–recapture (g‐CMR). We numerically validate the presented estimator (and corresponding variance estimates) and provide the R‐code for the computation of estimates of population size including confidence intervals. The presented method provides a new framework to precisely estimate population size based on the genetic analysis of a one‐time subsample. This is especially of value where traditional CMR methods or other DNA‐based (fecal or hair) capture–recapture methods fail or are too difficult to apply. The DNA source used is basically irrelevant, but in the present case the sampling of an annual hunting bag is to serve as data basis. In addition to the high quality of muscle tissue samples, hunting bags provide additional and essential information for wildlife management practices, such as age, weight, or sex. In cases where a g‐CMR method is ecologically and hunting‐wise appropriate, it enables a wide applicability, also through its species‐independent use.

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Determination of the minimum number of microsatellite markers for individual genotyping in wild boar (Sus scrofa) using a test with close relatives

Cited by 20 publications

References 42 publications

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system

Monitoring wild pig populations: a review of methods

Population size estimates based on the frequency of genetically assigned parent–offspring pairs within a subsample

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