Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions

Abstract

Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeatability, doubling the number of SNPs from 12 to 25 improved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering results of these 20 populations, based on the software STRUCTURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affiliation of birds to their original populations was correct (>95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered into five groups based on STRUCTURE, we used membership coefficient (Q) of the major cluster at each population as an indicator for clustering success level. This value was used to compare between three marker types; microsatellites, SNPs in or close to genes (g-SNPs) and SNPs in random fragments (r-SNPs). In this comparison, the same individuals were used (five to ten birds per population) and the same number of loci (14) used for each of the marker types. The average membership coefficients (Q) of the major cluster for microsatellites, g-SNPs and r-SNPs were 0.85, 0.7, and 0.64, respectively. Analysis based on microsatellites resulted in significantly higher clustering success due to their multi-allelic nature. Nevertheless, SNPs have obvious advantages, and are an efficient and cost-effective genetic tool, providing broader genome coverage and reliable estimates of genetic relatedness.

Conservation of Local Turkish and Italian Chicken Breeds: A Case Study

“…Until 2005, genotyping of the individual animals for the marker-assisted conservation scheme was carried out using the amplified fragment length polymorphism (AFLP) technique (De Marchi et al, 2006). After 2005, microsatellites were applied in the Veneto conservation scheme because they are well dispersed in the genome and highly polymorphic (Twito et al, 2007;Zanetti, 2009). About 30 microsatellites are currently routinely used for genotyping chicken breeds in the conservation scheme.…”

Evaluation of diversity between different Spanish chicken breeds, a tester line, and a White Leghorn population based on microsatellite markers

“…Genetic relationships between a wide range of chicken types from Europe, Asia, and Africa have been analyzed in the AVIANDIV project (Hillel et al, 2003), and Berthouly et al (2008) studied genetic diversity of French and Asian breeds, comparing them with those of the AVI-ANDIV project. Finally, Twito et al (2007) compared the biodiversity of 20 chicken breeds with SNP and microsatellite markers, noting that analysis based on microsatellites resulted in significantly higher clustering success due to their multiallelic nature.…”

Phylogenetic Analysis of South East Asian Countries Chickens Based on Mitochondrial DNA Variations

“…They established the theory of monophyletic origin of the domestic chicken that descended mainly from RJF subspecies of Southeast Asia. This result was supported by the analysis of microsatellite DNAs (Hillel et al, 2003) and single nucleotide polymorphism (SNP) genotypes in a wide range of distant chicken populations (Twito et al, 2007). In addition, SNP analysis at chicken lysozyme gene for species of genus Gallus and different domestic chickens revealed more closer relationship of RJF with domestic chickens than that of other fowl species (Downing et al, 2010).…”