Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle.

Kwondo Kim,Kelsey Caetano-Anollés,Tae-Jeong Choi,Yong-Min Cho,Bong-Hwan Choi,Byoungho Park,Heebal Kim,Hyung-Chul Kim,Eung-Woo Park,Jin-Young Jeong,Dongahn Yoo,Samsun Sung,Dajeong Lim,Jaehoon Jung,Marinus F W Te Pas

doi:10.1371/journal.pone.0193701

Abstract

Artificial selection has been demonstrated to have a rapid and significant effect on the phenotype and genome of an organism. However, most previous studies on artificial selection have focused solely on genomic sequences modified by artificial selection or genomic sequences associated with a specific trait. In this study, we generated whole genome sequencing data of 126 cattle under artificial selection, and 24,973,862 single nucleotide variants to investigate the relationship among artificial selection, genomic sequences and trait. Using runs of homozygosity detected by the variants, we showed increase of inbreeding for decades, and at the same time demonstrated a little influence of recent inbreeding on body weight. Also, we could identify ~0.2 Mb runs of homozygosity segment which may be created by recent artificial selection. This approach may aid in development of genetic markers directly influenced by artificial selection, and provide insight into the process of artificial selection.

Highlights

Artificial selection creates genetic signatures on a genome as well as alteration of phenotypes [1,2,3]
We aimed to investigate the changes of inbreeding in Hanwoo population during the decades of selection program, and identify genomic regions related to inbreeding induced by artificial selection and a trait
As the length of Runs of homozygosity (ROH) which is autozygous, decreases over generations, it is necessary to set a suitable threshold of ROH length in order to investigate the effects of recent inbreeding on a genome

Summary

Introduction

Artificial selection creates genetic signatures on a genome as well as alteration of phenotypes [1,2,3]. These genetic signatures refer to any types of sequence alteration which can be generated from selection process. Extended linkage disequilibrium (LD), and reduced nucleotide diversity are examples of the genetic signatures [4, 5]. In the artificial selection process, one of the factors that give rise to such genetic signatures is inbreeding, which is the production of offspring from mating or breeding of individuals that are genetically close [6]. Breeders allow only certain individuals with desirable characteristics to reproduce over the course of decades resulting in intensive inbreeding [7].

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Conclusion