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. 2024 Mar 8:11:1359312.
doi: 10.3389/fvets.2024.1359312. eCollection 2024.

Association between polymorphisms in NOBOX and litter size traits in Xiangsu pigs

Jiajin Huang  1   2   3 , Yong Ruan  1   2   3 , Meimei Xiao  1   2   3 , Lingang Dai  1   2   3 , Chuanmei Jiang  1   2   3 , Jifeng Li  1   2   3 , Jiali Xu  1   2   3 , Xiang Chen  1   2   3 , Houqiang Xu  1   2   3
Affiliations

Association between polymorphisms in NOBOX and litter size traits in Xiangsu pigs

Jiajin Huang et al. Front Vet Sci. .

Abstract

The newborn ovary homeobox gene (NOBOX) regulates ovarian and early oocyte development, and thus plays an essential role in reproduction. In this study, the mRNA expression level and single nucleotide polymorphism (SNP) of NOBOX in various tissues of Xiangsu pigs were studied to explore the relationship between its polymorphism and litter size traits. Also, bioinformatics was used to evaluate the effects of missense substitutions on protein structure and function. The results revealed that NOBOX is preferentially expressed in the ovary. Six mutations were detected in the NOBOX sequence, including g.1624 T>C, g.1858 G>A, g.2770 G>A, g.2821 A>G, g.5659 A>G, and g.6025 T>A, of which g.1858 G>A was a missense mutation. However, only g.1858 G>A, g.5659 A>G, and g.6025 T>A were significantly associated with litter size traits (p < 0.05). Further prediction of the effect of the missense mutation g.1858 G>A on protein function revealed that p.V82M is a non-conservative mutation that significantly reduces protein stability and thus alters protein function. Overall, these findings suggest that NOBOX polymorphism is closely related to the litter size of Xiangsu pigs, which may provide new insights into pig breeding.

Keywords: NOBOX gene; litter size traits; missense mutation; pig; polymorphism.

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Conflict of interest statement

The 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
(A) Tissue expression of NOBOX in Xiangsu pig. Different capital letters indicated that the difference between different tissues was extremely significant (p < 0.01). (B) The results of gel electrophoresis imaging of PCR amplification products. M: DL2000 marker, N1–N6: NOBOX gene Exon1–Exon6.
Figure 2
Figure 2
SNP locus of NOBOX in Xiangsu pig. (A) g.1624 T>C, (B) g.1858 G>A, (C) g.2770 G>A, (D) g.2821 A>G, (E) g.5659 A>G, (F) g.6025 T>A.
Figure 3
Figure 3
Phylogenetic tree (left) and motif structural analysis (right) for eight species. Fifteen significant motifs were identified. The length of the color block shows the position, strength and significance of a particular motif site. The length of the color block shows the position, strength and significance of a particular motif site. The length of the motif is proportional to the negative logarithm of the p-value of the motif site, truncated at the height for a p-value of 1 × 10−10. The colors were generated through motif analysis performed via the MEME suit system.
Figure 4
Figure 4
Conservative analysis of NOBOX SNP amino acid mutation sites. The red circle corresponds to p.V82M.
Figure 5
Figure 5
Modelled tertiary structure of the protein encoded by NOBOX. Different colors in the figure represent different secondary structures, (A) wild-type, (B) mutant type.
Figure 6
Figure 6
Analysis of linkage disequilibrium. r2 represents the correlation between a pair of loci, and D′ denotes the difference between the observed and the expected frequency of a given haplotype.
See this image and copyright information in PMC

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