Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs.

Yong Li,Bin Li,Lilin Yin,Xuewen Xu,Shuhong Zhao,Ran Wang,Xinyun Li,Qiang Wei,Zepu Miao,Manman Yang,Hu Han,Junran Shen,Ming Fang,Tao Chen

doi:10.3389/fgene.2020.00183

Abstract

Birth weight of pigs is an important economic factor in the livestock industry. The identification of the genes and variants that underlie birth weight is of great importance. In this study, we integrated two genotyping methods, single nucleotide polymorphism (SNP) chip analysis and restriction site associated DNA sequencing (RAD-seq) to genotype genome-wide SNPs. In total, 45,175 and 139,634 SNPs were detected with the SNP chip and RAD-seq, respectively. The genome-wide association study (GWAS) of the combined SNP panels identified two significant loci located at chr1: 97,745,041 and chr4: 112,031,589, that explained 6.36% and 4.25% of the phenotypic variance respectively. To reduce interval containing causal variants, we imputed sequence-level SNPs in the GWAS identified regions and fine-mapped the causative variants into two narrower genomic intervals: a ∼100 kb interval containing 71 SNPs and a broader ∼870 kb interval with 432 SNPs. This fine-mapping highlighted four promising candidate genes, SKOR2, SMAD2, VAV3, and NTNG1. Additionally, the functional genes, SLC25A24, PRMT6 and STXBP3, are also located near the fine-mapping region. These results suggest that these candidate genes may have contribute substantially to the birth weight of pigs.

Highlights

The birth weight of pigs is an important economic trait in the livestock industry
The region on chromosome 4 was determined to be significant for the restriction site associated DNA sequencing (RAD-seq) dataset but not for the single nucleotide polymorphism (SNP) chip dataset; where the reverse was true for the region on chromosome 1 (Figures 2C,E)
To increase the accuracy of fine mapping, we imputed the merged RADseq and SNP chip SNPs at a sequence level using the SNPs of high-coverage resequenced pigs as a reference panel

Summary

Introduction

The birth weight of pigs is an important economic trait in the livestock industry. It is closely associated with early survival, weaning weight, and growth rate after weaning (Quiniou et al, 2002; Smith et al, 2007). Pigs have been selectively bred to produce larger litters, with this increase in litter size, the average birth weight has decreased (Bergstrom et al, 2009; De Almeida et al, 2014). Birth weight reflects the intrauterine growth of piglets which is affected by both the maternal supply of nutrition and genetic factors (Roehe, 1999; Zohdi et al, 2012). Fine-Mapping for Pig Birth Weight is substantially affected by own (fetal) genetic factors as well as maternal genetic effects. It is a worthwhile endeavor to determine which genes or variants underly this variation in birth weight

Methods

Results

Discussion

Conclusion