Genome-Wide Association Study Identified a Quantitative Trait Locus and Two Candidate Genes on Sus scrofa Chromosome 2 Affecting Vulvar Traits of Suhuai Pigs

Yanzhen Yin; Liming Hou; Chenxi Liu; Kaijun Li; Hao Guo; Peipei Niu; Qiang Li; Ruihua Huang; Pinghua Li

doi:10.3390/genes13081294

Genome-Wide Association Study Identified a Quantitative Trait Locus and Two Candidate Genes on Sus scrofa Chromosome 2 Affecting Vulvar Traits of Suhuai Pigs

Genes (Basel). 2022 Jul 22;13(8):1294. doi: 10.3390/genes13081294.

Authors

Yanzhen Yin^{1

2}, Liming Hou^{1

2

3}, Chenxi Liu^{1

2}, Kaijun Li^{1

2}, Hao Guo^{1

2}, Peipei Niu³, Qiang Li⁴, Ruihua Huang^{1

2

3}, Pinghua Li^{1

2

3}

Affiliations

¹ Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China.
² Key Laboratory in Nanjing for Evaluation and Utilization of Livestock and Poultry (Pigs) Resources, Ministry of Agriculture and Rural Areas, Nanjing Agricultural University, Nanjing 210095, China.
³ Huaian Academy, Nanjing Agricultural University, Huaian 223005, China.
⁴ Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China.

Abstract

Vulvar size and angle are meaningful traits in pig production. Sows with abnormal vulva generally show reproductive disorders. In order to excavate candidate loci and genes associated with pig's vulvar traits, 270 Suhuai pigs with vulvar phenotype were genotyped by a porcine single nucleotide polymorphisms (SNP) Chip. Then, Chip data were imputed using resequenced data of 30 Suhuai pigs as a reference panel. Next, we estimated the heritability and performed a genome-wide association study (GWAS) for vulvar traits. The heritabilities for the traits vulvar length (VL), vulvar width (VW) and vulvar angle (VA) in this pig population were 0.23, 0.32 and 0.22, respectively. GWAS based on Chip data identified nine significant SNPs on the Sus scrofa chromosomes (SSC) 2, 7, 9 and 13 for VL or VW. GWAS based on imputed data identified 11 new quantitative trait loci (QTL) on SSC1, 2, 7, 8, 9, 11, 13, 16 and 17 for VL or VW. The most significant QTL for VL on SSC2 were refined to a 3.48-3.97 Mb region using linkage disequilibrium and linkage analysis (LDLA). In this refined region, FGF19 and CCND1, involved in the development of the reproductive tract, cell growth and vulvar cancer, could be new candidate genes affecting VL. Our results provided potential genetic markers for the breeding of vulvar traits in pigs and deepened the understanding of the genetic mechanism of vulvar traits.

Keywords: Suhuai pigs; candidate genes; genome-wide association study; linkage disequilibrium and linkage analysis; vulvar traits.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Female
Genome-Wide Association Study* / veterinary
Phenotype
Quantitative Trait Loci*
Sus scrofa* / genetics
Swine / genetics
Vulva

Grants and funding

This research was funded by the National Key R&D Program of China, grant number: 2021YFD13011011 and 2021YFD1301105; Jiangsu Agriculture Science and Technology Innovation Fund (JASTIF), Grant Number: CX(20)1003; Jiangsu seed industry revitalization project, Grant Number: JBGS(2021)024; the Key Project of Jiangsu Agricultural New Variety Innovation, Grant Number: PZCZ201732.