Consensus genetic structuring and typological value of markers using multiple co-inertia analysis

Denis Lalo?; Thibaut Jombart; Anne-B?atrice Dufour; Katayoun Moazami-Goudarzi
September 2007
Genetics Selection Evolution;Sep2007, Vol. 39 Issue 5, p545
Academic Journal
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?.


Related Articles

  • Extensive Long-Range and Nonsyntenic Linkage Disequilibrium in Livestock Populations: Deconstruction of a Conundrum. Lipkin, E.; Straus, K.; Stein, R. Tal; Bagnato, A.; Schiavini, F.; Fontanesi, L.; Russo, V.; Medugorac, I.; Foerster, M.; Sölkner, J.; Dolezal, M.; Medrano, J. F.; Friedmann, A.; Soller, M. // Genetics;Feb2009, Vol. 181 Issue 2, p691 

    Great interest was aroused by reports, based on microsatellite markers, of high levels of statistically significant long-range and nonsyntenic linkage disequilibrium (LD) in livestock. Simulation studies showed that this could result from population family structure. In contrast, recent...

  • A genetic profile of the Kalahari Red goat breed from southern Africa. Kotze, A.; Swart, H.; Grobler, J. P.; Nemaangani, A. // South African Journal of Animal Science;2004, Vol. 34 Issue 5, p10 

    The erosion of the Kalahari Red with red Boer goats is a major concern among breeders. Little empiric information is available with no comprehensive system of monitoring special characteristics. Eighteen microsatellite markers were applied to investigate the genetic diversity of the breed and to...

  • Genetic characterisation of the Blanca Andaluza goat based on microsatellite markers. Martínez, A. M.; Carrera, M. P.; Acosta, J. M.; Rodríguez-Gallardo, P. P.; Cabello, A.; Camacho, E.; Delgado, V. // South African Journal of Animal Science;2004, Vol. 34 Issue 5, p17 

    This is a genetic characterisation of the Blanca Serrana Andaluza goat breed based on microsatellite markers. Fifty animals from five herds were typed with a set of 27 microsatellites proposed by the FAO and ISAG for biodiversity studies. Our results showed that this is an extremely endangered...

  • Genetic variation of three commercial and three indigenous goat populations in South Africa. Visser, C.; Hefer, C. A.; Van Marle-Köster, E.; Kotze, A. // South African Journal of Animal Science;2004, Vol. 34 Issue 5, p24 

    Three commercial and three indigenous goat populations from South Africa were studied for genetic variation using ten microsatellite markers. Heterozygosity values of between 0.62 and 0.69 were obtained for the populations, except for the SA Boer Goat, which had the lowest variation (0.49)....

  • Testing Linkage Hypotheses in Hybrid Analysis of Alternatively Distributed Behavioral Traits with Incomplete Penetrance. Kulikov, A. V.; Bazovkina, D. V. // Russian Journal of Genetics;Aug2003, Vol. 39 Issue 8, p896 

    The use of polymorphic microsatellite markers for mapping alternatively distributed behavioral traits with incomplete penetrance was studied with special reference to inheritance of predisposition to catalepsy in mice. Using only backcrosses as a segregating population, the major gene for...

  • Genetic and Molecular Markers of the Queensland Fruit Fly, Bactrocera tryoni. Zhao, J. T.; Frommer, M.; Sved, J. A.; Gillies, C. B. // Journal of Heredity;Sep/Oct2003, Vol. 94 Issue 5, p416 

    Twenty-six microsatellite markers, along with two restriction fragment length polymorphism (RFLP) markers and three morphological markers, have been mapped to five linkage groups, corresponding to the five autosomes of the Queensland fruit fly, Bactrocera tryoni. All these molecular and genetic...

  • Early male production is not linked to a reproductive strategy in the Japanese paper wasp, Polistes chinensis antennalis (Hymenoptera: Vespidae). Koji Tsuchida; Takaharu Saigo; Sumiko Tsujita; Kazuki Takeuchi // Journal of Ethology;Jan2004, Vol. 22 Issue 1, p119 

    Diploid males in haplo-diploid insects are sterile, because they produce diploid sperm. Our previous report revealed that early males of the Japanese paper wasp Polistes chinensis antennalis are diploid but did not reveal how often this occurs. We analyzed the genotypes of early males using six...

  • Kin structure and colony male reproduction in the hornet Vespa crabro (Hymenoptera: Vespidae). Jun-ichi Takahashi; Jun Nakamura; Shin-ichi Akimoto; Eisuke Hasegawa // Journal of Ethology;Jan2004, Vol. 22 Issue 1, p43 

    We estimated queen mating frequency, genetic relatedness among workers, and worker reproduction in Vespa crabro flavofasciata using microsatellite DNA markers. Of 20 colonies examined, 15 contained queens inseminated by a single male, 3 colonies contained queens inseminated by two males, and 2...

  • Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome. Menotti-Raymond, M.; David, V. A.; Agarwala, R.; Schäffer, A. A.; Stephens, R.; O'Brien, S. J.; Murphy, W. J. // Cytogenetic & Genome Research;2003, Vol. 102 Issue 1-4, p272 

    Effective utilization of the domestic cat as an animal model for hereditary and infectious disease requires the development and implementation of high quality gene maps incorporating microsatellites and conserved coding gene markers. Previous feline linkage and radiation hybrid maps have lacked...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics