Abstract
BackgroundDomesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype.ResultsPrincipal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis.ConclusionsThese findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.
Highlights
Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors
Genetic variation in Xichuan black-bone chicken To identify genetic variations, we resequenced the genomes of 5 Xichuan black-bone chickens
We identified 5,062,529 single nucleotide polymorphisms (SNPs), including 247,054 homozygous SNPs, 830,606 insertion/deletion polymorphisms (InDels) (372,903 insertions and 457,703 deletions), 1279 copy number variants (CNVs), and 11,433 Structural variations (SVs) (Supplementary Fig. S1)
Summary
Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Chickens (Gallus Gallus domesticus) were the first domesticated bird species and were subjected for more than 8000 years to the combined effects of natural selection and human-driven artificial selection Compared with their wild progenitors (red junglefowl, Gallus gallus), chickens present many characteristics associated with domestication that impact behavior, morphology, physiology, egg production, and skin color. A variety of studies have used whole-genome high-throughput DNA sequencing to reveal the genetic basis for traits acquired by natural and artificial selection in domesticated animals This approach has recently been applied to dogs [7], pigs [8, 9], chickens [10], sheep [11], rabbits [12], cattle [13, 14], and ducks [15, 16]
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