The influences of diet and environmental factors on gut microbial profiles have been widely acknowledged; however, the specific roles of host genetics remain uncertain. To unravel host genetic effects, we raised 47 Jeju crossbred (Jeju × Thoroughbred) foals that exhibited higher genetic diversity. Foals were raised under identical environmental conditions and diets. Microbial composition revealed that Firmicutes, Bacteroidetes, and Spirochaetes were the predominant phyla. We identified 31 host–microbiome associations by utilizing 47,668 single nucleotide polymorphisms (SNPs) and 734 taxa with quantitative trait locus (QTL) information related to horse growth. The taxa involved in 31 host–microbiome associations were functionally linked to carbohydrate metabolism, energy metabolic processes, short-chain fatty acid (SCFA) production, and lactic acid production. Abundances of these taxa were affected by specific SNP genotypes. Most growth-associated SNPs are found between genes. The rs69057439 and rs69127732 SNPs are located within the introns of the VWA8 and MFSD6 genes, respectively. These genes are known to affect energy balance and metabolism. These discoveries emphasize the significant effect of host SNPs on the development of the intestinal microbiome during the initial phases of life and provide insights into the influence of gut microbial composition on horse growth.

Different dietary patterns affect the gut microbial compositions and diversity. Consistently, microbiome alterations are linked to digestion, immunity, and productivity. Sasa quelpaertensis Nakai (SQ) is a perennial bamboo species rich in proteins and fiber. Previous studies have confirmed the health benefits of SQ; however, the effects of SQ supplementation on gut microbiome and production performance are unclear. Herein, Landrace pigs were supplemented with SQ extract (SQE) and gut microbial compositions as opposed to the control group were assessed using 16S rRNA sequencing. Additionally, the influences of SQE supplementation on average daily gain (ADG) and backfat thickness (BF) were assessed after slaughter. In the SQE group, Firmicutes and Actinobacteria phyla increased significantly, whereas Bacteroidetes and Spirochaetes phyla markedly decreased (p < 0.05). The expression level of Bifidobacterium and Lactobacillus genera increased, whereas that of Treponema, Prevotella, and Turicibacter decreased (p < 0.05). The microbial richness was similar between groups; however, microbial diversity decreased in the SQE supplementation group. Additionally, the SQE supplementation in pigs resulted in a slight increase in ADG. In contrast, BF in the SQE group decreased notably (p < 0.05). These results underscore the significant influence of SQE supplementation on the gut microbiota and demonstrate the potential of SQ as a valuable feed resource for enhancing animal productivity.

Swine breeding programs aim to improve both growth performance and reproductive efficiency to enhance overall productivity. Although Duroc pigs have traditionally been selected mainly for productive traits, the genetic relationship between growth performance and reproductive traits across successive parities remains poorly understood. Therefore, this study estimated genetic parameters for productive traits, adjusted days to 105 kg (DAYS105) and backfat thickness (BF), and reproductive traits, total number born (TNB) and number born alive (NBA), in Duroc pigs using data from the Korean National Pig Breeding Network. A total of 93,467 pedigree, 82,696 productive, and 22,554 reproductive records collected between 2000 and 2024 were analyzed. Genetic parameters were estimated using restricted maximum likelihood under multiple-trait animal and repeatability models, and genetic correlations between productive traits and parity-specific NBA (parities 1–5) were evaluated. Heritability estimates were moderate for DAYS105 (0.39 ± 0.01) and BF (0.36 ± 0.01), but low for TNB (0.10 ± 0.01) and NBA (0.09 ± 0.01). Parity-specific analyses revealed clear differences in genetic architecture across parities, with NBA heritability increasing from 0.10 ± 0.02 at first parity to 0.22 ± 0.02 at second parity and gradually declining thereafter. Genetic correlations between productive traits and NBA were generally weak or unfavorable, with a moderately positive genetic correlation between DAYS105 and NBA (rg = 0.50 ± 0.13), indicating a potential antagonistic relationship because lower DAYS105 is the desired breeding direction. Genetic correlations for NBA were moderate to high between adjacent parities but lower between the first and later parities, suggesting partially different genetic control of reproductive performance across parities. These findings highlight the importance of incorporating parity-specific reproductive traits in multi-trait genetic evaluation models. The results provide new insights into the genetic trade-off between growth and reproductive traits in Duroc pigs and offer practical implications for designing balanced breeding strategies in national pig breeding programs.

