Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data.

The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

Genome-wide association studies for economically important traits in mink using copy number variation.

Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.

Impact of glucose and pyruvate on adenosine triphosphate production and sperm motility in goats.

OBJECTIVE: This study evaluates goat sperm motility in response to metabolic substrates and various inhibitors, aiming to assess the relative contribution of glycolysis and mitochondrial oxidation for sperm movement and adenosine triphosphate (ATP) production. METHODS: In the present study, two main metabolic substrates; 0 to 0.5 mM glucose and 0 to 30 mM pyruvate were used to evaluate their contribution to sperm movements of goats. Using a 3-chloro-1,2-propanediol (3-MCPD), a specific inhibitor for glycolysis, and carbonyl cyanide 3-chlorophenylhydrazone as an inhibitor for oxidative phosphorylation, cellular mechanisms into ATP-generating pathways in relation to sperm movements and ATP production were observed. Data were analysed using one-way analysis of variance for multiple comparisons. RESULTS: Sperm motility analysis showed that either glucose or pyruvate supported sperm movement during 0 to 30 min incubation. However, the supporting effects were abolished by the addition of a glycolysis inhibitor or mitochondrial uncoupler, concomitant with a significant decrease in ATP production. Although oxidative phosphorylation produces larger ATP concentrations than those from glycolysis, sperm progressivity in relation to these two metabolic pathways is comparable. CONCLUSION: Based on the present study, we suggest that goat sperm use glucose and pyruvate to generate cellular energy through glycolysis and mitochondrial respiration pathways to maintain sperm movement.

Corrigendum: Population genomics of American mink using genotype data.

[This corrects the article DOI: 10.3389/fgene.2023.1175408.].

Population genomics of American mink using genotype data.

Understanding the genetic structure of the target population is critically important to develop an efficient genomic selection program in domestic animals. In this study, 2,973 American mink of six color types from two farms (Canadian Centre for Fur Animal Research (CCFAR), Truro, NS and Millbank Fur Farm (MFF), Rockwood, ON) were genotyped with the Affymetrix Mink 70K panel to compute their linkage disequilibrium (LD) patterns, effective population size (Ne), genetic diversity, genetic distances, and population differentiation and structure. The LD pattern represented by average r 2, decreased to <0.2 when the inter-marker interval reached larger than 350 kb and 650 kb for CCFAR and MFF, respectively, and suggested at least 7,700 and 4,200 single nucleotide polymorphisms (SNPs) be used to obtain adequate accuracy for genomic selection programs in CCFAR and MFF respectively. The Ne for five generations ago was estimated to be 76 and 91 respectively. Our results from genetic distance and diversity analyses showed that American mink of the various color types had a close genetic relationship and low genetic diversity, with most of the genetic variation occurring within rather than between color types. Three ancestral genetic groups was considered the most appropriate number to delineate the genetic structure of these populations. Black (in both CCFAR and MFF) and pastel color types had their own ancestral clusters, while demi, mahogany, and stardust color types were admixed with the three ancestral genetic groups. This study provided essential information to utilize the first medium-density SNP panel for American mink in their genomic studies.

The Complete Mitochondrial Genome and Phylogenetic Analyses of To Chicken in Vietnam.

Indigenous chicken breeds have both cultural significance and economic value since they possess unique genetic characteristics that enable them to adapt to the local environment and contribute to biodiversity, food security, and sustainable agriculture in Vietnam. To (Tò in Vietnamese) chicken, a Vietnamese indigenous chicken breed, is popularly raised in Thai Binh province; however, little known is about the genetic diversity of this breed. In this study, we sequenced the complete mitochondrial genome of To chicken for a better understanding of the diversity and origin of the breed. The results of sequencing showed that the mitochondrial genome of To chicken spans a total length of 16,784 base pairs and comprises one non-coding control region (known as the displacement-loop (D-loop) region), two ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. The phylogenetic tree analyses and estimated genetic distances based on 31 complete mitochondrial genome sequences indicated that To chicken has a close genetic distance with the Laotian native chicken breed, Lv'erwu breed in China, and Nicobari black and Kadaknath breeds in India. The result of the current study might be important for conservation, breeding, and further genetic studies of To chicken.

