Single-marker and haplotype-based genome-wide association studies for the number of teats in two heavy pig breeds.

S Bovo,M Gallo,S Dall'Olio,S Tinarelli,V J Utzeri,G Schiavo,L Fontanesi,A Ribani,M Ballan

doi:10.1111/age.13095

Abstract

SummaryThe number of teats is a reproductive‐related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single‐marker and haplotypes‐based genome‐wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype‐based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single‐marker and haplotype‐based genome‐wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs.

Highlights

The number of piglets weaned per sow and per year is one of the most important indicators of economic sustainability of pig farming
A few other studies proposed that polymorphic sites close to the VRTN gene and variability in other genes located on SSC7 could affect the number of teats and vertebrae in pigs (Zhang et al 2016; Park et al 2018)
Descriptive statistics on the number of teats in the two heavy pig breeds Descriptive statistics on the number of teats in Italian Large White and Italian Landrace breeds are reported in Tables S2 and S3 respectively

Summary

Introduction

The number of piglets weaned per sow and per year is one of the most important indicators of economic sustainability of pig farming. Porcine chromosome (SSC) 7 has been reported to harbor one of the most important QTL affecting this trait segregating in several populations (Mikawa et al 2007, 2011; Duijvesteijn et al 2014; Rohrer & Nonneman 2017; Dall’Olio et al 2018; van Son et al 2019; Moscatelli et al 2020) This QTL has pleiotropic effects on the number of vertebrae due to variability in the vertebrae development associated gene known as vertnin (VRTN) (Mikawa et al 2011; Arakawa et al 2015), which encodes for a DNA binding factor (Duan et al 2018). A few other studies proposed that polymorphic sites close to the VRTN gene and variability in other genes located on SSC7 (latent transforming growth factor binding protein 2 or LTBP2 and BRMS1-like transcriptional repressor or BRMS1L) could affect the number of teats and vertebrae in pigs (Zhang et al 2016; Park et al 2018)

Methods

Results

Discussion

Conclusion