Abstract Domestic organisms provide valuable models for studying the impact of population bottlenecks, inbreeding, and artificial selection on the accumulation of deleterious variants. While previous studies largely focused on coding variants, our study investigated both coding and non-coding contributions to genetic load in diverse chicken breeds, revealing the consequences of inbreeding and artificial selection on genome-wide patterns of deleterious variation. Using representative chicken populations with different selection histories, we show that domestication processes significantly impact the genetic load in chicken populations. Village chickens, which have experienced only the initial domestication, exhibit comparable levels of neutral heterozygosity and realized load as their wild progenitor Red Jungle Fowl. In contrast, breed chickens that have undergone more intense artificial selection show a significant decrease in neutral heterozygosity, an increase in the ratio of zerofold to fourfold heterozygosity, and a higher realized genetic load in both coding and non-coding regions. However, signals of purging of loss-of-function and non-coding deleterious variants were also detected in domestic chicken. Inbreeding is a major contributor to the increase of genome-wide realized load. We found selection against recently inbred individuals carrying long ROHs covering more coding regions, and an enrichment of homozygous non-coding deleterious variants in ROHs of no less than 2Mb. Additionally, we found that artificial selection drastically elevated the relative allele frequency of deleterious variants within sweep regions. These findings have implications for the importance of genetic background evaluation of breeding flocks and strategic management to maintain long-term health in domestic populations.
Huang et al. (Wed,) studied this question.