Coat color inheritance in American mink.

BACKGROUND: Understanding the genetic mechanisms underlying coat color inheritance has always been intriguing irrespective of the animal species including American mink (Neogale vison). The study of color inheritance in American mink is imperative since fur color is a deterministic factor for the success of mink industry. However, there have been no studies during the past few decades using in-depth pedigree for analyzing the inheritance pattern of colors in American mink. METHODS: In this study, we analyzed the pedigree of 23,282 mink extending up to 16 generations. All animals that were raised at the Canadian Center for Fur Animal Research (CCFAR) from 2003 to 2021 were used in this study. We utilized the Mendelian ratio and Chi-square test to investigate the inheritance of Dark (9,100), Pastel (5,161), Demi (4,312), and Mahogany (3,358) colors in American mink. RESULTS: The Mendelian inheritance ratios of 1:1 and 3:1 indicated heterozygous allelic pairs responsible for all studied colors. Mating sire and dam of the same color resulted in the production of offspring with the same color most of the time. CONCLUSION: Overall, the results suggested that color inheritance was complex and subjected to a high degree of diversity in American mink as the genes responsible for all four colors were found to be heterozygous.

Editorial: Role of Non-Coding RNAs in Animals.

The importance of non-coding RNAs (ncRNAs), such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and circular RNAs (circRNA), in gene regulation is increasingly being appreciated in many species [...].

A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison).

Availability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole genome was covered by 15 chromosomes. In total, 25,377 genes were predicted across the American mink genome using the NCBI Eukaryotic Genome Annotation Pipeline. In addition, gene orthology, demographic history, synteny blocks, and phylogenetic relationships were studied in connection with the genomes of other related Carnivora. Furthermore, population-based statistics of 100 sequenced mink were presented using the newly assembled genome. Remarkable improvements were observed in genome contiguity, the number of scaffolds, and annotation compared to the first draft of mink genome assembly (NNQGG.v01). This high-quality genome assembly will support the development of efficient breeding strategies as well as conservation programs for American mink.

Environmental Effects and Genetic Parameters for Growth Traits of Lohi Sheep.

Estimating genetic parameters for growth traits is crucial to plan breeding strategies for improving meat production in indigenous sheep breeds. The study first tested the effects of environmental and maternal effects on five growth traits, including birth weight (BWT), weight at 120 days (WT120), weight at 180 days (WT180), weight at 270 days (WT270) and weight at 365 days of age (WT365) and then estimated genetic parameters for these traits using data obtained in 1215 Lohi sheep. The effects of factors, including year (YOB), season (SOB) and type of birth (TOB), age of dam (AOD) and sex on growth traits of Lohi sheep, were examined using analysis of variance (ANOVA) in R software. Sex, TOB and YOB significantly affected all studied traits. The estimates of direct and maternal heritability for BWT and WT120 were 0.15 ± 0.08 and 0.20 ± 0.06, and 0.45 ± 0.16, 0.21 ± 0.08, respectively. The direct heritability estimates for WT180, WT270 and WT365 were 0.20 ± 0.07, 0.21 ± 0.07 and 0.19 ± 0.08, respectively. Due to the high heritability estimate obtained for WT120 compared to other studied traits, and its strong genetic correlation (>0.9) with post-weaning growth traits, it is recommended that selection must be practiced on WT120 to improve the growth performance of Lohi sheep. The results could be used for the development of genetic/genomic selection programs aiming to improve the production performance of the Lohi sheep.

Genetic and Phenotypic Parameters for Pelt Quality and Body Length and Weight Traits in American Mink.

