Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population

A meta-analysis of genome-wide association studies revealed significant QTL and candidate genes for loin muscle area in three breeding pigs

Loin muscle area (LMA) is an important production trait in pigs and is highly correlated with lean meat percentage. However, the genetic architecture of LMA has not yet been fully elucidated. This study conducted genome-wide association studies (GWAS) and meta-analyses of LMA in Duroc (n = 337), Landrace (n = 662), and Yorkshire pigs (n = 3,176) using imputed whole-genome sequencing to identify new QTLs and candidate genes associated with LMA traits. A total of 108, 34, and 232 significant variants were identified in the Duroc, Landrace, and Yorkshire populations, respectively. The meta-analysis revealed 143 genome-wide significant SNPs and 276 suggestive SNPs, among which 213 were not identified in single population GWAS. Notably, 229 and 413 SNPs were located on SSC16 in the Yorkshire population and meta-analysis, respectively. Based on the 2-LOD drop-off interval, the SSC16 QTL in the Yorkshire population was further narrowed to a 679.835 kb interval (from 32.818 Mb to 33.498 Mb). The most significant variant within this QTL, 16_33228254 (P = 4.45 × 10-9), explained 1.11% phenotypic variance, representing a potential novel locus for LMA. Further bioinformatics analysis determined seven promising candidate genes (NDUFS4, ARL15, FST, ADAM12, DAB2, PLPP1, and SGMS2) with biological processes such as myoblast fusion and positive regulation of transforming growth factor beta receptor signaling pathway. Among them, ARL15 was previously reported in LMA studies, while the other six genes represent novel candidate genes. These findings reveal potential functional genes and pathways associated with LMA, providing valuable insights for future genetic improvement in pigs.

Genome-Wide Association Integrating a Transcriptomic Meta-Analysis Suggests That Genes Related to Fat Deposition and Muscle Development Are Closely Associated with Growth in Huaxi Cattle

Growth traits are among the most important economic phenotypes targeted in the genetic improvement of beef cattle. To understand the genetic basis of growth traits in Huaxi cattle, we performed a genome-wide association study (GWAS) on body weight, eye muscle area, and back fat thickness across five developmental stages in a population of 202 Huaxi cattle. Additionally, publicly available RNA-seq data from the longissimus dorsi muscle of both young and adult cattle were analyzed to identify key genes and genetic markers associated with growth in Huaxi cattle. In total, 7.19 million high-quality variant loci (SNPs and INDELs) were identified across all samples. In the GWAS, the three multilocus models (FarmCPU, MLMM, and BLINK) outperformed the conventional single-locus models (CMLM, GLM, and MLM). Consequently, GWAS analysis was conducted using multilocus models, which identified 99 variant loci significantly associated with growth traits and annotated a total of 83 candidate genes (CDGs). Additionally, 23 of the 83 CDGs overlapped with significantly differentially expressed genes identified from public RNA-seq datasets of longissimus dorsi muscle between young and adult cattle. Furthermore, gene functional enrichment (KEGG and GO) analyses revealed that over 30% of the pathways and GO terms were associated with muscle development and fat deposition, crucial factors for beef production. Specifically, key genes identified included MGLL, SGMS1, SNX29 and AKAP6, which are implicated in lipid metabolism, adipogenesis, and muscle growth. In summary, this study provides new insights into the genetic mechanisms underlying growth traits in Huaxi cattle and presents promising markers for future breeding improvements.

Genome-Wide Association Analysis of Boar Semen Traits Based on Computer-Assisted Semen Analysis and Flow Cytometry

Semen quality and persistence are critical for evaluating the usability of individual boars in AI, a standard practice in pig breeding. We conducted GWASs on various semen traits of Duroc boars, including MOT, DEN, ABN, MMP, AIR, and ROS levels. These traits were assessed using FCM and CASA. A total of 1183 Duroc boars were genotyped using the GeneSeek GGP Porcine 50 K SNP BeadChip. The GWAS was performed using three different models: GLM, MLM, and FarmCPU. Additionally, trait heritability was estimated using single- and multiple-trait PBLUP models, yielding 0.19, 0.29, 0.13, 0.18, 0.11, and 0.14 heritability for MOT, DEN, ABN, MMP, AIR, and ROS, respectively. All semen traits exhibited low heritability except ABN, which demonstrated medium heritability. Nine candidate genes (GPX5, AWN, PSP-II, CCDC62, TMEM65, SLC8B1, TRPV4, UBE3B, and SIRT5) were potentially associated with semen traits. These genes are associated with antioxidant and mitochondrial functions in porcine sperm. Our findings provide insight into the genetic architecture of semen traits in Duroc boars, and the identified SNPs and candidate genes may enhance economic outcomes in the pig breeding industry while improving sperm quality through targeted breeding strategies.