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Melanoma prevalence in gray horses reaches up to 50% and more. Several studies have documented a genetic melanoma predisposition which is referred to the 4.6 kb duplication in intron 6 of STX17 and its surrounding haplotype. However, the genetic background and mechanisms responsible for differences in etiopathogenesis of equine dermal melanomatosis still remain unknown. In the current study, we performed a genome wide association analysis in 141 Lipizzan horses and subsequently identified one candidate gene on chromosome 24 putatively involved in melanoma pathogenesis in gray horses. The associated SNP was located in the intronic region of DPF3, a gene which is involved in humans in cell growth, proliferation, apoptosis and motility of cancer cells. The replication study in 1210 horses from seven breeds demonstrated, that the G/G genotype of the DPF3 associated SNP exhibits putative melanoma suppression effects. As a conclusion DPF3 represents a candidate gene, which might play an essential role for gray horses coping with high genetic melanoma related tumor load., (Copyright © 2021. Published by Elsevier Inc.)

As one of the key components of pattern recognition receptors, Toll-like receptors (TLRs) play pivotal roles in the innate immune system. However, little information is available about the TLR genes in Sebastes schlegelii. In the present study, 17 TLR genes were identified and classified based on the whole genome database. Tandem duplication events in TLR1, TLR2, TLR5 and TLR13 played major role in the expansion of S. schlegelii TLR genes; both TLR2-3 and TLR2-4 had the same largest number of introns/exons, 11 exons and 10 introns. The syntenic analysis showed neighboring genes of TLR genes were most conserved in S. schlegelii and in L. crocea. Phylogenetic and evolutionary analysis showed that these TLR genes were divided into five subfamilies and exhibited different selection pressures. Meanwhile, the expression patterns of TLR genes in the intestine after E. tarda infection were investigated by qRT-PCR. Finally, protein and protein interaction (PPI) network analysis indicated that TLR genes interacted with IFN-inducible genes, inflammatory cytokines, and participated in MyD88-dependent pathway. In summary, this study provided valuable information for further functional characterization of TLR genes in S. schlegelii., Competing Interests: Declaration of competing interest The authors declare no competing interest., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Objectives: Pituitary-dependent hyperadrenocorticism is the most common cause of naturally occurring hypercortisolism in dogs. CRHR1 expression in human and dog corticotrophinomas suggested that this gene affects pituitary tumorigenesis. The present study aimed to investigate mutations in the CRHR1 coding region in poodles with pituitary-dependent hyperadrenocorticism., Methods: Fifty poodles with pituitary-dependent hyperadrenocorticism and 50 healthy poodles were studied. Genomic DNA was amplified by PCR and analyzed by Sanger sequencing., Results: The novel CRHR1 p.V97M mutation was identified in one dog. This valine residue, located in the amino-terminal extracellular domain, exhibits high affinity for its corticotropin-releasing hormone (CRH) ligand. Bioinformatic analysis revealed structural rearrangements in the mutant protein, with a 17% increase in the surface binding affinity between CRHR1 and CRH. In vitro functional studies showed that mutant CRHR1 induced higher ACTH secretion than the wild type after stimulation with human CRH., Conclusion: These results suggest that germline activating mutations in CRHR1 may be a rare cause of pituitary hyperadrenocorticism in poodles.

The possibility of using genetic control strategies to increase disease resistance to infectious diseases relies on the identification of markers to include in the breeding plans. Possible incomplete exposure of mastitis-free (control) animals, however, is a major issue to find relevant markers in genetic association studies for infectious diseases. Usually, designs based on elite dairy sires are used in association studies, but an epidemiological case-control strategy, based on cows repeatedly field-tested could be an alternative for disease traits. To test this hypothesis, genetic association results obtained in the present work from a cohort of Italian Holstein cows tested for mastitis over time were compared with those from a previous genome-wide scan on Italian Holstein sires genotyped with 50k single nucleotide polymorphisms for de-regressed estimated breeding values for somatic cell counts (SCCs) on Bos taurus autosome (BTA6) and BTA14. A total of 1121 cows were selected for the case-control approach (cases=550, controls=571), on a combination of herd level of SCC incidence and of within herd individual level of SCC. The association study was conducted on nine previously identified markers, six on BTA6 and four on BTA14, using the R statistical environment with the 'qtscore' function of the GenABEL package, on high/low adjusted linear score as a binomial trait. The results obtained in the cow cohort selected on epidemiological information were in agreement with those obtained from the previous sire genome-wide association study (GWAS). Six out of the nine markers showed significant association, four on BTA14 (rs109146371, rs109234250, rs109421300, rs109162116) and two on BTA6 (rs110527224 and rs42766480). Most importantly, using mastitis as a case study, the current work further validated the alternative use of historical field disease data in case-control designs for genetic analysis of infectious diseases in livestock.

