Abstract
Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current commercial stocks bred for efficient meat and egg production. In‐depth characterizations of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.
Highlights
The chicken is one of the major agricultural species, and the poultry industry today produces more than 120 million tons of meat and over 1.2 trillion eggs each year (FAO, 2020)
Hundreds of chicken breeds have been established across the world (Figure 1a,b), ranging from extensively kept indigenous breeds to highly specialized chicken stocks used in industrial-scale egg or meat production
Selection signatures in domestic stocks resulting from past breeding processes for production traits, and traits related to regional adaptation, could be compared with patterns resulting from admixture events and relationships among populations could be used to make demographic inferences for comparisons with historical description of population dynamics and crossings
Summary
The chicken is one of the major agricultural species, and the poultry industry today produces more than 120 million tons of meat and over 1.2 trillion eggs each year (FAO, 2020). Its domestication started about 10,000 year ago (International Chicken Polymorphism Map, 2004; Xiang et al, 2014), likely following a commensal pathway where the initial interactions were an adaptation of wild junglefowl to human-created niches, followed by an over time increased human intent to keep, control, intensively breed and commercialize the use of chicken in agriculture (Zeder, 2012). During this process, hundreds of chicken breeds have been established across the world (Figure 1a,b), ranging from extensively kept indigenous breeds to highly specialized chicken stocks used in industrial-scale egg (layers) or meat (broilers) production. Our results were in agreement with available historical records about the origin and ancestry of key breeds used in the breeding of current stocks used for commercial egg and meat production
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