The genomic characteristics affect phenotypic diversity from the perspective of genetic improvement of economic traits

The genetic improvement of economic traits suggests that chicken is an excellent model for exploring the genetic changes and molecular mechanisms underlying phenotypic diversity and artificial selection. Here, the sequencing data including 477 samples from 25 breeds worldwide were used to reveal the genomic patterns of chicken domestication. We analyzed 7.4 Tb clean data with 14.83 per individ-ual to identify 23,504,766 SNPs, 3,289,782 InDels, and 27,027 SVs. The diversity analysis indicates that high-intensity artificial selection would accelerate popula-tion differentiation. We also found that the human-driven traits are controlled by polygenes and major genes, such as the primary candidates SOX5 and IGF1 for body size, and NEDD4 for sperm storage capacity. Our findings provide an impor-tant reference for understanding how genomic patterns shape phenotypes in livestock.

Automated summary

The genetic improvement of economic traits in chicken makes it an excellent model for studying the genetic changes and molecular mechanisms underlying phenotypic diversity and artificial selection. By analyzing the sequencing data of 477 samples from 25 breeds, we identified SNPs, InDels, and SVs, and found that high-intensity artificial selection accelerates population differentiation. We also discovered that human-driven traits in chicken are controlled by polygenes and major genes, such as SOX5 and IGF1 for body size, and NEDD4 for sperm storage capacity. Our findings provide important insights into how genomic patterns shape livestock phenotypes.