Genetic diversity and genealogical origins of domestic chicken

This paper reviews some important features of the chicken genome, genealogical origins and the current status of the genetic diversity of the chicken. The small chicken genome exhibits six times more single nucleotide polymorphisms (>7,000,000 SNPs) than mammalian genomes and considerable microsatellite content (375,000). An obvious debate is still dedicated to whether chicken origin is monophyletic or polyphyletic. Modern genetic analysis conducted across the world's chicken population has determined no restricted phylo-geographical centre of domestication, as has been shown for other livestock species. Wild, unselected native and some fancy and conserved chicken populations showed high microsatellite and SNP diversity. Within-population diversity was higher than between-population diversity in selected or inbred chicken populations, whereas village chickens almost showed no sub-division in clusters. There is a variable degree of mitochondrial-DNA control-region (mtDNA-CR) sequence diversity within native chicken populations. Although commercial broilers exhibited considerable diversity in all marker types, they have lost >50% of SNP alleles found in their ancestors. Moreover, the linkage disequilibrium (LD) within broiler lines extends over shorter distances than in other inbred livestock populations. Domestic chickens are still genetically diverse and further conservation efforts are warranted to maintain the large between-population diversity.