Abstract
Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models for individual-specific allele frequencies that directly capture a wide range of complex structure from genome-wide genotypes. As measured by magnitude of differentiation, selection pressure on SNPs within genes is substantially greater than that on intergenic regions. Additionally, broad regions of chromosome 6 harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull genomes can support genetic management strategies that capture structural complexity and promote sustainable genetic breadth.
Highlights
Recognizing the importance of cattle genome diversity in genome-wide association studies, genomic predictions, and optimal breeding, there have been substantial efforts to obtain genome-wide genotypes of multiple breeds in diverse geographical locations[1,2,3]
This study provides detailed assessment of population structure among a diverse panel of whole genome sequences (~4.0 million single nucleotide polymorphism (SNP) per bull)
We enable interactive exploration of this population structure by creating an online app visualizing logistic factors (LFs) according to user-specified parameters
Summary
Recognizing the importance of cattle genome diversity in genome-wide association studies, genomic predictions, and optimal breeding, there have been substantial efforts to obtain genome-wide genotypes of multiple breeds in diverse geographical locations[1,2,3]. The structural complexity of cattle has previously been studied based on array-based genome profiles or selected genetic markers, focusing on regions and breeds[4,5,6,7,8,9], a population genomic study involving whole genome sequences related to European and Western ancestry has not been performed. Logistic factor analysis (LFA) uses recently developed probabilistic models of individual allele frequencies underlying genotypes that are appropriate for a wide range of population structures (e.g., discrete, continuous, or admixture)[10]. By modeling each single nucleotide polymorphism (SNP) by the population structure estimated by logistic factors (LFs), genetic differentiation can be directly tested and inferred. This study provides detailed assessment of population structure among a diverse panel of whole genome sequences (~4.0 million SNPs per bull). We present an interactive visualization, which enables exploration of underlying population structure by LFs
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