Decoding genetic architecture of dog complex traits by constructing fine-scale genomic ancestry of admixture

Domestic animals and plants exhibit remarkable phenotypic diversity in terms of morphology, behavior, and physiology, which can be attributed to the complex interbreeding process of various breeds and artificial selection. Here we develop a method that can efficiently construct fine-scale interbreeding history of local segments along the genome. Since ancestral breeds usually exhibit diverse phenotypes, the method provides a valuable approach for unraveling the genetic architecture of complex traits in admixed breeds. Simulated data demonstrates that the method performs well, even in scenarios involving complex interbreeding with up to 19 ancestral breeds. The method is applied to analyze three mixed dog breeds, Irish Wolfhound, Giant Schnauzer, and Miniature Schnauzer, representing instances of body-size enlargement and miniaturization. Numerous novel ancestor breed-specific genes determining body size are identified, including FGFR2, WDR11, and FARS2. We also validate genes reported in previous GWAS or genomic sweep scans, such as LCORL, STC2, NPR2, and FGF4. These findings highlight the validity of the method as a valuable tool for investigating the genetic basis underlying ancestry-specific traits in domestic animals and plants with complex interbreeding histories.