Genome-Wide Identification of Discriminative Genetic Variations in Beef and Dairy Cattle via an Information-Theoretic Approach

Soo-Jin Kim,Heebal Kim,Jung-Woo Ha

doi:10.3390/genes11060678

Abstract

Analyzing the associations between genotypic changes and phenotypic traits on a genome-wide scale can contribute to understanding the functional roles of distinct genetic variations during breed development. We performed a whole-genome analysis of Angus and Jersey cattle breeds using conditional mutual information, which is an information-theoretic method estimating the conditional independency among multiple factor variables. The proposed conditional mutual information-based approach allows breed-discriminative genetic variations to be explicitly identified from tens of millions of SNP (single nucleotide polymorphism) positions on a genome-wide scale while minimizing the usage of prior knowledge. Using this data-driven approach, we identified biologically relevant functional genes, including breed-specific variants for cattle traits such as beef and dairy production. The identified lipid-related genes were shown to be significantly associated with lipid and triglyceride metabolism, fat cell differentiation, and muscle development. In addition, we confirmed that milk-related genes are involved in mammary gland development, lactation, and mastitis-associated processes. Our results provide the distinct properties of Angus and Jersey cattle at a genome-wide level. Moreover, this study offers important insights into discovering unrevealed genetic variants for breed-specific traits and the identification of genetic signatures of diverse cattle breeds with respect to target breed-specific properties.

Highlights

Manipulating domesticated animals by inbreeding and artificial selection has led to the development of a multitude of individual cattle breeds
We performed a comparative genome-wide analysis for identifying discriminative genetic variations between Angus and Jersey cattle using enhanced methods based on the information-theoretic approach (Figure 1)
The genomes of the Angus and Jersey cattle were sequenced to approximately 15.79× coverage average, with a total of 840,132,997,679 bp in 8,401,720,919 reads

Summary

Introduction

Manipulating domesticated animals by inbreeding and artificial selection has led to the development of a multitude of individual cattle breeds. Many cattle breeds have become highly specialized for meat or milk production subsequent to strong genetic selection for these traits. In this context, investigating the associations between genetic variations and phenotypes has significant potential for understanding the heritability of complex traits in cattle. Such a study will identify distinct genetic factors that are likely to relate to breed-specific characteristics. The Angus breed has been intensively selected over the last few decades to reduce several recessive genetic disorders [1]

Methods

Results

Discussion

Conclusion