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

Abstract

The 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.

Keywords: ARL4C; FRMD4A; HOXB1; Sus scrofa; VRTN; Landrace; Large White; morphological trait; single nucleotide polymorphism.

Figure 1

Distribution of the number of teats within the Italian Large White (ILW) and Italian Landrace (IL) populations.

Figure 2

Manhattan plots of the genome‐wide association studies on the number of teats in the Italian Large White (a) and in the Italian Landrace (b) populations. Single‐marker analysis is on the top part of each plot and haplotype‐based analysis is on the bottom part of each plot. Each dot represents a DNA marker or a haplotype. The red lines identify the significance thresholds (Bonferroni correction; α = 0.05).

Figure 3

Boxplots showing the allelic effects of the top associated haplotype regions for the number of teats. (a) Genome region SSC7:97435001 bp in Italian Large White pigs and (b) genome region SSC15:134400001 bp in Italian Landrace pigs. Haplotypes have been treated as bi‐allelic variants (H = haplotype allele and N = other N alleles). The red line indicates the average value.