| Description |
The evolutionary dynamics underlying domestication for animal and plant are of significance. Chicken, an important model organism, has been subjected to intensive human-driven selection, leading to remarkable phenotypic diversity in morphology and physiology. Identifying the genetic dynamics underlying domestication and divergence would provide promising insight into the mechanisms by which genetic variations shape phenotypic diversity. We sequenced 62 chickens from 6 breeds with divergent characteristics, consist of meat-production breeds (Xinghua, XH; Beijing You, YOU; Recessive White, RW), egg-production breed (White Leghorn, WL), ornamental breed (Luxi Dou, DOU), medical breed (Silkie, SILK), as well as Red Jungle Fowl, profiled the whole-genome genetic variations in terms of 15904909 SNPs, 1327453 INDELs, 10445 segmental duplications and 30732 deletions, which exhibit substantial power to distinguish chicken genealogy with distinct origination, selection purpose and geographical distribution. Putative selective sweeps analysis based on self-developed method revealed that all modern chickens have undertaken multiple pivotal systems involving nervous, cardiovascular, skeletal and muscular development, calibrating the distinguishing between wild and modern breeds. For meat-purpose breeds, several intriguing genes/regions potentially associated with lipid metabolism have been identified. For egg-purpose breed, the reproduction system has been subject to human-driven reconstruction. We creatively introduced the conception of entropy and accurately exploited species islands and breed specific islands, which hightlights the breed differentiation. Four significant copy number variations reflected the genomic differentiations in breeds, namely EDN3, TACR3, SOCS2, SMARCE1/KRT222. This study traced the genomic dynamics and functional changing patterns during breed divergence underlying intensive domestication, provided promising insight into the putative genetic architectures of complex traits. |