Understanding the genetics of fur characteristics and skin size is important for developing effective breeding programs in the mink industry. Therefore, the objectives of this study were to estimate the genetic and phenotypic parameters for pelt quality traits including live grading overall quality (LQU), live grading nap size (LNAP), dried pelt size (DPS), dried pelt nap size (DNAP) and overall quality of dried pelt (DQU), and body length and weight traits, including November body weight (Nov_BW), November body length (Nov_BL), harvest weight (HW) and harvest length (HL) in American mink. Dried pelt quality traits on 1195 mink and pelt quality traits on live animals on 1680 were collected from mink raised at two farms, in Nova Scotia and Ontario. A series of univariate analyses were implemented in ASReml 4.1 software to identify the significance (p < 0.05) of random effects (maternal genetic effects, and common litter effects) and fixed effects (farm, sex, color type, year, and age) for each trait. Subsequently, bivariate models were used to estimate the genetic and phenotypic parameters using ASReml 4.1. Heritability (±SE) estimates were 0.41 ± 0.06 for DPS, 0.23 ± 0.10 for DNAP, 0.12 ± 0.04 for DQU, 0.28 ± 0.06 for LQU, 0.44 ± 0.07 for LNAP, 0.29 ± 0.10 for Nov_BW, 0.28 ± 0.09 for Nov_BL, 0.41 ± 0.07 for HW and 0.31 ± 0.06 for HL. DPS had high positive genetic correlations (±SE) with Nov_BW (0.89 ± 0.10), Nov_BL (0.81 ± 0.07), HW (0.85 ± 0.05) and HL (0.85 ± 0.06). These results suggested that body weight and length measured on live animals in November of the first year were reliable indicators of dried pelt size. DQU had favorable genetic correlations with Nov_BL (0.55 ± 0.24) and HL (0.46 ± 0.20), and nonsignificant genetic correlations with DNAP (0.13 ± 0.25), Nov_BW (0.25 ± 0.25) and HW (0.06 ± 0.20), which made body length traits an appealing trait for selection for increased pelt size. High positive genetic correlation (±SE) was observed between LNAP and DNAP (0.82 ± 0.22), which revealed that nap size measurement on live animals is a reliable indicator trait for dried pelt nap size. However, nonsignificant (p > 0.05) low genetic correlation (±SE) was obtained between LQU and DQU (0.08 ± 0.45), showing that indirect selection based on live grading might not lead to the satisfactory improvement of dried pelt overall quality. The estimated genetic parameters for live grading, dried pelt quality, and body weight and body length traits may be incorporated into breeding programs to improve fur characteristics in Canadian mink populations.

Genome-Wide Detection of Selection Signatures for Pelt Quality Traits and Coat Color Using Whole-Genome Sequencing Data in American Mink.

Domestication and selection are the major driving forces responsible for creating genetic variability in farmed species. American mink has been under selection for more than 100 years for improved body size and pelt quality. This study aimed to identify the genomic regions subjected to selection for pelt quality traits, and coat color using the whole genome sequences of 100 mink raised in the Canadian Centre for Fur Animal Research (CCFAR) at Dalhousie Agriculture Campus (Truro, NS, Canada), and Millbank fur farm (Rockwood, ON, Canada). Measurements of three dried pelt characteristics (including pelt size (n = 35), overall quality of fur (n = 27), and nap size (n = 29)), and three coat color of Black, Stardust, and Pastel (Stardust_ Black (n = 38), and Pastel_Black (n = 41)) were used to assign animals to pairwise groups. Signatures of selection were detected using integrated measurement of fixation index (Fst), extended haplotype homozygosity (XP-EHH), and nucleotide diversity (θπ) tests. In total, overlapping top 1% of Fst and XP-EHH harbored 376 genes for pelt quality traits (110 for nap size, 163 for overall quality of fur, and 98 pelt size), and 194 genes for coat color (123 for Pastel_Black and 71 for Stardust_Black) were detected in different groups. Integrating results of Fst, and XP-EHH with the θπ test supported 19 strongly selected regions on chromosomes 3, 4, 5, 6, 7, 8, 9, and 10 that contained 33 candidate genes related to fur quality, hair follicle function, and pelt size traits. Gene ontology revealed numerous genes related to the hair cycle process and molting cycle process, epidermis development, Wnt signaling pathway and muscle development. This study provided the first map of putative selection signals related to pelt quality and coat color in American mink, which could be used as a reference for future studies attempting to identify genes associated with economically important traits in mink.

