Immune response of 107 vaccinated Holstein cattle was initially obtained prior to the ELISA test. Five cattle with high and low bovine viral diarrhea virus (BVDV) type I antibody were identified as the final experimental animals. Blood samples from these animals were then utilized to determine significant differentially expressed genes (DEGs) using the RNA-seq transcriptome analysis and enrichment analysis. Our analysis identified 261 DEGs in cattle identified as experimental animals. Functional enrichment analysis in gene ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed the DEGs potentially induced by the inactivated BVDV type I vaccine, and might be responsible for the host immune responses. Our findings suggested that inactivated vaccine induced upregulation of genes involved in different GO annotations, including antigen processing and presentation of peptide antigen (via MHC class I), immune response, and positive regulation of interferon-gamma production. The observed downregulation of other genes involved in immune response might be due to inhibition of toll-like receptors (TLRs) by the upregulation of the Bcl-3 gene. Meanwhile, the result of KEGG pathways revealed that the majority of DEGs were upregulated and enriched to different pathways, including cytokine-cytokine receptor interaction, platelet activation, extracellular matrix (ECM) receptor interaction, hematopoietic cell lineage, and ATP-binding cassette (ABC) transporters. These significant pathways supported our initial findings and are known to play a vital role in shaping adaptive immunity against BVDV type 1. In addition, type 1 diabetes mellitus pathways tended to be significantly enriched. Thus, further studies are needed to investigate the prevalence of type 1 diabetes mellitus in cattle vaccinated with inactivated and live BVDV vaccine.

This study was conducted to estimate the genetic parameters of different feeding pattern traits, including average daily feed intake (ADFI), average occupation time per day (AOTD), average occupation time per visit (AOTV), average daily feeding rate (ADFR), average feeding rate per feeding visit (AFRV), average feed intake per feeding visit (AFIV), and average number of visits per day (ANVD), and their genetic relationship to production traits, such as on-test average daily gain (ADG), backfat thickness (BFT), loin muscle area (LMA), lean percentage (LP), and feed efficiency traits, such as feed conversion ratio (FCR) and five measures of residual feed intake (RFI1 to RFI5), in Duroc pigs (DD). The non-heritable common spatial pen effect was also estimated in all studied traits. The feeding pattern traits used in this study were derived from filtered feeding visits of 602 DD pigs. Using three animal models and the REML method, the genetic parameters revealed low to moderate heritability for ADFI (0.19 to 0.32) and AFIV (0.18 to 0.33), moderate heritability for ANVD (0.28 to 0.35) and AOTV (0.21 to 0.31), and high heritability for AOTD (0.73), ADFR (0.62 to 0.64), and AFRV (0.59 to 0.63). The addition of a common spatial pen effect in models 2 and 3 had a substantial impact, ranging from 8% to 23%, on the total variability of most feeding pattern traits, with the exception of AOTD, which only had a percentage variance of 0.30% due to the pen effect. The genetic and phenotypic correlation revealed that ADFI had consistent moderate to high genetic and phenotypic correlation with production and feed efficiency (FE) traits. However, selection against ADFI would negatively affect on-test ADG. Interestingly, the AOTD had no genetic correlation with ADG (0.04), low to moderate positive genetic correlation with FCR (0.27) and all RFI measures (0.24 to 0.33), and moderate negative correlation with LP (−0.39), indicating that selection for DD pigs with lower AOTD would not influence on-test ADG but may increase LP and improve feed efficiency by lowering FCR and all RFI measures. However, the corresponding phenotypic correlation of AOTD with production and feed efficiency traits was mostly weak, which can be attributed to the low residual or environmental correlation between these correlated traits. At the genetic level, the feeding pattern traits showed potential in improving feed efficiency and production traits. However, further studies are needed to evaluate their impact at phenotypic level.

