Background: In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. Copy number variation (CNV), an important source of genetic diversity, can affect a variety of complex traits and diseases and has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs using SNP genotyping data from 6627 animals. We also performed a copy number variation region (CNVR)-based genome-wide association studies (GWAS) for growth and fatness traits in two Duroc populations. Results: Our study identified 953 nonredundant CNVRs in U.S. and Canadian Duroc pigs, covering 246.89 Mb (~ 10.90%) of the pig autosomal genome. Of these, 802 CNVRs were in U.S. Duroc pigs with 499 CNVRs were in Canadian Duroc pigs, indicating 348 CNVRs were shared by the two populations. Experimentally, 77.8% of nine randomly selected CNVRs were validated through quantitative PCR (qPCR). We also identified 35 CNVRs with significant association with growth and fatness traits using CNVR-based GWAS. Ten of these CNVRs were associated with both ADG and AGE traits in U.S. Duroc pigs. Notably, four CNVRs showed significant associations with ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. In Canadian Duroc pigs, nine CNVRs were significantly associated with both ADG and AGE traits. Further bioinformatic analysis identified a subset of potential candidate genes, including PDGFA, GPER1, PNPLA2 and BSCL2. Conclusions: The present study provides a necessary supplement to the CNV map of the Duroc genome through large-scale population genotyping. In addition, the CNVR-based GWAS results provide a meaningful way to elucidate the genetic mechanisms underlying complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in the molecular-guided breeding of modern commercial pigs.

Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the analysis. Our findings revealed 60 significant single nucleotide polymorphisms (SNPs) associated with these body conformation traits in the crossbred pig population. Specifically, sixteen SNPs were significantly associated with BL, three SNPs with BH, thirteen SNPs with CC, twelve SNPs with AC, and sixteen SNPs with WC. Moreover, we identified several promising candidate genes located within the genomic regions associated with body conformation traits. These candidate genes include INTS10, KIRREL3, SOX21, BMP2, MAP4K3, SOD3, FAM160B1, ATL2, SPRED2, SEC16B, and RASAL2. Furthermore, our analysis revealed a novel significant quantitative trait locus (QTL) on SSC7 specifically associated with waist circumference, spanning an 84 kb interval. Overall, the identification of these significant SNPs and potential candidate genes in crossbred commercial pigs enhances our understanding of the genetic basis underlying body conformation traits. Additionally, these findings provide valuable genetic resources for pig breeding programs.

Meat quality is of importance in consumer acceptance and purchasing tendency of pork. However, the genetic architecture of pork meat quality traits remains elusive. Herein, we conducted genome-wide association studies to detect single nucleotide polymorphisms (SNPs) and genes affecting meat pH and meat color (L*, lightness; a*, redness; b*, yellowness) in 1518 three-way crossbred pigs. All individuals were genotyped using the GeneSeek Porcine 50K BeadChip. In sum, 30 SNPs and 20 genes are found to be associated with eight meat quality traits. Notably, we detect one significant quantitative trait locus (QTL) on SSC15 with a 143 kb interval for meat pH (pH_12h), together with the most promising candidate TNS1. Interestingly, two newly identified SNPs located in the TTLL4 gene demonstrate the highest phenotypic variance of pH_12h in this QTL, at 2.67%. The identified SNPs are useful for the genetic improvement of meat quality traits in pigs by assigning higher weights to associated SNPs in genomic selection.

The intuitive impression of pork is extremely important in terms of whether consumers are enthusiastic about purchasing it. Flesh color and intramuscular fat (IMF) are indispensable indicators in meat quality assessment. In this study, we determined the flesh color and intramuscular fat at 45 min and 12 h after slaughter (45 mFC, 45 mIMF, 12 hFC, and 12 hIMF) of 1518 commercial Duroc × Landrace × Large White (DLY) pigs. We performed a single nucleotide polymorphism (SNP) genome-wide association study (GWAS) analysis with 28,066 SNPs. This experiment found that the correlation between 45 mFC and 12 hFC was 0.343. The correlation between 45 mIMF and 12 hIMF was 0.238. The heritability of the traits 45 mFC, 12 hFC, 45 mIMF, and 12 hIMF was 0.112, 0.217, 0.139, and 0.178, respectively, and we identified seven SNPs for flesh color and three SNPs for IMF. Finally, several candidate genes regulating these four traits were identified. Three candidate genes related to flesh color were provided: SNCAIP and PRR16 on SSC2, ST3GAL4 on SSC5, and GALR1 on SSC1. A total of three candidate genes related to intramuscular fat were found, including ABLIM3 on SSC2, DPH5 on SSC4, and DOCK10 on SSC15. Furthermore, GO and KEGG analysis revealed that these genes are involved in the regulation of apoptosis and are implicated in functions such as pigmentation and skeletal muscle metabolism. This study applied GWAS to analyze the scoring results of flesh color and IMF in different time periods, and it further revealed the genetic structure of flesh color and IMF traits, which may provide important genetic loci for the subsequent improvement of pig meat quality traits.

Chest circumference (CC), abdominal circumference (AC), and waist circumference (WC) are regarded as important indicators for improving economic traits because they can reflect the growth and physiological status in pigs. However, the genetic architecture of CC, AC, and WC is still elusive. Here, we performed single-trait and multi-trait genome-wide association studies (GWASs) for CC, AC, and WC in 2,206 American origin Duroc (AOD) and 2,082 Canadian origin Duroc (COD) pigs. As a result, one novel quantitative trait locus (QTL) on Sus scrofa chromosome (SSC) one was associated with CC and AC in COD pigs, which spans 6.92 Mb (from 170.06 to 176.98 Mb). Moreover, multi-trait GWAS identified 21 significant SNPs associated with the three conformation traits, indicating the multi-trait GWAS is a powerful statistical approach that uncovers pleiotropic locus. Finally, the three candidate genes (ITGA11, TLE3, and GALC) were selected that may play a role in the conformation traits. Further bioinformatics analysis indicated that the candidate genes for the three conformation traits mainly participated in sphingolipid metabolism and lysosome pathways. For all we know, this study was the first GWAS for WC in pigs. In general, our findings further reveal the genetic architecture of CC, AC, and WC, which may offer a useful reference for improving the conformation traits in pigs.