Abstract
BackgroundUnderstanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs.ResultsWe performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China. Population genetic analyses revealed the genetic structures of these populations were mostly related to the geographic locations. Notably, we detected 294 and 1263 candidate regions under selection using the di and iHS approaches, respectively. A series of group-specific and breed-specific candidate genes were identified, which are involved in immune response, sexual maturation, stature related, birth and bone weight, embryonic development, coat colors and adaptation. Furthermore, haplotype diversity and network pattern for candidate genes, including LPGAT1, LCORL, PPP1R8, RXFP2 and FANCA, suggest that these genes have been under differential selection pressures in various environmental conditions.ConclusionsOur results shed insights into diverse selection during breed formation in Chinese local cattle. These findings may promote the application of genome-assisted breeding for well-adapted local breeds with economic and ecological importance.
Highlights
Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs
Sample selection and genotyping We genotyped a total of 179 samples using Illumina BovineHD Single nucleotide polymorphism (SNP) array from eight cattle breeds including Yanhuang cattle (YHC), Menggu cattle (MGC), Caidamu cattle (CDM), Liangshan cattle (LSC), Pingwu cattle (PWC), Zhaotong cattle (ZTC), Wenshan cattle (WSC) and Nandan cattle (NDC)
We observed the distributions of minor allele frequency (MAF) display distinct patterns across breeds, which may reflect the diverse population history, genetic structure and geographic origin of breed formation
Summary
Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs. As an important domesticated farm animal, is raised for many purposes, including meat, dairy, leather, and labor. China has rich cattle genetic resources, and these breeds can be divided into different groups based on their locations, morphologies and sex chromosome polymorphisms [5,6,7]. Previous genetic analyses using mtDNA and Y microsatellite (Y-STR) data indicated that Chinese cattle breeds are influenced by the two above subspecies, with cattle in the north and northeast China are primarily of Bos t. Taurus ancestry and cattle in southern China are predominantly of Bos t. Indicus [5,6,7,8,9,10,11]. Modern farm animals are a result of selective breeding for many traits of economic and adaptive importance since
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