Native chickens in Ethiopia are characterized in a fragmented manner for their performance characteristics and genotypes. This review aimed to explore the production and reproduction performance characteristics as well as the morphometric and morphological diversity of Ethiopian native chickens. The investigation was performed on four production performance characteristics, including average egg per clutch, average clutch/hen/year, average egg set/hen, and average egg/hen/year, as well as six reproductive performance characteristics, including age at first laying, age of male chickens at first bred, age at which female chickens are first bred, the reproductive life span of males and females, and fertility percentage in various parts of Ethiopia. Some economically practical morphometric characteristics of native chickens, such as shank length, chest circumference, comb length, body weight, body length, keel length, wattle length, neck length, back length, and morphological diversity, were also summarized. Regarding performance characteristics, there were some variations in eggs’ average production performance per clutch (13.56-15.4 eggs) and clutch/hen/year (3.0-4.29) in Ethiopia. The average reproduction performance characteristics of Ethiopian native chickens for age at first laying (6.90-7.13 months), age of male chickens at first bred (5.87-6.15 months), female at first bred (5.20-5.93 months), the reproductive life span of males (3.79 years) and hens (3.56 years), and chicks hatched from set eggs revealed variation across Ethiopia. In various locations of Ethiopia, the average trait values reported for Ethiopian native chickens under the farmer’s management differed in terms of morphometric and morphological features. The variation observed in performance characteristics, as well as morphometrics and morphological characteristics for Ethiopian native chicken ecotype population, can help the native breed classification, unique trait conservation, and breed improvement intervention programs.

Residual feed intake (RFI) gained attention as a potential alternative to the feed conversion ratio (FCR). Thus, this study aimed to estimate genetic parameters for different feed efficiency (FE) traits (FCR, RFI1 to RFI5) and their genetic correlation to on-test daily weight gain (ADG), backfat (BFT), loin muscle area (LMA), lean percentage (LP), and total feed intake (FI) for 603 Male Duroc (DD), 295 Landrace (LL), and 341 Yorkshire (YY). The common spatial pen effect was also estimated in these traits. Five RFI measures were estimated by regressing daily feed intake on initial testing age (ITA), initial testing weight (IBW), and ADG for RFI1; other models were the same as RFI1 except for additional BFT for RFI2; LMA for RFI3; BFT and LMA for RFI4; BFT, LMA, and average metabolic body weight (AMBW) instead of IBW for RFI5. Genetic parameters estimated using two animal models and the REML method showed moderate heritability for FCR in all breeds (0.22 and 0.28 for DD, 0.31 and 0.39 for LL, 0.17 and 0.22 for YY), low heritability for the majority of RFI measures in DD (0.15 to 0.23) and YY (0.14 to 0.20) and moderate heritability for all RFI measures in LL (0.31 to 0.34). Pen variance explained 7% to 22% for FE and 0% to 9% for production traits’ phenotypic variance. The genetic correlation revealed that selection against less complex RFI1 in DD and LL and RFI2 in YY would bring the most advantageous reduction to FI (0.71 for DD, 0.49 for LL, 0.43 YY) without affecting ADG in all breeds (0.06 for DD, −0.11 for LL, 0.05 for YY), decrease in BFT, and increase in LP in DD (0.51 in BFT, −0.77 in LP) and LL (0.45 in BFT, −0.83 in LP). Therefore, inclusion of these breed-specific RFI measures in the future selection criteria would help improve feed efficiency in the swine industry.

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.

Meat quality and carcass characteristics have gained the attention of breeders due to their increasing economic value. Thus, this study investigated the genomic prediction efficiencies of genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) for traits associated with meat quality, sensory characteristics, and fatty-acid composition. A total of 1237 Duroc finishing pigs with 654 individuals genotyped using the Illumina Porcine SNP 60k marker panel were used in this study. Prediction accuracy and bias for GBLUP and ssGBLUP were evaluated using a five-replicates of five-fold cross-validation. Estimation of genetic parameters for traits associated with meat quality, including lightness, yellowness, redness, pH at 24 h post-mortem, moisture content, fat content, water-holding capacity, cooking loss except for shear force (0.19), as well as fatty-acid composition (palmitic, stearic, oleic, linoleic, and linolenic fatty acids), revealed moderate to high heritability estimates ranging from 0.25 to 0.72 and 0.27 to 0.50, respectively, whereas all traits related to sensory characteristics (color, flavor, tenderness, juiciness, and palatability) showed low heritability estimates ranging from 0.08 to 0.14. Meanwhile, assessment of genomic prediction accuracy revealed that ssGBLUP exhibited higher prediction accuracy than GBLUP for meat quality traits, fatty-acid composition, and sensory characteristics, with percentage improvements ranging from 1.90% to 56.07%, 0.73% to 23.21%, and 0.88% to 11.85%, respectively. In terms of prediction bias, ssGBLUP showed less bias estimates than GBLUP for the majority of traits related to meat quality traits, sensory characteristics, and fatty-acid composition of Duroc meat. In this study, ssGBLUP outperformed GBLUP in terms of prediction accuracy and bias for the majority of traits. Through selection and breeding, our findings could be used to promote meat production with improved nutritional value.