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. 2024 Dec 18;25(1):1217.
doi: 10.1186/s12864-024-11109-0.

Revealing genes related teat number traits via genetic variation in Yorkshire pigs based on whole-genome sequencing

Jialin Wei #  1 , Jingchun Sun #  1   2 , Yi Pan  1 , Minghao Cao  1 , Yulong Wang  1 , Tiantian Yuan  1 , Ao Guo  1 , Ruihua Han  3 , Xiangdong Ding  4 , Gongshe Yang  1 , Taiyong Yu  1 , Rongrong Ding  5
Affiliations

Revealing genes related teat number traits via genetic variation in Yorkshire pigs based on whole-genome sequencing

Jialin Wei et al. BMC Genomics. .

Abstract

Background: Teat number is one of the most important indicators to evaluate the lactation performance of sows, and increasing the teat number has become an important method to improve the economic efficiency of farms. Therefore, it is particularly important to deeply analyze the genetic mechanism of teat number traits in pigs. In this study, we detected Single Nucleotide Ploymorphism (SNP), Insertion-Deletion (InDel) and Structural variant (SV) by high-coverage whole-genome resequencing data, and selected teat number at birth and functional teat number as two types of teat number traits for genome-wide association study (GWAS) to reveal candidate genes associated with pig teat number traits.

Results: In this study, we used whole genome resequencing data from 560 Yorkshire sows to detect SNPs, InDels and SVs, and performed GWAS for the traits of born teat number and functional teat number, and detected a total of 85 significant variants and screened 214 candidate genes, including HEG1, XYLT1, SULF1, MUC13, VRTN, RAP1A and NPVF. Among them, HEG1 and XYLT1 were the new candidate genes in this study. The co-screening and population validation of multiple traits suggested that HEG1 may have a critical effect on the born teat number.

Conclusion: Our study shows that more candidate genes associated with pig teat number traits can be identified by GWAS with different variant types. Through large population validation, we found that HEG1 may be a new key candidate gene affecting pig teat number traits. In conclusion, the results of this study provide new information for exploring the genetic mechanisms affecting pig teat number traits and genetic improvement of pigs.

Keywords: GWAS; Structural variation; Teat number; Whole genome sequencing.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: The study was approved by the Institutional Animal Care and Use Committee of the Northwest A & F University (approval number: NWAFU-314021167). All experiments strictly followed the guidelines of this committee. The experimental animals were not anesthetized or euthanized in this study. All experimental protocols were approved by the aforementioned committee and in accordance with ARRIVE guidelines ( https://arriveguidelines.org ). Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
SV discovery process overview
Fig. 2
Fig. 2
GWAS of born teat number based on SNPs and population validation. (a) GWAS of TTN based on SNPs. N = 560 Yorkshire pigs. The horizontal solid line represents Bonferroni threshold (-Log10(0.05/678,204) = 7.1324). The horizontal dashed line represents the suggestive significance threshold line (-Log10(1/678,204) = 5.8314). (b) Magnification of the gene region with significant variants in TTN, RTN and LTN GWAS result. Different color and shaped points distinguish three traits. (c) Population validation in 1169 Yorkshire pigs base on target sequencing with GWAS candidate significant SNP in TTN. The blue box represent sow population with reference variant; and the red box is sow population with mutation
Fig. 3
Fig. 3
GWAS of born teat number traits. (a) TTN GWAS base on InDels. (b) TTN GWAS base on SVs. (c) Candidate genes from GWAS screens for SNPs, Indels, and SVs, respectively, plotted on a Wayne diagram. (d) Magnified Manhattan plot of LTN GWAS result and LD heatmap of the magnified region. (e) Magnified Manhattan plot of GWAS result in TTN
Fig. 4
Fig. 4
GWAS of FTTN base on SNPs, InDels, SVs, respectively. (a) GWAS result of FTTN base on SNPs. N = 427 pig samples. (b) GWAS result of FTTN base on InDels. (c) GWAS result of FTTN base on SVs
Fig. 5
Fig. 5
GWAS of FRTN base on SNPs, InDels, SVs, respectively. N = 430 pig samples. The dotted red box indicates that the same region of interest was detected by the three variant types GWAS results in Chr7. (a) GWAS of FRTN base on SNPs. There is no significant variation on Chr7, but trends can be detected. (b) GWAS of FRTN base on InDels. (c) GWAS of FRTN base on SVs
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