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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00272

A QTL for number of teats shows breed specific effects on number of vertebrae in pigs: Bridging the gap between molecular and quantitative genetics

 Maren Van Son1*,  Marcos S. Lopes2, 3,  Henry J. Martell4,  Martijn F. Derks5, Lars Erik Gangsei6, 7, Jørgen Kongsro1,  Mark N. Wass4, Eli H. Grindflek1 and Barbara Harlizius3
  • 1Norsvin (Norway), Norway
  • 2Topigs Norsvin, Brazil
  • 3Topigs Norsvin (Netherlands), Netherlands
  • 4University of Kent, United Kingdom
  • 5Wageningen University & Research, Netherlands
  • 6Animalia (Norway), Norway
  • 7Norwegian University of Life Sciences, Norway

Modern breeding schemes for livestock species accumulate a large amount of genotype and phenotype data which can be used for genome-wide association studies. Many chromosomal regions harboring effects on quantitative traits have been reported from these studies, but the underlying causative mutations remain mostly undetected. In this study, we combine large genotype and phenotype data available from a commercial pig breeding scheme for three different breeds (Duroc, Landrace, and Large White) to pinpoint functional variation for a region on porcine chromosome 7 affecting number of teats (NTE). Our results show that refining trait definition by counting number of vertebrae (NVE) and ribs (RIB) helps to reduce noise from other genetic variation and increases heritability from 0.28 up to 0.62 NVE and 0.78 RIB in Duroc. However, in Landrace, the effect of the same QTL on NTE mainly affects NVE and not RIB, which is reflected in reduced heritability for RIB (0.24) compared to NVE (0.59). Further, differences in allele frequencies and accuracy of rib counting incluence genetic parameters. Correction for the top SNP does not detect any other QTL effect on NTE, NVE, or RIB in Landrace or Duroc. At the molecular level, haplotypes derived from 660K SNP data detects a core haplotype of seven SNPs in Duroc. Sequence analysis of 16 Duroc animals shows that two functional mutations of the Vertnin (VRTN) gene known to increase number of thoracic vertebrae (ribs) reside on this haplotype. In Landrace, the linkage disequilibrium extends over a region of more than 3 Mb also containing both VRTN mutations. Here, other modifying loci are expected to cause the breed-specific effect. Additional variants found on the wildtype haplotype surrounding the VRTN region in all sequenced Landrace animals point towards breed specific differences which are expected to be present also across the whole genome. This Landrace specific haplotype contains two missense mutations in the ABCD4 gene, one of which is expected to have a negative effect on the protein function. Together, the integration of largescale genotype, phenotype and sequence data shows exemplarily how population parameters are influenced by underlying variation at the molecular level.

Keywords: Teats, vertebrae, Ribs, QTL, fine mapping, Spine development, mammary gland, SSC7

Received: 28 Aug 2018; Accepted: 12 Mar 2019.

Edited by:

Tad S. Sonstegard, Recombinetics (United States), United States

Reviewed by:

Dan Nonneman, Agricultural Research Service, United States Department of Agriculture, United States
Eui-Soo Kim, Recombinetics (United States), United States  

Copyright: © 2019 Van Son, Lopes, Martell, Derks, Gangsei, Kongsro, Wass, Grindflek and Harlizius. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Maren Van Son, Norsvin (Norway), Hamar, Norway,