Genetic and phenotypic correlations between Aleutian disease tests with body weight, growth, and feed efficiency traits in mink.

The ineffectiveness of vaccination, medicine, and culling strategy leads mink farmers to control Aleutian disease (AD) by selecting AD-resilient mink based on AD tests. However, the genetic background of AD tests and their correlations with economically important or AD-resilient traits are limited. This study estimated the genetic and phenotypic correlations between four AD tests and seven body weight (BW) traits, six growth parameters from the Richards growth model, and eight feed-related traits. Univariate models were used to test the significance (P < 0.05) of fixed effects (sex, color type, AD test year, birth year, and row-by-year), random effects (additive genetic, maternal genetic, and permanent environmental), and a covariate of age using ASReml 4.1. Likewise, pairwise bivariate analyses were conducted to estimate the phenotypic and genetic correlations among the studied traits. Both antigen- and virus capsid protein-based enzyme-linked immunosorbent assay tests (ELISA-G and ELISA-P) showed significant (P < 0.05) moderate positive genetic correlations (±SE) with maturation rate (from 0.36 ± 0.18 to 0.38 ± 0.19). ELISA-G showed a significant negative genetic correlation (±SE) with average daily gain (ADG, -0.37 ± 0.16). ELISA-P showed a significant positive moderate genetic correlation (±SE) with off-feed days (DOF, 0.42 ± 0.17). These findings indicated that selection for low ELISA scores would reduce the maturation rate, increase ADG (by ELISA-G), and minimize DOF (by ELISA-P). The iodine agglutination test (IAT) showed significant genetic correlations with DOF (0.73 ± 0.16), BW at 16 weeks of age (BW16, 0.45 ± 0.23), and BW at harvest (HW, -0.47 ± 0.20), indicating that selection for lower IAT scores would lead to lower DOF and BW16, and higher HW. These estimated genetic correlations suggested that the selection of AD tests would not cause adverse effects on the growth, feed efficiency, and feed intake of mink. The estimates from this study might strengthen the previous finding that ELISA-G could be applied as a reliable and practical indicator trait in the genetic selection of AD-resilient mink in AD-positive farms.

The selection of Aleutian disease-resistant individuals based on Aleutian disease (AD) tests is seen as a potential method to control AD effectively. However, the knowledge regarding the genetic background of AD tests is limited. This study estimated the genetic and phenotypic correlations between Aleutian disease tests and body weight, growth, and feed-related traits in mink. The estimates in this study indicated that the growth, feed efficiency, and feed intake of mink would not be adversely influenced by the selection of AD tests. In the meantime, the estimates further illustrate that the antigen-based enzyme-linked immunosorbent assay test could be applied as the most reliable and practical indicator trait to select AD-resilient mink in AD-positive farms.

Genome-wide detection of copy number variation in American mink using whole-genome sequencing.

BACKGROUND: Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS: A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS: This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.

Identification of potential crucial genes and key pathways shared in Inflammatory Bowel Disease and cervical cancer by machine learning and integrated bioinformatics.

