Genome-wide analysis of genetic diversity and selection signatures in Fuzhou cattle

Abstract

The Fuzhou cattle breed, native to northeast China, is widely recognized for its adaptability, disease resistance, and docility. Despite being known for these qualities, its population has declined recently, and there is a significant lack of genomic studies on this species. We sequenced 21 samples from a primary breeding farm to determine the genetic structure, diversity, and selection signature to address this. Additionally, we combined 100 published genomic datasets from diverse geographical regions to characterize the genomic variation of Fuzhou cattle. There were 53 752 978 bi-allelic SNPs retained for downstream analysis. In population structure analysis, Fuzhou cattle show a predominantly East Asian taurine ancestry, with strong genetic affinities to Hanwoo and Yanbian cattle. Despite high nucleotide diversity within the Bos taurine lineage, genetic diversity analysis also revealed significant levels of inbreeding in Fuzhou cattle populations, indicating the need for conservation. Utilizing various methods such as θπ, iHS, F_ST, π-ratio, and XP-EHH, we identified genes associated with traits like growth, meat quality, energy metabolism, and immunity. Several genes related to cold adaptation were identified, including PLIN5, PLB1, and CPT2. These findings provide a basis for conservation strategies to safeguard the genetic resources of Fuzhou cattle.