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. 2024 Oct 6;14(19):2874.
doi: 10.3390/ani14192874.

Genome-Wide Association Study of Reproductive Traits in Large White Pigs

Yifeng Hong  1 , Cheng Tan  2   3   4 , Xiaoyan He  3   4 , Dan Wu  3   4 , Yuxing Zhang  3   4 , Changxu Song  1 , Zhenfang Wu  1   2   3   4
Affiliations

Genome-Wide Association Study of Reproductive Traits in Large White Pigs

Yifeng Hong et al. Animals (Basel). .

Abstract

(1) Background: Reproductive performance is crucial for the pork industry's success. The Large White pig is central to this, yet the genetic factors influencing its reproductive traits are not well understood, highlighting the need for further research. (2) Methods: This study utilized Genome-Wide Association Studies to explore the genetic basis of reproductive traits in the Large White pig. We collected data from 2237 Large White sows across four breeding herds in southern China, focusing on eight reproductive traits. Statistical analyses included principal component analysis, linkage disequilibrium analysis, and univariate linear mixed models to identify significant single-nucleotide polymorphisms and candidate genes. (3) Results: Forty-five significantly related SNPs and 17 potential candidate genes associated with litter traits were identified. Individuals with the TT genotype at SNP rs341909772 showed an increase of 1.24 in the number of piglets born alive (NBA) and 1.25 in the number of healthy births (NHBs) compared with those with the CC genotype. (4) Conclusions: The SNPs and genes identified in this study offer insights into the genetics of reproductive traits in the Large White pig, potentially guiding the development of breeding strategies to improve litter size.

Keywords: GWAS; Large White pigs; SNPs; candidate genes; litter traits.

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Conflict of interest statement

Authors Xiaoyan He, Dan Wu, and Yuxing Zhang were employed by Wens Foodstuff Group Co., Ltd. This company provided the pigs used in this study from a swine breeding herd that it owns and manages. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Manhattan plots of GWAS with SNPs for litter traits at the first parity in the Large White populations. In the Manhattan plots, the yellow and red lines represent the 5% genome-wide and chromosome-wide (suggestive) Bonferroni-corrected thresholds, respectively.
Figure 2
Figure 2
Manhattan plots of GWAS with SNPs for litter traits at the second parity in the Large White populations. In the Manhattan plots, the yellow and red lines represent the 5% genome-wide and chromosome-wide (suggestive) Bonferroni-corrected thresholds, respectively.
Figure 3
Figure 3
The genotype effect plot of the pleiotropic SNP rs341909772, which is associated with both NBA and NHB in the Large White population at the second parity, is displayed. On the left, the plot shows the effect of SNP rs341909772 on NBA, and on the right, the effect on NHB (** p < 0.001).
Figure 4
Figure 4
The regional association plot illustrates the primary signal (rs332278643) associated with NWB on SSC15 in the Large White population at the second parity. The plot displays negative log10 p-values of SNPs (y-axis) according to their chromosomal positions (x-axis). The red line indicates the genome-wide significance level. The primary SNPs are marked by red triangles. The left and right panels of the figure show the association results for NWB before and after conditional analysis on rs332278643, respectively. The color of the dots in the plot represents the level of linkage disequilibrium (LD) with the primary signal (rs332278643), where redder dots indicate higher LD levels, and yellower dots indicate lower LD levels.
See this image and copyright information in PMC

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