BACKGROUND: Recently, Inflammatory Bowel Disease (IBD) has been proven as a risk factor for the increasing incidence of cervical cancer (CC) development. In this study, we identify these potential hub genes and their significant pathways that commonly interact between IBD and CC and these pathological mechanisms. To this end, we use bioinformatics and systems biology approaches to analyze the miRNA-mRNA, TFs-mRNA regulatory network. METHODS AND FINDINGS: The reanalysis dataset from Gene Expression Omnibus (GEO) and the cancer genome atlas (TCGA) found these common differentially expressed genes (DEGs) between IBD and CC, clustered via weighted gene co-expression network analysis, and the vital modules significantly related to cervical cancer were identified. These hub genes of the key module were identified and explored in biological mechanism pathway analysis. Organelle fission, nuclear envelope, protein serine/threonine kinase activity, and the Human T-cell leukemia virus 1 infection pathway were the major enriched pathways for the common DEGs. Due to the high connectivity, the common DEGs with protein-protein interaction (PPI) network disclosed hub proteins (CDK1, MAD2L1, and CCNB1). This study also showed the classification algorithms of ten hub genes (MAD2L1, CCNB2, CDK1, CCNA2, BUB1B, KIF11, TTK, BUB1, CCNB1, ASPM) with accuracy >0.90 suggesting the novel biomarker potential of the hub genes. The microRNAs (miRNA), and transcription factors (TFs) mRNA regulatory network, five transcription factors, and twelve miRNAs are strongly linked to three hub genes. Gene drug interaction analysis found seven drugs compound that interacts with the hub gene. CONCLUSIONS: In the current study, our procedure has hypothesized the comprehensive understanding of disease mechanisms vital for both CC and IBD that may mediate their interaction. Our results suggest the further investigation of the molecules for the treatment of IBD and CC.

Applying Machine Learning Algorithms for the Classification of Mink Infected with Aleutian Disease Using Different Data Sources.

American mink (Neogale vison) is one of the major sources of fur for the fur industries worldwide, whereas Aleutian disease (AD) is causing severe financial losses to the mink industry. A counterimmunoelectrophoresis (CIEP) method is commonly employed in a test-and-remove strategy and has been considered a gold standard for AD tests. Although machine learning is widely used in livestock species, little has been implemented in the mink industry. Therefore, predicting AD without using CIEP records will be important for controlling AD in mink farms. This research presented the assessments of the CIEP classification using machine learning algorithms. The Aleutian disease was tested on 1157 individuals using CIEP in an AD-positive mink farm (Nova Scotia, Canada). The comprehensive data collection of 33 different features was used for the classification of AD-infected mink. The specificity, sensitivity, accuracy, and F1 measure of nine machine learning algorithms were evaluated for the classification of AD-infected mink. The nine models were artificial neural networks, decision tree, extreme gradient boosting, gradient boosting method, K-nearest neighbors, linear discriminant analysis, support vector machines, naive bayes, and random forest. Among the 33 tested features, the Aleutian mink disease virus capsid protein-based enzyme-linked immunosorbent assay was found to be the most important feature for classifying AD-infected mink. Overall, random forest was the best-performing algorithm for the current dataset with a mean sensitivity of 0.938 ± 0.003, specificity of 0.986 ± 0.005, accuracy of 0.962 ± 0.002, and F1 value of 0.961 ± 0.088, and across tenfold of the cross-validation. Our work demonstrated that it is possible to use the random forest algorithm to classify AD-infected mink accurately. It is recommended that further model tests in other farms need to be performed and the genomic information needs to be used to optimize the model for implementing machine learning methods for AD detection.

The Role of miR-29s in Human Cancers-An Update.

MicroRNAs (miRNAs) are small non-coding RNAs that directly bind to the 3' untranslated region (3'-UTR) of the target mRNAs to inhibit their expression. The miRNA-29s (miR-29s) are suggested to be either tumor suppressors or oncogenic miRNAs that are strongly dysregulated in various types of cancer. Their dysregulation alters the expression of their target genes, thereby exerting influence on different cellular pathways including cell proliferation, apoptosis, migration, and invasion, thereby contributing to carcinogenesis. In the present review, we aimed to provide an overview of the current knowledge on the miR-29s biological network and its functions in cancer, as well as its current and potential applications as a diagnostic and prognostic biomarker and/or a therapeutic target in major types of human cancer.

