Genome-wide Analysis of Genetic Diversity and Differentiation of Different Feather Color Population in Yantai Cankang Chicken (Gallus gallus domesticus)
1 School of Animal Science and Technology/Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan 528225, China; 2 Sichuan Academy of Animal Husbandry Science/Animal Genetic Breeding and Reproduction Key Laboratory of Sichuan province, Chengdu 610066, China; 3 Jining Rencheng District Animal Husbandry and Veterinary Development Center, Jining 273199, China; 4 Shandong Bairiji Poultry Breeding Ltd. Co., Jining 272073; 5 Jining City Animal and Veterinary Development Center, Jining 272002, China
Abstract：The Yantai Cankang chicken (Gallus gallus domesticus) exhibits significant phenotypic differentiation within this breed, though whether distinct resource populations have formed remains to be determined. In this study, production phenotypes and blood samples were collected from roosters, mottled hens, yellow partridge hens and black partridge hens, for whole-genome resequencing analysis, whole genome data from 101 individuals were obtained and jointly analyzed with genomic data from 3 other local breeds in Jining city. A comprehensive assessment of different subpopulations of Yantai Cankang chicken was conducted at both mitochondrial and whole-genome levels, focusing on genetic diversity, population structure, genetic relationships, and runs of homozygosity (ROH) distribution characteristics. The results indicated significant genetic differentiation between Yantai Cankang chicken and other local breeds. Despite the presence of multiple feather color groups within the breed, no distinct subpopulations were formed in terms of production phenotypes or genomics, characterized by low genetic differentiation among populations, high genetic diversity, and low inbreeding coefficients. Relatively, roosters exhibited comparatively lower inbreeding coefficients. In conclusion, the Yantai Cankang chicken population demonstrated a favorable conservation status, specialized line breeding and industrial development could be appropriately enhanced. This study provides a scientific foundation for the conservation, selective breeding, and industrial development and utilization of Yantai Cankang chicken genetic resources.
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