Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in 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 number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.

During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic architecture of tenderloin weight (TLNW) and rib weight (RIBW)—important components of pig carcass economic value—remain unknown. In this study, we conducted genome-wide association studies (GWAS) for TLNW and RIBW traits in a population of 431 Duroc × Landrace × Yorkshire (DLY) pigs. In our study, the most significant single nucleotide polymorphism (SNP) associated with TLNW was identified as ASGA0085853 (3.28 Mb) on Sus scrofa chromosome 12 (SSC12), while for RIBW, it was Affx-1115046258 (172.45 Mb) on SSC13. Through haplotype block analysis, we discovered a novel quantitative trait locus (QTL) associated with TLNW, spanning a 5 kb region on SSC12, and a novel RIBW-associated QTL spanning 1.42 Mb on SSC13. Furthermore, we hypothesized that three candidate genes, TIMP2 and EML1, and SMN1, are associated with TLNW and RIBW, respectively. Our research not only addresses the knowledge gap regarding TLNW, but also serves as a valuable reference for studying RIBW. The identified SNP loci strongly associated with TLNW and RIBW may prove useful for marker-assisted selection in pig breeding programs.

Internal organ weight is an essential indicator of growth status as it reflects the level of growth and development in pigs. However, the associated genetic architecture has not been well explored because phenotypes are difficult to obtain. Herein, we performed single-trait and multi-trait genome-wide association studies (GWASs) to map the genetic markers and genes associated with six internal organ weight traits (including heart weight, liver weight, spleen weight, lung weight, kidney weight, and stomach weight) in 1518 three-way crossbred commercial pigs. In summation, single-trait GWASs identified a total of 24 significant single- nucleotide polymorphisms (SNPs) and 5 promising candidate genes, namely, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, as being associated with the six internal organ weight traits analyzed. Multi-trait GWAS identified four SNPs with polymorphisms localized on the APK1, ANO6, and UNC5C genes and improved the statistical efficacy of single-trait GWASs. Furthermore, our study was the first to use GWASs to identify SNPs associated with stomach weight in pigs. In conclusion, our exploration of the genetic architecture of internal organ weights helps us better understand growth traits, and the key SNPs identified could play a potential role in animal breeding programs.