Identification of loci affecting teat number by genome-wide association studies on three pig populations.

Jianhong Tang,Nengshui Ding,Huashui Ai,Lusheng Huang,Liyu Zhou,Jun Ren,Yuanmei Guo,Ying Su,Xiaopeng Wang,Hui Zhang,Leilei Cui,Zhiyan Zhang,Bin Yang,Yi Long,Chengbin Wang

doi:10.5713/ajas.15.0980

Jianhong Tang, Nengshui Ding + Show 13 more

Open Access

https://doi.org/10.5713/ajas.15.0980

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Abstract

ObjectiveThree genome-wide association studies (GWAS) and a meta-analysis of GWAS were conducted to explore the genetic mechanisms underlying variation in pig teat number.MethodsWe performed three GWAS and a meta-analysis for teat number on three pig populations, including a White Duroc×Erhualian F2 resource population (n = 1,743), a Chinese Erhualian pig population (n = 320) and a Chinese Sutai pig population (n = 383).ResultsWe detected 24 single nucleotide polymorphisms (SNPs) that surpassed the genome-wide significant level on Sus Scrofa chromosomes (SSC) 1, 7, and 12 in the F2 resource population, corresponding to four loci for pig teat number. We highlighted vertnin (VRTN) and lysine demethylase 6B (KDM6B) as two interesting candidate genes at the loci on SSC7 and SSC12. No significant associated SNPs were identified in the meta-analysis of GWAS.ConclusionThe results verified the complex genetic architecture of pig teat number. The causative variants for teat number may be different in the three populations

Highlights

Experiment animals were from three pig populations, including the White Duroc×Erhualian F2 resource population, Chinese Erhualian and Sutai populations
928 F2 pigs and their F1 and F0 ancestors, 320 Erhualian and 383 Sutai pigs were genotyped for 62193 single nucleotide polymorphisms (SNPs) on the Illumina Porcine 60K Beadchip [7]
Confidence regions were determined by log of odds ratio (LOD) dropoff 2 from the peak SNPs

Summary

Objective

Three genome-wide association studies (GWAS) and a meta-analysis of GWAS were conducted to explore the genetic mechanisms underlying variation in pig teat number. Methods: We performed three GWAS and a meta-analysis for teat number on three pig populations, including a White Duroc×Erhualian F2 resource population (n = 1,743), a Chinese Erhualian pig population (n = 320) and a Chinese Sutai pig population (n = 383). Results: We detected 24 single nucleotide polymorphisms (SNPs) that surpassed the genome- wide significant level on Sus Scrofa chromosomes (SSC) 1, 7, and 12 in the F2 resource population, corresponding to four loci for pig teat number. No significant associated SNPs were identified in the meta-analysis of GWAS. Conclusion: The results verified the complex genetic architecture of pig teat number. The causative variants for teat number may be different in the three populations

INTRODUCTION

MATERIALS AND METHODS

RESULTS

DISCUSSION