Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome.

Martijn F L Derks,Martien A M Groenen,Hendrik-Jan Megens,Barbara Harlizius,Mirte Bosse,Ole Madsen,Bert Dibbits,Marcos S Lopes,Tosso Leeb

doi:10.1371/journal.pgen.1007661

Martijn F L Derks, Martien A M Groenen + Show 7 more

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https://doi.org/10.1371/journal.pgen.1007661

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Abstract

Livestock populations can be used to study recessive defects caused by deleterious alleles. The frequency of deleterious alleles including recessive lethal alleles can stay at high or moderate frequency within a population, especially if recessive lethal alleles exhibit an advantage for favourable traits in heterozygotes. In this study, we report such a recessive lethal deletion of 212kb (del) within the BBS9 gene in a breeding population of pigs. The deletion produces a truncated BBS9 protein expected to cause a complete loss-of-function, and we find a reduction of approximately 20% on the total number of piglets born from carrier by carrier matings. Homozygous del/del animals die mid- to late-gestation, as observed from high increase in numbers of mummified piglets resulting from carrier-by-carrier crosses. The moderate 10.8% carrier frequency (5.4% allele frequency) in this pig population suggests an advantage on a favourable trait in heterozygotes. Indeed, heterozygous carriers exhibit increased growth rate, an important selection trait in pig breeding. Increased growth and appetite together with a lower birth weight for carriers of the BBS9 null allele in pigs is analogous to the phenotype described in human and mouse for (naturally occurring) BBS9 null-mutants. We show that fetal death, however, is induced by reduced expression of the downstream BMPER gene, an essential gene for normal foetal development. In conclusion, this study describes a lethal 212kb deletion with pleiotropic effects on two different genes, one resulting in fetal death in homozygous state (BMPER), and the other increasing growth (BBS9) in heterozygous state. We provide strong evidence for balancing selection resulting in an unexpected high frequency of a lethal allele in the population. This study shows that the large amounts of genomic and phenotypic data routinely generated in modern commercial breeding programs deliver a powerful tool to monitor and control lethal alleles much more efficiently.

Highlights

Domesticated animals are excellent models to study the effect of inbreeding on fitness, and the role of selection in inbreeding depression
Drift effects are expected to be less severe because recessive lethal alleles from founder boars are less likely to rise in frequency very rapidly, because of a lower male selection intensity compared to cattle breeding [6]
Genomic loci that harbour recessive lethal alleles can be identified by searching for haplotypes showing reduced or missing homozygosity

Summary

Introduction

Domesticated animals are excellent models to study the effect of inbreeding on fitness, and the role of selection in inbreeding depression. Breeding of domesticated animals increases inbreeding by applying artificial insemination that allows breeding populations to be sired by a small number of elite males. The frequency of deleterious alleles including recessive lethal alleles can rise in populations as a consequence of drift due to small effective population size, and due to selection [1]. In cattle breeds, several high frequency lethal alleles have been described [3, 4] reaching carrier frequencies up to 32% [5], that can be traced back to prime bulls that were used extensively in the past decades. Drift effects are expected to be less severe because recessive lethal alleles from founder boars are less likely to rise in frequency very rapidly, because of a lower male selection intensity compared to cattle breeding [6]

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