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

  • Twito T
  • Weigend S
  • Blum S
 et al. 
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Abstract

Marth et al., 1999; Zhou and Lamont, 1999; Parker et al., 2004). Knowledge of genetic relationships between popula-tions may be useful for further genetic studies and for de-veloping conservation strategies (Baali-Cherif and Besnard, 2005). These studies also assist in tracing the history of do-mestication and evolution of the species under study (Vish-wanathan et al., 2004; Gaines et al., 2005). SNPs (single nucleotide polymorphisms) are single base changes in a DNA sequence. SNPs are usually bi-allelic, due to the low frequency of single nucleotide mutation, estimat-ed to be between 1 ! 10 –9 and 5 ! 10 –9 per nucleotide and year at neutral positions in mammals (Martinez-Arias et al., 2001). 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 differ-ent chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phy-logenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeat-ability, doubling the number of SNPs from 12 to 25 im-proved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering re-sults of these 20 populations, based on the software STRUC-TURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affilia-tion of birds to their original populations was correct (1 95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered

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