Data on 125 dry-cured hams from purebred Duroc pigs were used to examine whether the favorable effect of the T allele in the promoter region of the stearoyl-CoA desaturase gene (AY487830:g.2228T>C) on monounsaturated fatty acid (MUFA) content in green ham is maintained after the curing process. It is shown that pigs carrying the T allele produced dry-cured hams with increased C16:1, C18:1n-9, C18:1n-7, and MUFA and decreased C18:0 and saturated fatty acid (SFA) content. The TT pigs had 1.39% more MUFA and 1.62% less SFA than the CC animals, while gilts had 0.74% more MUFA and 0.34% less SFA than barrows. The correlation between MUFA in green and dry-cured hams (n=53) was high (r=0.88), with TT pigs being more effective in retaining increased MUFA in green hams until the end of the curing period. It is concluded that increasing the presence of the T allele could have more impact than gender to produce hams with a high level of MUFA., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

This study aimed to verify genetic effects of the bovine adiponectin (ADIPOQ) gene on carcass traits of Hanwoo cattle. The measured carcass traits were marbling score (MAR), backfat thickness (BFT), loineye area (LEA), and carcass weight (CAW). Selection of primers was based on the bovine ADIPOQ sequence, and the analysis amplified approximately 267 and 333 bp genomic segments, including 67 bp of insertions in the promoter region. Sequencing analysis confirmed genetic variants (g.81966235C>T, g.81966377T>C, and g.81966364D>I) that showed significant effects on MAR. The present results suggest that the identified SNPs are useful genetic markers for the improvement of carcass traits in Hanwoo cattle., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

The aim of this study was to estimate genetic correlations between milk yield, somatic cell score (SCS), mastitis, and claw and leg disorders (CLDs) during first lactation in Holstein cows by using a threshold-linear random regression test-day model. We used daily records of milk, fat and protein yields; somatic cell count (SCC); and mastitis and CLD incidences from 46 771 first-lactation Holstein cows in Hokkaido, Japan, that calved between 2000 and 2009. A threshold animal model for binary records (mastitis and CLDs) and linear animal model for yield traits were applied in our multiple trait analysis. For both liabilities and yield traits, additive genetic effects were used as random regression on cubic Legendre polynomials of days on milk. The highest positive genetic correlations between yields and disease incidences (0.36 for milk and mastitis, 0.56 for fat and mastitis, 0.24 for protein and mastitis, 0.32 for milk and CLD, 0.44 for fat and CLD and 0.31 for protein and CLD) were estimated at about the time of peak milk yield (36 to 65 days in milk). Selection focused on early lactation yield may therefore increase the risk of mastitis and CLDs. The positive genetic correlations of SCS with mastitis or CLD incidence imply that selection to reduce SCS in the early stages of lactation would decrease the incidence of both mastitis and CLD.

