Abstract
Working with weakly congruent markers means that consensus genetic structuring of populations requires methods explicitly devoted to this purpose. The method, which is presented here, belongs to the multivariate analyses. This method consists of different steps. First, single-marker analyses were performed using a version of principal component analysis, which is designed for allelic frequencies (%PCA). Drawing confidence ellipses around the population positions enhances %PCA plots. Second, a multiple co-inertia analysis (MCOA) was performed, which reveals the common features of single-marker analyses, builds a reference structure and makes it possible to compare single-marker structures with this reference through graphical tools. Finally, a typological value is provided for each marker. The typological value measures the efficiency of a marker to structure populations in the same way as other markers. In this study, we evaluate the interest and the efficiency of this method applied to a European and African bovine microsatellite data set. The typological value differs among markers, indicating that some markers are more efficient in displaying a consensus typology than others. Moreover, efficient markers in one collection of populations do not remain efficient in others. The number of markers used in a study is not a sufficient criterion to judge its reliability. "Quantity is not quality".
Highlights
Today, a large number of studies are aimed at investigating the genetic structuring of populations within species
Under the coordination of the FAO, an initiative called the measurement of domestic animal diversity (MoDAD) was started in order to provide technical recommendations for studies in farm animals [24]
We provide a short background to multiple co-inertia analysis (MCOA), we describe the typological value and we study the interest and efficiency of this method using a bovine data set
Summary
A large number of studies are aimed at investigating the genetic structuring of populations within species. Among the many DNA tools available, microsatellites are the most widely used mainly because of their high variability Within this context, an FAO/ISAG advisory group has been formed to recommend species-specific lists of microsatellite loci (about 30 per species) for the major farm animal species (cattle, buffalo, yak, goat, sheep, pig, horse, donkey, chicken and camelids; http://dad.fao.org/en/refer/library/guidelin/marker.pdf). An FAO/ISAG advisory group has been formed to recommend species-specific lists of microsatellite loci (about 30 per species) for the major farm animal species (cattle, buffalo, yak, goat, sheep, pig, horse, donkey, chicken and camelids; http://dad.fao.org/en/refer/library/guidelin/marker.pdf) The adherence to such recommendations permits reasonable comparisons of parallel or overlapping studies of genetic diversity and it is a necessary prerequisite to combine results in meta-analyses [60]. They underline that the recommended markers are well known and used in 79% of the projects
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