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. 2025 Feb 19;15(4):603.
doi: 10.3390/ani15040603.

Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms

Huipeng Du  1 , Jianchao Hu  1 , Zhiyan Zhang  1 , Zhongzi Wu  1
Affiliations

Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms

Huipeng Du et al. Animals (Basel). .

Abstract

Pigs are essential agricultural animals, and among the various breeds, the Meishan pig, a native breed of China, is renowned for its high reproductive performance. This breed has been introduced to many countries to enhance local pig breeding programs. However, there have been limited genomic and population genetics studies focusing on Meishan pigs. We created a chromosomal-level genomic assembly using high-depth PacBio sequencing and Illumina sequencing data collected from a Meishan pig. Additionally, we analyzed whole-genome sequencing (WGS) data from Chinese boars and Meishan pigs to identify domestication selection signals within the Meishan breed. The assembled genome of the Meishan pig (MSjxau) was found to be 2.45 Gb in size, with a scaffold length of 139.17 Mb. The quality value was 37.06, and the BUSCO score was 96.2%, indicating good completeness, continuity, and accuracy. We annotated transposable elements, segmental duplication, and genes in the MSjxau genome. By combining these data with 28 publicly available genomes, we provide a high-quality structural variants resource for pigs. Furthermore, we identified 716 selective sweep intervals between Chinese wild pigs and Meishan pigs, where the selected gene PGR may be linked to the high fertility observed in Meishan pigs. Our study offers valuable genomic and variation resources for pig breeding and identifies several genes associated with the domestication of the Meishan pig. This lays the groundwork for further investigation into the genetic mechanisms behind complex traits in pigs.

Keywords: PacBio sequencing; domestication region; high fecundity; meishan pig genome; structural variation.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
The genome assembly of the Meishan pig. (A) Workflow for the genome assembly of Meishan pig. (B) The frequency distribution of k-mer for Meishan pig genome (k = 31). (C) The distribution of contigs on the chromosome, with green and gray representing different contigs. (D) BUSCO evaluates the completeness of genome assembly.
Figure 2
Figure 2
Genome annotation of Meishan pig assembly. (A) Distribution of features in the Meishan pig genome. For the outer to inner regions, each circle represents the GC content, transposable elements number, gene number and collinearity of repetitive sequences in the 500 kb nonoverlapping windows. (B) Sequence divergence of repetitive elements in the Meishan pig assembly. (C) Sequence consistency between Meishan pigs and Sscrofa11.1.
Figure 3
Figure 3
Statistical analysis of structural variations (SVs) in Meishan pigs. (A) The distribution of the number of structural variations detected in different pig breeds. (B) The statistical distribution of the number of structural variations in outgroup, Asian, and European populations. (C) Comparison and statistical analysis of the number of structural variations. PHA, Phacochoerus africanus; POT, Potamochoerus porcus; BMX, Bamaxiang pig; WZS, Wuzhishan pig; LC, Luchuan pig; DNXE, Diannan small-ear pig; TT, Tibetan pig; MS, Meishan pig; SWT, Shawutou pig; TC, Tunchang pig; RC, Rongchang pig; NX, Ningxiang pig; HUAI, Huai pig; LWH, Laiwu pig; CH, Chenghua pig; AQLB, Anqingliubai pig; MIN, Min pig; KORE, Korean minipig; NANC, Nanchukmacdon pig; OSS, Ossabaw minipig; DU, Duroc pig; DLY, Duroc × Landrace × Yorkshire pig; BBH, Babraham pig; LR, Landrace pig; LW, Largewhite pig; EWB, European wild pig; EUP, European pig; ASP, Asian pig; OUT, outgroup.
Figure 4
Figure 4
Selective regions on SVs between the CWB and the Meishan genome assembly. (A) Statistic Fst was plotted for selected SVs with threshold Fst value ≥ 0.01. (B) Pathway enrichment of a gene set. (C) Local display of Fst and nucleotide diversity ratio in chr9:31.9-32.2 Mb region. Note that the PGR gene overlaps with this selective sweep region.
Figure 5
Figure 5
The degree of haplotype sharing in pairwise comparisons among 16 populations. (A) Haplotype sharing in interval chr4:82,660,001-82,730,000; (B) Haplotype sharing in interval chr9:32,050,001-32,070,000. AWB, Asian wild pig; MS, Meishan pig; WZS, Wuzhishan pig; LC, Luchuan pig; BMX, Bamaxiang pig; LA, Lean pig; EHL, Erhualian pig; TT, Tibetan pig; LWU, Laiwu pig; MIN, Min pig; HT, Heitao pig; EWB, European wild pig; PT, Pietrain pig; LW, Largewhite pig; LR, Landrace pig; DU, Duroc pig.
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References

    1. Warr A., Affara N., Aken B., Beiki H., Bickhart D.M., Billis K., Chow W., Eory L., Finlayson H.A., Flicek P. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience. 2020;9:giaa051. doi: 10.1093/gigascience/giaa051. - DOI - PMC - PubMed
    1. Ye R.-S., Li M., Chen T., Wei X.-C., Qi Q.-E., Cheng X., Li C.-Y., Jiang Q.-Y., Xi Q.-Y., Zhang Y.-L. miRNAome, mRNAome and degradome analysis of Tibetan minipigs anterior pituitary. Gen. Comp. Endocrinol. 2018;259:104–114. doi: 10.1016/j.ygcen.2017.11.009. - DOI - PubMed
    1. Zak L.J., Gaustad A.H., Bolarin A., Broekhuijse M.L., Walling G.A., Knol E.F. Genetic control of complex traits, with a focus on reproduction in pigs. Mol. Reprod. Dev. 2017;84:1004–1011. doi: 10.1002/mrd.22875. - DOI - PubMed
    1. Chen K., Baxter T., Muir W.M., Groenen M.A., Schook L.B. Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa) Int. J. Biol. Sci. 2007;3:153. doi: 10.7150/ijbs.3.153. - DOI - PMC - PubMed
    1. Tong X., Chen D., Hu J., Lin S., Ling Z., Ai H., Zhang Z., Huang L. Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences. Nat. Commun. 2023;14:5126. doi: 10.1038/s41467-023-40434-3. - DOI - PMC - PubMed

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