Effectiveness of microsatellite and single nucleotide polymorphism markers for parentage analysis in European domestic pigs

Yu, Guowu; Tang, Qianzi; Long, Keren; Che, Tiandong; Li, M.Z.; Shuai, Surong

doi:10.4238/2015.february.13.15

Cited by 22 publications

(19 citation statements)

References 33 publications

(31 reference statements)

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“…If we limit the overview to vertebrates alone, we can distinguish different types of research. Some studies have compared the effectiveness of the two markers: (i) for the purpose of performing kinship analyses [9][10][11][12][13], (ii) to infer diversity parameters e.g., [14,15], and (iii) to analyze genetic relationships between populations [16][17][18][19][20]. This last group is of particular interest for this study as it aims to enrich knowledge about the precise issue of the inference of population genetic structure.…”

Section: Introductionmentioning

confidence: 99%

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance

Laoun

Harkat

Lafri

et al. 2020

Genes

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Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, FST), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise FST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number.

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Section: Introductionmentioning

confidence: 99%

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance

Laoun

Harkat

Lafri

et al. 2020

Genes

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“…The study indicated that the number of SNP loci required was also related to the species population size of the estimated model. When the population was larger, the number of SNP loci required to meet the accuracy requirements of the identification was higher (Turakulov and Easteal 2003;Yu et al 2015).…”

Section: Resultsmentioning

confidence: 99%

Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey (Rhinopithecus roxellana)

Chen

Hou

et al. 2020

Conservation Genet Resour

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Microsatellite markers are popular for assigning parentage, but single-nucleotide polymorphisms (SNPs) have only been applied in this area recently. To evaluate these two markers which have been previously studied in golden snub-nosed monkeys, we genotyped 12 individuals using 37 microsatellite loci and 37 SNP markers. The data showed that 32 of 37 microsatellite loci were polymorphic, and most microsatellite loci were high informative (mean PIC = 0.599). Meanwhile, 24 of 37 SNP markers were polymorphic and most were low informative (mean PIC = 0.244). For microsatellites, the combined exclusion probability with one-parent-unknown/known (CE-1P/CE-2P) nearly reached 1, while for the SNP markers, CE-2P only reached 0.9582. Under the condition of one parent known/unknown, the CE-2P and CE-1P could meet the international human parental standard (0.9973) by using five or nine microsatellite loci respectively. For SNP markers, we doubled the loci (n = 48) and simulated parentage testing, and the data showed that the CE-2P was 0.998 while the CE-1P was still low. This result indicated that the SNP loci which we used here had low polymorphism and that more loci need to be developed in the future. In addition, we corrected one case of failed identification by excluding siblings and reducing the range of candidate paternities.

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“…Parentage analysis and parentage verification are very important for an efficient genetic management in livestock breeding (Yu et al, 2015). Traditionally, pedigree records are the foundation of the breeding programs, but if this records are incomplete or inaccurate, these data can lead to unexpected and undesired consequences and errors in further breeding.…”

Section: Introductionmentioning

confidence: 99%

12-plex highly polymorphic microsatellite marker set for parentage analysis in Banija spotted pigs

Margeta

Škorput

Šalamon

et al. 2019

JCEA

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Microsatellites (MS) have been, for the last two decades, widely used for parentage analysis in all types of livestock, including pigs. Conservation efforts on Banija spotted pigs included genetic characterization of the breed with MS markers. Since recent comparison of pedigree and MS data revealed some inconsistencies, the aim of this study was to develop a set of highly polymorphic and heterozygous MS markers, which could be used for parentage analysis and to prevent pedigree errors. 12 MS markers with the polymorphic information content (PIC) above 0.62 were chosen and combined into a single multiplex polymerase chain reaction (PCR). The combined non-exclusion probability for one candidate parent (NE-1P) was 0.00246149, the combined NE-1P given the genotype of a known parent of the opposite sex (NE-2P) was 0.00003739 and combined non-exclusion probability for a candidate parent pair (NE-PP) was 0.00000003. Due to a high information content of selected MS markers it was possible to obtain high accuracy in parentage assignment, which was confirmed by analyzing actual data with known genetic relationships.

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Effectiveness of microsatellite and single nucleotide polymorphism markers for parentage analysis in European domestic pigs

Cited by 22 publications

References 33 publications

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance

Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey (Rhinopithecus roxellana)

12-plex highly polymorphic microsatellite marker set for parentage analysis in Banija spotted pigs

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