The Domestichick Project: from 57K to Whole Genome Sequence Data.

The red junglefowl (Gallus gallus) is considered as the main ancestor of the domestic chicken, but the genus Gallus includes three other species : Gallus sonneratii (grey junglefowl), Gallus varius (green junglefowl) and Gallus lafayetii (Sri Lanka junglefowl). Deep genome sequencing (25-30X) has been undertaken for these species in order to analyze with a great accuracy the genetic diversity within the genus Gallus and to better understand the genetic make-up of domestic chickens.

The individuals to be sequenced have been chosen according to their geographic origin (Vietnam, Thailand, Japan, Taiwan for wild Gallus; Europe, Africa, Asia, South America for domestic chickens) and on the basis of the genotypes obtained on the 57K SNP Illumina iSelect chicken array, in order to best represent the diversity of the sample. In total 18 wild individuals and 18 domestic chickens, 1 per breed, mostly females, were sequenced in paired-end.

The total number of SNPs detected as compared to the reference genome GalGal4 reached 42 millions. Some regions exhibited a strong differentiation between G. sonneratii and G. gallus (on chromosomes 7 and 28 for instance) whereas others exhibited a very low variability, suggesting a strong selective pressure (on chromosomes 5 and 18 for instance). The analysis of heterozygosity on the Z chromosome provides new insight into the pseudo-autosomal region. A HMM model applied to all data showed that the contribution of G. sonneratii to the genetic make-up of chickens could vary from 0.14 to 1.22% according to the breed.