High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development.

Naomi Duijvesteijn,Barbara Harlizius,Egbert F Knol,Jacqueline M Veltmaat

doi:10.1186/1471-2164-15-542

Abstract

BackgroundSelection pressure on the number of teats has been applied to be able to provide enough teats for the increase in litter size in pigs. Although many QTL were reported, they cover large chromosomal regions and the functional mutations and their underlying biological mechanisms have not yet been identified. To gain a better insight in the genetic architecture of the trait number of teats, we performed a genome-wide association study by genotyping 936 Large White pigs using the Illumina PorcineSNP60 Beadchip. The analysis is based on deregressed breeding values to account for the dense family structure and a Bayesian approach for estimation of the SNP effects.ResultsThe genome-wide association study resulted in 212 significant SNPs. In total, 39 QTL regions were defined including 170 SNPs on 13 Sus scrofa chromosomes (SSC) of which 5 regions on SSC7, 9, 10, 12 and 14 were highly significant. All significantly associated regions together explain 9.5% of the genetic variance where a QTL on SSC7 explains the most genetic variance (2.5%). For the five highly significant QTL regions, a search for candidate genes was performed. The most convincing candidate genes were VRTN and Prox2 on SSC7, MPP7, ARMC4, and MKX on SSC10, and vertebrae δ-EF1 on SSC12. All three QTL contain candidate genes which are known to be associated with vertebral development. In the new QTL regions on SSC9 and SSC14, no obvious candidate genes were identified.ConclusionsFive major QTL were found at high resolution on SSC7, 9, 10, 12, and 14 of which the QTL on SSC9 and SSC14 are the first ones to be reported on these chromosomes. The significant SNPs found in this study could be used in selection to increase number of teats in pigs, so that the increasing number of live-born piglets can be nursed by the sow. This study points to common genetic mechanisms regulating number of vertebrae and number of teats.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-542) contains supplementary material, which is available to authorized users.

Highlights

Selection pressure on the number of teats has been applied to be able to provide enough teats for the increase in litter size in pigs
The Genome-Wide Association Study (GWAS) resulted in 212 Single Nucleotide Polymorphisms (SNPs) with a Bayes Factor (BF) >10 of which 6 SNPs had a BF > 100 (Figure 2)
Instead of a sliding window of N number of SNPs, which is often used to account for linkage disequilibrium (LD) [47], regions were defined based on distances between significant SNPs (

Summary

Introduction

Selection pressure on the number of teats has been applied to be able to provide enough teats for the increase in litter size in pigs. The number of mammary glands varies among mammalian species, but even in humans, who normally form one pair of breasts, there are at least 6 other positions that additional breasts can randomly occupy on either side of the body [21] Their positions range from armpit (axilla) to groin (inguen), span the same region where pigs form their mammary glands and teats. On both sides lateral to the ventral midline, one can draw imaginary fluent lines from both axillae to both inguenae, called mammary lines or milk lines. These lines exist as histologically and molecularly distinct bands in the surface ectoderm, connecting all positions where mammary glands may form on either side of the body in any given mammalian species [22,23,24]

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