The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs

Abstract

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in animal genetic improvement. Despite recent advances in high-throughput genotyping technologies, the resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2259 whole genome-sequenced animals representing 44 pig breeds. We evaluated software combinations and breed composition to optimize the imputation procedure and achieved an average concordance rate in excess of 96%, a non-reference concordance rate of 88%, and an r2 of 0.85. We demonstrated in two case studies that genotype imputation using this resource can dramatically improve the resolution of genetic mapping. A public web server has been developed to allow the pig genetics community to fully utilize this resource. We expect this resource to facilitate genetic mapping and accelerate genetic improvement in pigs.

Genomic and Phenotypic Consequences of Bi-Directional Introgression Between Chinese and European Pig Breeds

“…4; supplementary Table S15 and S16). Due to limited space, BMP2 particularly stands out for its strong association with growth traits in pigs (Li et al 2021; Ding et al 2023). This gene is located within regions indicative of introgression between Southern Chinese indigenous pigs and Canadian Duroc or Pietrain (defined as regions where rIBD > 0).…”

“…In our previous body length genome-wide association study (GWAS) (Ding et al 2023), we identified a high-confidence candidate variant (chr17:15643342:C>T) located upstream of the BMP2 gene. Given the high correlation coefficient between body length and body height (supplementary Fig.…”

“…To the best of our knowledge, this is the first report of bi-directional introgression of haplotypes and SVs around the BMP2 locus between European commercial pigs and Chinese indigenous breeds. Prior GWAS studies have identified BMP2 as a promising candidate gene correlated with the body length and loin muscle depth in pigs (Ding et al 2023; Miao et al 2023). The introduction of European-origin haplotypes and SVs at the BMP2 locus, especially during the mid-20th century through the admixture of Lichahei breed with Duroc and Landrace, likely contributed to the larger body size observed in Lichahei pigs (Xie et al 2023).…”

“…We obtained genome-wide resequencing data from diverse sources, including 129 pigs newly reported in this study, along with 88 pigs retrieved from our prior study (Ding et al 2023). Among them, we included 30 American Duroc (ADUR), 29 Canadian Duroc (CDUR), 29 Taiwan Duroc (TDUR), 30 French Large White (LW), 23 Wen’s Landrace (WLR), 29 French Landrace (FLR), 29 Norwegian Landrace (NLR), and 18 Lichahei pigs (LIC), all sourced from Wen’s Food Group Co., Ltd. (Yunfu, Guangdong, China).…”

The efficient phasing and imputation pipeline of low‐coverage whole genome sequencing data using a high‐quality and publicly available reference panel in cattle

“…In humans, reference panels are large and diverse, such as the 1000 Genomes Project [9], the UK10K Project [10], the Genome of the Netherlands [11], 64976 human haplotypes from European ancestry [12], and ChinaMAP [13], so that the imputation accuracy based on them could be high. Livestock panels have been reported in pigs [14,15] and cattle [16] but were not publicly available. The establishment of both an efficient imputation pipeline and a public reference panel on cattle is crucial for research and cattle breeding improvement.…”