Increased Genetic Load in Breed Chickens and Reduced Coding Content in Long ROH

Area of Science:

• Genomics
• Animal Genetics
• Evolutionary Biology

Background:

• Domestic organisms serve as models for studying genetic variation.
• Previous research focused on coding variants, neglecting non-coding contributions to genetic load.
• Understanding genetic load is crucial for domestic animal health and management.

Purpose of the Study:

• To investigate the impact of domestication, inbreeding, and artificial selection on genetic load in chickens.
• To analyze both coding and non-coding deleterious variants in diverse chicken breeds.
• To reveal genome-wide patterns of deleterious variation resulting from selective breeding.

Main Methods:

• Comparative analysis of chicken populations with varying selection histories.
• Assessment of neutral heterozygosity and realized genetic load.
• Examination of coding and non-coding variants, including loss-of-function and non-coding deleterious variants.
• Analysis of runs of homozygosity (ROHs) and sweep regions.

Main Results:

• Village chickens show genetic load similar to Red Jungle Fowl, while breed chickens exhibit reduced heterozygosity and increased genetic load.
• Inbreeding significantly increases genome-wide realized load, with selection against individuals with long ROHs.
• Artificial selection elevates deleterious variant frequencies in sweep regions, impacting both coding and non-coding DNA.

Conclusions:

• Domestication and artificial selection profoundly alter genetic load in domestic chickens.
• Inbreeding is a primary driver of increased genetic load.
• Findings emphasize the importance of genetic background evaluation and strategic management for domestic populations.