Objective: Understanding the individual- and population-level polymorphisms of major histocompatibility complex (MHC) genes is crucial for identifying associations between MHC variations and immune phenotypes. To support this, we developed NGSMHC, a streamlined bioinformatics tool for efficient and accurate MHC genotyping using nextgeneration sequencing (NGS) data in non-human species.Methods: NGSMHC constructs phased haplotype contigs of selected MHC genes from BAM-format mapping data and determines the best matching MHC alleles and genotypes via nucleotide BLAST analysis against a user-provided reference set of MHC alleles. We evaluated NGSMHC using short-read whole-genome sequencing (WGS) data from 12 pigs, focusing on swine leukocyte antigen (SLA) genes. The typing results from NGSMHC were compared to those obtained using polymerase chain reaction sequence-based typing (PCR-SBT). In addition, we tested NGSMHC on a publicly available long-read WGS dataset with known SLA genotypes.Results: The short-read WGS data showed an average read depth of 20.9× across the SLA region, enabling typing of SLA-2, SLA-3, SLA-DRB1, and SLA-DQB1 using NGSMHC. The concordance rates between NGSMHC and PCR-SBT were 88% for SLA-3, 92% for SLA-DRB1, and 100% for SLA-DQB1. However, SLA-2 typing showed lower concordance (58%), likely due to its high sequence similarity with other SLA class I genes and complex intra-locus polymorphisms. In contrast, NGSMHC accurately identified all tested SLA genotypes—including SLA-1, SLA-2, SLA-3, SLA-DRA, SLA-DRB1, SLA-DQA, and SLADQB1—when applied to the long-read WGS data.Conclusion: NGSMHC is a simple and effective tool for MHC genotyping using NGS data, particularly for non-human species. Its accuracy is significantly improved by longread sequencing, underscoring the importance of read length in precise MHC allele determination.

Background: The HorvathMammalMethylChip40 enables standardized DNA methylation profiling across diverse mammalian species by targeting evolutionarily conserved CpG sites; appropriate preprocessing and quality control are essential for reliable downstream analysis. Methods: This technical protocol describes a reproducible Mammalian Methylation Array workflow using SeSAMe for preprocessing and limma for epigenome-wide association study (EWAS); the workflow was demonstrated using blood-derived methylation data from 826 domestic dogs and 279 cattle to assess age-, sex-, and population-associated methylation patterns. Results: The processed Korean dog samples exhibited generally consistent bimodal β-value distributions. EWAS identified 16,275 age-associated and 1,702 sex-associated CpG sites in dogs, whereas 20,508 CpG sites were significantly associated with age in cattle. In addition, 230 CpG sites exhibited significant age-by-group interaction effects between Korean and U.S. dogs, indicating population differences in age-associated methylation patterns. Conclusion: This protocol provides a practical framework for preprocessing Mammalian Methylation Array data and identifying phenotype-associated CpG sites, thereby supporting downstream genomic annotation and functional interpretation.

This study estimated genetic parameters and genetic trends for production (days to 105 kg, DAYS105; backfat thickness, BFT) and reproductive traits (total number born, TNB; number born alive, NBA) in Korean Landrace and Yorkshire pigs using data collected from 2000 to 2024. Heritabilities for production traits were moderate to high (0.43-0.52), whereas those for reproductive traits were low (0.08-0.12). A negative genetic correlation (-0.15 to -0.18) was observed between DAYS105 and BFT, suggesting a genetic antagonism where selection for faster growth could lead to increased backfat thickness. Analysis of genetic trends over the 25 year period revealed substantial genetic progress, characterized by a continuous reduction in DAYS105 and an increase in litter size traits (TNB and NBA) for both breeds. The Yorkshire population showed higher accuracy in estimated breeding values compared to Landrace, attributed to its larger reference population size. These results highlight the confirmed effectiveness of the national breeding program and suggest the need for a balanced selection index considering unfavorable correlations, as well as the expansion of reference populations for further genetic improvement in maternal pig lines.