Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

Abstract

-In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of populationspecific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.genetic distance / polymorphism / red jungle fowl / DNA markers / domesticated chicken

Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication

“…Using peak frequencies rather than correcting for actual alleles results in a systematic overestimation of the actual number of alleles and hence heterozygosity. Nevertheless, as expected [9,20,44], the effective number of peaks does correlate strongly with the effective number of alleles as do heterozygosity (Fig. 1) and the inferred genetic distances (see supplementary material online version only: http://www.gse-journal.org) when comparing to individually genotyped pigs.…”

“…[2]). Gene diversity (H m ) was measured for all loci and all populations by using peak frequencies instead of allele frequencies according to Hillel et al [20]. An average H was calculated from H m for each population across loci, but only for loci that had a higher than 75% success ratio overall.…”

“…Pooling DNA samples provides a cost effective method for any study that aims at assessing relative differences of allele frequency among populations [44] and can be applied to microsatellite markers [9,20,42] and SNP e.g. [46].…”

“…Three distance measures available from the Phylip package (Phylip 3.64 [14]) were considered: Nei standard (D s [29]), Reynolds (D r [36]), and Cavalli-Sforza chord (D c [5,20]). Hillel et al [20] found a significant and large degree of correlation between these three distance measures in chicken lines for pooled samples.…”

“…Several meaningful population statistics and comparisons can be deduced from allele frequency data. Although individual genotyping is the most accurate method to estimate allele frequencies in populations, it has been shown that pooled sampling methods [9,16,20,[42][43][44], and references therein can perform very adequately as well, at a fraction of the cost of labor and consumables.…”