Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs

Abstract

Background Carcass length is very important for body size and meat production for swine, thus understanding the genetic mechanisms that underly this trait is of great significance in genetic improvement programs for pigs. Although many quantitative trait loci (QTL) have been detected in pigs, very few have been fine-mapped to the level of the causal mutations. The aim of this study was to identify potential causal single nucleotide polymorphisms (SNPs) for carcass length by integrating a genome-wide association study (GWAS) and functional assays. Results Here, we present a GWAS in a commercial Duroc × (Landrace × Yorkshire) (DLY) population that reveals a prominent association signal (P = 4.49E−07) on pig chromosome 17 for carcass length, which was further validated in two other DLY populations. Within the detected 1 Mb region, the BMP2 gene stood out as the most likely causal candidate because of its functions in bone growth and development. Whole-genome gene expression studies showed that the BMP2 gene was differentially expressed in the cartilage tissues of pigs with extreme carcass length. Then, we genotyped an additional 267 SNPs in 500 selected DLY pigs, followed by further whole-genome SNP imputation, combined with deep genome resequencing data on multiple pig breeds. Reassociation analyses using genotyped and imputed SNP data revealed that the rs320706814 SNP, located approximately 123 kb upstream of the BMP2 gene, was the strongest candidate causal mutation, with a large association with carcass length, with a ~ 4.2 cm difference in length across all three DLY populations (N = 1501; P = 3.66E−29). This SNP segregated in all parental lines of the DLY (Duroc, Large White and Landrace) and was also associated with a significant effect on body length in 299 pure Yorkshire pigs (P = 9.2E−4), which indicates that it has a major value for commercial breeding. Functional assays showed that this SNP is likely located within an enhancer and may affect the binding affinity of transcription factors, thereby regulating BMP2 gene expression. Conclusions Taken together, these results suggest that the rs320706814 SNP on pig chromosome 17 is a putative causal mutation for carcass length in the widely used DLY pigs and has great value in breeding for body size in pigs.

Structural variants and tandem repeats in the founder individuals of four F2 pig crosses and implications to F2 GWAS results

“…In the case of the CRCL peak (SSC17, Fig. 3 D), BMP2 (bone morphogenetic protein 2) was suggested as a strong candidate in previous studies conducted on these crosses [ 7 , 22 ] but also in other pig populations (Duroc × (Landrace × Yorkshire), [ 42 ]). In the latter study, the authors indicated that a SNP (rs320706814) was the main cause of the effect on carcass length.…”

“…However, we could not confirm the SNP effect in our population, as this SNP was not significantly associated nor in LD with the significant SNPs, small indels, SVs, or TRs we have identified. Li et al [ 42 ] did not exclude the option that the causative mutation could be in fact a non-SNP or non-small indel variant. Therefore, coupled with our findings, it could be hypothesized that the nearby TR-enriched lncRNAs (upstream: ENSSSCG00000043546 , ENSSSCG00000047884 ; downstream: ENSSSCG00000044805 ) could drive the molecular mechanisms involving the BMP2 in carcass length variation in the current F 2 crosses.…”

Genome-Wide Association Studies for Flesh Color and Intramuscular Fat in (Duroc × Landrace × Large White) Crossbred Commercial Pigs

“…It may be that some SNP sites had been deleted because the labeling density and conditions were too strict. Subsequently, new SNPs on IMF can be selected by increasing the labeling density or selecting a looser quality control condition [ 43 ]. Although only three SNPs were screened on 12 hIMF, both SSC2 (H3GA0054148) and SSC15 (WU_10.2_15_140224592) reached a loose genome-wide significant threshold (1/28066).…”

“…Haplotype block analysis was carried out using PLINK v1.90 [ 28 ] and Haploview [ 41 ] software. According Gebriel et al [ 42 ], the search for genes was within the SNP locus and 500 Kb upstream and downstream of the GWAS-significant SNP [ 43 ] on Sscrofa11.1 in the Ensembl database ( accessed on 13 October 2022). Gene function annotation was performed on the screened genes, and KOBAS 3.0 [ 44 ] was used to further perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on all of the screened genes.…”

Nucleotide resolution genetic mapping in pigs by publicly accessible whole genome imputation

“…Remarkably, this variant explained 13.65% of the total phenotypic variance and the homozygous C/C animals were on average 4.01 cm longer than the T/T homozygotes (Figure 4b,c). BMP2 has been repeatedly shown to be associated with growth traits in pigs and a recent study implicated a regulatory variant upstream of the BMP2 gene and validated its functional impact using reporter genes (Li et al, 2021a). This regulatory variant was the third most significant SNP under this peak in our analysis.…”