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Open Access Research article

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

Naomi Duijvesteijn1*, Jacqueline M Veltmaat2, Egbert F Knol1 and Barbara Harlizius1

Author Affiliations

1 TOPIGS Research Center IPG, PO Box 43, 6640AA Beuningen, The Netherlands

2 Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61, Biopolis Drive, Singapore, Singapore 138673

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BMC Genomics 2014, 15:542  doi:10.1186/1471-2164-15-542

Published: 30 June 2014

Abstract

Background

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. 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.

Results

The 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.

Conclusions

Five 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.

Keywords:
Pigs; Number of teats; Vertebrae; Genome-wide association study; Somites; De-regressed breeding values