Association of Lactoferrin and Toll-like Receptor 2 Genotypes with Mastitis and Milk Components in Vietnamese Holstein Cattle.

Mastitis is one of the most widespread diseases in dairy cows and causes huge losses for the dairy industry. Molecular markers can be used for the quick diagnosis of mastitis infection, consequently reducing the loss caused by this disease. Lactoferrin (LTF) and Toll-like receptor 2 (TLR2) have been suggested as candidate genes for mastitis; however, their associations with the mastitis incidence and milk components have not been reported in Vietnamese Holstein cows. This study examined the association of TLR2 and LTF polymorphisms with subclinical mastitis and milk components in the Holstein breed raised in Vietnam. Among 192 samples, we identified 44 mastitis-positive samples (22.92%). The mastitis significantly reduced the fat and lactose components in milk (p < 0.001) but increased the protein concentration in milk. A total of 94 (49%) and 98 (51%) cows had AA and AB genotypes for the LTF gene, respectively. No significant association was found between the LTF genotypes and the milk component traits or mastitis incidence (p > 0.05). The interaction between LTF and mastitis incidence was significantly associated with the protein percentage (p = 0.01). A total of 78, 76, and 38 cows had genotypes GG, GT, and TT for the TLR2 gene, respectively. TLR2 genotypes were not significantly associated with mastitis incidence (p > 0.05) but were significantly associated with pH value (p = 0.03). The interaction between TLR2 and mastitis incidence was significantly associated with the fat (p = 0.02) and protein percentage (p = 0.04). Further studies are required to confirm the roles of LTF and TFL2 in mastitis in the Holstein breed in Vietnam.

Application of Genetic, Genomic and Biological Pathways in Improvement of Swine Feed Efficiency.

Despite the significant improvement of feed efficiency (FE) in pigs over the past decades, feed costs remain a major challenge for producers profitability. Improving FE is a top priority for the global swine industry. A deeper understanding of the biology underlying FE is crucial for making progress in genetic improvement of FE traits. This review comprehensively discusses the topics related to the FE in pigs including: measurements, genetics, genomics, biological pathways and the advanced technologies and methods involved in FE improvement. We first provide an update of heritability for different FE indicators and then characterize the correlations of FE traits with other economically important traits. Moreover, we present the quantitative trait loci (QTL) and possible candidate genes associated with FE in pigs and outline the most important biological pathways related to the FE traits in pigs. Finally, we present possible ways to improve FE in swine including the implementation of genomic selection, new technologies for measuring the FE traits, and the potential use of genome editing and omics technologies.

Immune-related biomarkers shared by inflammatory bowel disease and liver cancer.

It has been indicated that there is an association between inflammatory bowel disease (IBD) and hepatocellular carcinoma (HCC). However, the molecular mechanism underlying the risk of developing HCC among patients with IBD is not well understood. The current study aimed to identify shared genes and potential pathways and regulators between IBD and HCC using a system biology approach. By performing the different gene expression analyses, we identified 871 common differentially expressed genes (DEGs) between IBD and HCC. Of these, 112 genes overlapped with immune genes were subjected to subsequent bioinformatics analyses. The results revealed four hub genes (CXCL2, MMP9, SPP1 and SRC) and several other key regulators including six transcription factors (FOXC1, FOXL1, GATA2, YY1, ZNF354C and TP53) and five microRNAs (miR-124-3p, miR-34a-5p, miR-1-3p, miR-7-5p and miR-99b-5p) for these disease networks. Protein-drug interaction analysis discovered the interaction of the hub genes with 46 SRC-related and 11 MMP9- related drugs that may have a therapeutic effect on IBD and HCC. In conclusion, this study sheds light on the potential connecting mechanisms of HCC and IBD.