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. 2024 Aug 23;14(17):2449.
doi: 10.3390/ani14172449.

Genetic Structure and Genome-Wide Association Analysis of Growth and Reproductive Traits in Fengjing Pigs

Lei Xing  1 , Xuelin Lu  1 , Wengang Zhang  1 , Qishan Wang  2 , Weijian Zhang  1
Affiliations

Genetic Structure and Genome-Wide Association Analysis of Growth and Reproductive Traits in Fengjing Pigs

Lei Xing et al. Animals (Basel). .

Abstract

The Fengjing pig is one of the local pig breed resources in China and has many excellent germplasm characteristics. However, research on its genome is lacking. To explore the degree of genetic diversity of the Fengjing pig and to deeply explore its excellent traits, this study took Fengjing pigs as the research object and used the Beadchip Array Infinium iSelect-96|XT KPS_PorcineBreedingChipV2 for genotyping. We analyzed the genetic diversity, relatedness, inbreeding coefficient, and population structure within the Fengjing pig population. Our findings revealed that the proportion of polymorphic markers (PN) was 0.469, and the effective population size was 6.8. The observed and expected heterozygosity were 0.301 and 0.287, respectively. The G-matrix results indicated moderate relatedness within the population, with certain individuals exhibiting closer genetic relationships. The NJ evolutionary tree classified Fengjing boars into five family lines. The average inbreeding coefficient based on ROH was 0.318, indicating a high level of inbreeding. GWAS identified twenty SNPs significantly associated with growth traits (WW, 2W, and 4W) and reproductive traits (TNB and AWB). Notably, WNT8B, RAD21, and HAO1 emerged as candidate genes influencing 2W, 4W, and TNB, respectively. Genes such as WNT8B were verified by querying the PigBiobank database. In conclusion, this study provides a foundational reference for the conservation and utilization of Fengjing pig germplasm resources and offers insights for future molecular breeding efforts in Fengjing pigs.

Keywords: Fengjing pigs; SNP chip; genetic diversity; genome-wide association study.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
(A) G-matrix heat map of Fengjing pigs in the conserved population. Each tiny square exhibits the kinship value between different individuals. The closer the color of the squares is to red, the closer the kinship between individuals. (B) The phylogenetic tree of Fengjing boars. The numbers are boar ear numbers, and samples marked with the same color in the evolutionary tree diagram were assessed to be of the same lineage. (C) Phylogenetic tree of all individuals in this population. Individuals with the same color belong to the same familial lineage.
Figure 1
Figure 1
(A) G-matrix heat map of Fengjing pigs in the conserved population. Each tiny square exhibits the kinship value between different individuals. The closer the color of the squares is to red, the closer the kinship between individuals. (B) The phylogenetic tree of Fengjing boars. The numbers are boar ear numbers, and samples marked with the same color in the evolutionary tree diagram were assessed to be of the same lineage. (C) Phylogenetic tree of all individuals in this population. Individuals with the same color belong to the same familial lineage.
Figure 2
Figure 2
(A), Distribution of ROH numbers on the chromosomes in Fengjing pigs. (B) Distribution of ROH numbers in Fengjing pigs. (C) Distribution of ROH length in Fengjing pigs. (D) Distribution of the inbreeding coefficient based on runs of homozygosity in Fengjing pigs.
Figure 3
Figure 3
The Manhattan plots and quantile–quantile plots of the GWAS results of the growth traits. (A) The Manhattan plots and quantile–quantile plots of the GWAS results of the WW trait. (B) The Manhattan plots and quantile–quantile plots of the GWAS results of the 2W trait. (C) The Manhattan plots and quantile–quantile plots of the GWAS results of the 4W trait. The red line in the Manhattan plots represents the level of significance. The red line in the quantile–quantile plots is the middle line assuming that the expected value equals the observed value.
Figure 4
Figure 4
GO annotation and KEGG pathway analysis for candidate genes. (A) The GO enrichment analysis of WW candidate genes. (B) The KEGG pathways of WW candidate genes. (C) The GO enrichment analysis of 2W candidate genes. (D) The KEGG pathways of 2W candidate genes. (E) The GO enrichment analysis of 4W candidate genes. (F) The KEGG pathways of 4W candidate genes.
Figure 5
Figure 5
The Manhattan plots and quantile–quantile plots of the GWAS results of the reproduction traits. (A) The Manhattan plots and quantile–quantile plots of the GWAS results of the TNB trait. (B) The Manhattan plots and quantile–quantile plots of the GWAS results of the AWB trait. The red line in the Manhattan plots represents the level of significance. The red line in the quantile–quantile plots is the middle line assuming that the expected value equals the observed value.
Figure 6
Figure 6
GO annotation and KEGG pathway analysis for candidate genes. (A) The GO enrichment analysis of the TNB candidate genes. (B) The KEGG pathways of the TNB candidate genes. (C) The GO enrichment analysis of the AWB candidate genes. (D) The KEGG pathways of the AWB candidate genes.
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References

    1. Yang J., Wu J., Ding W., Chen J., Xing J. The complete mitochondrial genome of the Fengjing pig. Mitochondrial DNA Part B. 2019;4:443–445. doi: 10.1080/23802359.2018.1555014. - DOI
    1. Chen H.-Y., Li S.-F., Gao X.-C., Li N., Liu Y.-H., Lu C.-G. Current status, conservation and exploitation of Fengjing pig resources. Shanghai Anim. Husb. Vet. Commun. 2021;1:46–47. doi: 10.14170/j.cnki.cn31-1278/s.2021.01.015. - DOI
    1. Ge Q., Gao C., Cai Y., Jiao T., Quan J., Guo Y., Zheng W., Zhao S. Evaluating genetic diversity and identifying priority conservation for seven Tibetan pig populations in China based on the mtDNA D-loop. Asian-Australas. J. Anim. Sci. 2020;33:1905–1911. doi: 10.5713/ajas.19.0752. - DOI - PMC - PubMed
    1. Wang H., Fu Y., Gu P., Zhang Y., Tu W., Chao Z., Wu H., Cao J., Zhou X., Liu B., et al. Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds. Animals. 2020;10:1792. doi: 10.3390/ani10101792. - DOI - PMC - PubMed
    1. Ahmed S.M., Hordofa B., Meressa B.H., Tamiru M. Population structure and genetic diversity of Nile tilapia (Oreochromis niloticus) using microsatellite markers from selected water bodies in southwest Ethiopia. Vet. Med. Sci. 2023;9:2095–2106. doi: 10.1002/vms3.1212. - DOI - PMC - PubMed

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