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. 2022 Jun 19;12(12):1584.
doi: 10.3390/ani12121584.

Identification of Genomic Regions and Candidate Genes for Litter Traits in French Large White Pigs Using Genome-Wide Association Studies

Jianmei Chen  1 , Ziyi Wu  1 , Ruxue Chen  1 , Zhihui Huang  1 , Xuelei Han  1 , Ruimin Qiao  1 , Kejun Wang  1 , Feng Yang  1 , Xin-Jian Li  1 , Xiu-Ling Li  1
Affiliations

Identification of Genomic Regions and Candidate Genes for Litter Traits in French Large White Pigs Using Genome-Wide Association Studies

Jianmei Chen et al. Animals (Basel). .

Abstract

The reproductive traits of sows are one of the important economic traits in pig production, and their performance directly affects the economic benefits of the entire pig industry. In this study, a total of 895 French Large White pigs were genotyped by GeneSeek Porcine 50K SNP Beadchip and four phenotypic traits of 1407 pigs were recorded, including total number born (TNB), number born alive (NBA), number healthy piglets (NHP) and litter weight born alive (LWB). To identify genomic regions and genes for these traits, we used two approaches: a single-locus genome-wide association study (GWAS) and a single-step GWAS (ssGWAS). Overall, a total of five SNPs and 36 genomic regions were identified by single-locus GWAS and ssGWAS, respectively. Notably, fourof all five significant SNPs were located in 10.72-11.06 Mb on chromosome 7, were also identified by ssGWAS. These regions explained the highest or second highest genetic variance in the TNB, NBA and NHP traits and harbor the protein coding gene ENSSSCG00000042180. In addition, several candidate genes associated with litter traits were identified, including JARID2, PDIA6, FLRT2 and DICER1. Overall, these novel results reflect the polygenic genetic architecture of the litter traits and provide a theoretical reference for the following implementation of molecular breeding.

Keywords: SNP; SsGWAS; genetic variants; pig; reproductive traits.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The Manhattan plots of genome-wide association study for four reproductive traits. (A) TNB: total number born; (B) NBA: number born alive; (C) NHP, number healthy piglets; (D) LWB: litter weight born alive. Each dot represents one SNP. The y-axis represents −log10(P). The x-axis represents the position of SNPs. The horizontal solid line depicts the chromosome-level significance threshold value.
Figure 2
Figure 2
The Manhattan plots of single-step genome-wide association study for four reproductive traits. (A) TNB: total number born; (B) NBA: number born alive; (C) NHP, number healthy piglets; (D) LWB: litter weight born alive. Each dot represents one window of 10 adjacent SNPs. The y-axis displays the proportion of genetic variances of each window. The x-axis represents the position of windows for chromosomes. The horizontal solid line depicts the significance level (proportion of genetic variances = 1%).
Figure 3
Figure 3
The 49 protein coding genes related to four reproductive traits. The blue circles represent genes and the orange diamonds represent traits. TNB: total number born; NBA: number born alive; NHP: number healthy piglets; LWB: litter weight born alive.
Figure 4
Figure 4
The analysis of 10.5–11.5 Mb region. (A) The Manhattan plot of genome-wide association study for NBA trait; (B) The Manhattan plot of single-step genome-wide association study for NBA trait; (C) genes distributed in 10.5–11.5 Mb region; (D) linkage disequilibrium analysis for 10.5–11.5 Mb region.
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References

    1. Ye J., Tan C., Hu X., Wang A., Wu Z. Genetic parameters for reproductive traits at different parities in Large White pigs. J. Anim. Sci. 2018;96:1215–1220. doi: 10.1093/jas/sky066. - DOI - PMC - PubMed
    1. Ogawa S., Konta A., Kimata M., Ishii K., Uemoto Y., Satoh M. Estimation of genetic parameters for farrowing traits in purebred Landrace and Large White pigs. Anim. Sci. J. 2019;90:23–28. doi: 10.1111/asj.13120. - DOI - PMC - PubMed
    1. Canario L., Roy N., Gruand J., Bidanel J.P. Genetic variation of farrowing kinetics traits and their relationships with litter size and perinatal mortality in French Large White sows. J. Anim. Sci. 2006;84:1053–1058. doi: 10.2527/2006.8451053x. - DOI - PubMed
    1. Song H., Zhang J., Jiang Y., Gao H., Tang S., Mi S., Yu F., Meng Q., Xiao W., Zhang Q., et al. Genomic prediction for growth and reproduction traits in pig using an admixed reference population. J. Anim. Sci. 2017;95:3415–3424. doi: 10.2527/jas2017.1656. - DOI - PubMed
    1. Ding R., Qiu Y., Zhuang Z., Ruan D., Wu J., Zhou S., Ye J., Cao L., Hong L., Xu Z., et al. Genome-wide association studies reveals polygenic genetic architecture of litter traits in Duroc pigs. Theriogenology. 2021;173:269–278. doi: 10.1016/j.theriogenology.2021.08.012. - DOI - PubMed

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