Background: Reproductive performance is critical in the pig industry, and improved sow performance could lead to increased economic benefits. GWAS and ROH analyses based on SNP array data were conducted to identify the breed-specific genetic architecture underlying the variation in NBA and TNB. Methods: A total of 7488 breeding pigs with phenotypic data from 1586 Duroc, 2256 Landrace, and 3646 Yorkshire breeds, along with 76,756 SNP markers from Korean grand-grand-parent (GGP) breeding farms, were used. Results: In the Duroc breeds, SNPs on SSC 9 and 17 were found to be associated with the SIDT2 and TGM2 genes, respectively. In the Landrace breed, PPP1R9A, LMTK2, and GTF2H3 on SSCs 9, 3, and 14, respectively, were associated with both TNB and NBA. With the Yorkshire breed genome, GRID1, DLGAP2, ZZEF1, PARG, RNF17, and NDUFAF5 in SSCs 14, 15, 12, 14, 11, and 17, respectively, were associated with NBA and TNB traits. These genes have distinct functions, ranging from synaptic transmission and cytoskeletal organization to DNA repair and cellular energy production. In the Duroc breed, six genes identified in the ROH islands were associated with various biological pathways, molecular functions, and cellular components. NT5DC1 was associated with metaphyseal chondrodysplasia, CRTAC1 with ion binding, CFAP43 with spermatogenic failure, CASC3 with intracellular mRNA localization, ERC2 with cellular component organization, and FOCAD with Focadhesin. In the Landrace and Yorkshire breeds, PDE6D was associated with GTPase inhibitor activity. Conclusions: Through GWAS and ROH analyses, we identified breed-specific SNP markers associated with NBA and TNB in three breed genotypes, providing insights for improving reproductive performance efficiency and contributing to future breeding strategies.

The purpose of this study was to estimate the homozygosity distribution and compute genomic and conventional inbreeding coefficients in three genetically diverse pig breed populations. The genomic and pedigree data of Duroc (1586), Landrace (2256), and Yorkshire (3646) were analyzed. We estimated and compared various genomic and pedigree inbreeding coefficients using different models and approaches. A total of 709,384 ROH segments in Duroc, 816,898 in Landrace, and 1,401,781 in Yorkshire, with average lengths of 53.59 Mb, 56.21 Mb, and 53.46 Mb, respectively, were identified. Relatively, the Yorkshire breed had the shortest ROH segments, whereas the Landrace breed had the longest mean ROH segments. Sus scrofa chromosome 1 (SSC1) had the highest chromosomal coverage by ROH across all breeds. Across breeds, an absolute correlation (1.0) was seen between F_ROH total and F_ROH1–2Mb, showing that short ROH were the primary contributors to overall F_ROH values. The overall association between genomic and conventional inbreeding was weak, with values ranging from 0.058 to 0.140. In contrast, total genomic inbreeding (F_ROH) and ROH classes showed a strong association, ranging from 0.663 to 1.00, across the genotypes. The results of genomic and conventional inbreeding estimates improve our understanding of the genetic diversity among genotypes.

The biometric characterization of autochthonous Ethiopian chickens has not been fully investigated in the study area. In this study, we aimed to conduct biometric trait characterization and multivariate discriminant analysis of traditionally bred autochthonous chickens in Ethiopia and assess the wide range of phenotypic diversity within these populations. A multi-stage sampling procedure was used, and data on biometric traits and body weight were collected from adult chickens. Principal component and correlation analyses were performed to explore the discriminating factors and relationships among traits. All autochthonous chickens showed clear sexual dimorphism, with the Agarfa chickens having the highest biometric traits and body weight. Across the study area, the majority of biometric values showed variation between age group 1 (AG-1) and age group 3 (AG-3). All autochthonous chickens showed a strong correlation between wingspan and back length (p ≤ 0.001). Roosters and hens also showed a strong correlation between the keel and neck length (p ≤ 0.001). Principal component 1 (PC1) and principal component 2 (PC2) explained 56.44%, 55.09%, and 47.86% of the total variation in the original variables for all autochthonous chickens, roosters, and hens, respectively. Univariate and multivariate analyses revealed the existence of biometric trait and body weight variations among autochthonous chickens from different districts. Therefore, genetic profiling should be performed to better understand the genetic potential of autochthonous Ethiopian chickens.

This study aimed to estimate carcass trait characteristics, proportions, and their correlation with the preslaughter body weight of indigenous chickens in Southeastern Ethiopia. Data from 42 healthy male chickens were collected and analyzed using SAS 2012 ver. 9.4, R software ver.4.3.1, and MetaboAnalyst 5.0. The results indicated significant fixed effect of districts on dressed carcass weight, drumsticks, thighs, wings, and gizzard between Goba and Agarfa chickens (p < 0.05). The fixed effect of age and the district–age interaction effect were not significant. Principal component analysis revealed that PC1, accounting for 96.8% of the total variation between Goba and Agarfa chickens, was contributed by preslaughter and dressed carcass weight. Among the carcass components, the key contributors to differentiation between the Goba and Agarfa indigenous chicken carcass yields were the drumstick, thigh, breast (with/without keel bone), and back with thoracic weight (VIP > 1); there was a higher yield in Goba chickens. Preslaughter weight exhibited stronger correlations with most other traits, while dressing percentages displayed a negative correlation with various carcass components and edible giblet yields across the study districts. This study provides useful insights into carcass component characteristics and yields of indigenous Ethiopian chickens, which can increase our understanding of carcass components and their relationships with other qualities for improvement and further studies on poultry production.

Reproductive performance is a critical aspect of livestock production and sustainability. The number of stillbirths (NS) and mummified (NM) piglets significantly affect reproductive efficiency in swine production. Identifying and understanding the genetic architecture and candidate genes influencing these reproductive loss traits are essential for genetic inheritance studies and selective breeding programs in the swine breeding industry. To elucidate the genetic architecture of these traits, we performed a genome-wide association study (GWAS) using porcine 70 K BeadChip arrays from 1,162 Duroc, 1,783 Landrace, and 2,366 Yorkshire pigs. Single-parity breed-specific genome-wide association (GWA) analyses revealed that SIDT2 on Chr9 was associated with NM in Duroc pigs, whereas GTF2H3, PPP1R9A, and LMTK2 on Chr14, 9, and 3, respectively, were associated with both traits in Landrace pigs. Several genes have been linked to NS and NM in Yorkshire pigs, including GRID1 (chr14), DLGAP2 (chr15), ZZEF1 (chr12), RNF17 (chr11), SEL1L2 (chr17), ASCC3 (chr1), KCND2 (chr18), AP5B1(chr2), KAT5 (chr2), and SPATS2 (chr5). Across the breeds, five genes (DLGAP2, RNF17, SEL1L2, AP5B1, and KAT5) were exclusively associated with NS, whereas the other five (SIDT2, NDUFAF5, AKAP12, RCC1L, and BIRC6) were specific to NM. In addition, eight genes (GTF2H3, PPP1R9A, LMTK2, GRID1, ZZEF1, ASCC3, KCND2, and SPATS2) were associated with both traits, suggesting shared molecular pathways involved in piglet mortality. This study showed genetic factors affecting reproductive performance loss in three commercial Korean pig breeds through first-parity GWA analysis and provided crucial genetic markers that breeders may use in marker-assisted breeding programs aimed at improving reproductive efficiency.