An immune response is mounted after binding of Toll-like receptors (TLRs) to pathogen-associated molecular patterns. The primary objective of this study was to test for the associations between bovine single-nucleotide polymorphisms (SNPs) and insertion-deletion (indel) mutations occurring in seven bovine TLR genes (TLRs 1, 2, 4, 5, 6, 9, and 10) that are known to recognize bacterial ligands and the most significant uterine diseases in dairy cows, including metritis (MET), clinical endometritis (CE), and cytologic endometritis (CYE). Custom allele-specific genotyping assays derived from multiple bovine TLR sequencing studies were utilized. Genotypes for 110 loci (SNPs and indels) that are known to be variable in domestic cattle were determined, resulting in 46 monomorphic loci, 64 loci with two alleles, and 35 loci that did not meet our inclusion criterion for minor allele frequency (≥0.10). The association between specific TLR genotypes and each of the uterine diseases (MET, CE, CYE) was evaluated by logistic regression with correction for confounding variables. Collectively, seven SNPs produced uncorrected P values ≤0.05 with respect to three different uterine diseases investigated, but none of the SNP associations endured correction for multiple testing (P values ≥ 0.05). Several confounding variables, including parity, dystocia, and ketosis before 17 DIM, remained significant after correction for multiple testing. Our analysis of these data suggest that some bovine TLR SNPs (i.e., TLRs 2, 4, 6, 9) may potentially elicit relatively small effects on uterine health in Holstein dairy cows and that some confounding variables are actually more predictive for the incidence of disease than any genetic markers evaluated herein., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Our previous transcriptome analysis using a cDNA microarray identified differentially-expressed transcripts in Tsaiya ducks (Anas platyrhynchos); we concluded that the ovalbumin gene might be involved in duck hatchability. In the present study, associations of single nucleotide polymorphism (SNP) genotypes of the duck ovalbumin gene with hatchability were investigated. To confirm the cDNA microarray analysis, real-time polymerase chain reaction (PCR) and Western blot analysis were used to validate ovalbumin gene expression. The messenger RNA and protein expression of the ovalbumin gene were higher (P < 0.05) in the low-hatchability group (1.00 ± 0.19; 30.36 ± 3.51 arbitrary units) than in high-hatchability counterparts (0.56 ± 0.07; 8.53 ± 2.97 arbitrary units), consistent with the previous cDNA microarray analysis. The PCR products (506 base pairs) of ovalbumin gene amplified by the primer pair of TovaF and TovaR from the genomic DNA templates of 10 ducks were sequenced and a g.385 C>T SNP site in the 506-base pair sequence of the ovalbumin gene identified. Genotyping of SNP of 187 ducks was then carried out by PCR restriction fragment length polymorphism and minisequencing methods. Based on SNP genotypes of the duck ovalbumin gene, there were three types: CC, TT, and CT. Birds with the CC and TT genotypes had higher hatchability (79.59 ± 3.40, 76.35 ± 1.77) (P < 0.05) than those with a CT genotype (65.77 ± 2.07). In conclusion, the ovalbumin gene was an important candidate gene that can be used for marker-assisted selection to increase hatchability in Tsaiya ducks., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Salmonella enterica serovar Enteritidis infection is a common concern in poultry production for its negative effects on growth as well as food safety for humans. Identification of molecular markers that are linked to resistance to Salmonella Enteritidis may lead to appropriate solutions to control Salmonella infection in chickens. This study investigated the association of candidate genes with resistance to Salmonella Enteritidis in young chickens. Two native breeds of Malaysian chickens, namely, Village Chickens and Red Junglefowl, were evaluated for bacterial colonization after Salmonella Enteritidis inoculation. Seven candidate genes were selected on the basis of their physiological role in immune response, as determined by prior studies in other genetic lines: natural resistance-associated protein 1 (NRAMP1), transforming growth factor β3 (TGFβ3), transforming growth factor β4 (TGFβ4), inhibitor of apoptosis protein 1 (IAP1), caspase 1 (CASP1), lipopolysaccharide-induced tumor necrosis factor (TNF) α factor (LITAF), and TNF-related apoptosis-inducing ligand (TRAIL). Polymerase chain reaction-RFLP was used to identify polymorphisms in the candidate genes; all genes exhibited polymorphisms in at least one breed. The NRAMP1-SacI polymorphism correlated with the differences in Salmonella Enteritidis load in the cecum (P = 0.002) and spleen (P = 0.01) of Village Chickens. Polymorphisms in the restriction sites of TGFβ3-BsrI, TGFβ4-MboII, and TRAIL-StyI were associated with Salmonella Enteritidis burden in the cecum, spleen, and liver of Village Chickens and Red Junglefowl (P < 0.05). These results indicate that the NRAMP1, TGFβ3, TGFβ4, and TRAIL genes are potential candidates for use in selection programs for increasing genetic resistance against Salmonella Enteritidis in native Malaysian chickens.

The prevention of unpleasant boar taint is the main reason for castration of male piglets. This study aimed to investigate how the malodorous compound skatole is affected by a single nucleotide polymorphism (g.2412 C>T at -586 ATG) in the porcine cytochrome p450 II E1 (CYP2E1) gene. 119 boars of two commercial Duroc-sired crossbred populations raised at different farms were investigated. Skatole and androstenone in backfat averaged 114±125 ng/g and 1206±895 ng/g melted fat, respectively. The frequency of the genotypes CC, CT, and TT was 25, 52, and 23%, respectively. CC boars had the highest average skatole levels (175 ng/g) compared to CT (92 ng/g) and TT (93 ng/g). Applying suggested sensory threshold levels for skatole (>150 ng/g) and androstenone (>2000 ng/g), 30% of the carcasses may be unacceptably tainted while the proportion of tainted carcasses is significantly higher within genotype CC (56.7%) compared to genotypes CT (24.3%) and TT (14.8%). Effective reduction of tainted carcasses appears feasible applying marker assisted selection., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

This study aimed to evaluate the effects of PRKAG3 Ile199Val and CAST Arg249Lys and CAST Ser638Arg polymorphisms on the quality traits of the French dry-cured ham Jambon de Bayonne and their interaction with salt reduction. Significant (p<0.05) and suggestive associations (p<0.10) between the polymorphisms and several quality traits of dry-cured ham, mainly related to processing and textural properties, were found. PRKAG3 Ile/Val and CAST 249Lys/638Arg presented the highest scores for sensory and processing properties, whatever the salt content., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Skeletal muscle and kidney-enriched inositol phosphatase (SKIP) was identified as a 5'-inositol phosphatase that hydrolyzes phosphatidylinositol (3,4,5)-triphosphate (PI(3,4,5)P3) to PI(3,4)P2 and negatively regulates insulin-induced phosphatidylinositol 3-kinase signaling in skeletal muscle. In this study, two new single nucleotide polymorphisms (SNPs) in porcine SKIP introns 1 and 6 were detected. The C1092T locus in intron 1 showed significant associations with some meat traits, whereas the A17G locus in intron 6 showed significant associations with some carcass traits. Expression analysis showed that porcine SKIP is upregulated at d 65 of gestation and Meishan fetuses have higher and prolonged expression of SKIP compared to Large White at d 100 of gestation. Ectopic expression of porcine SKIP decreased insulin-induced cell proliferation and promoted serum starvation-induced cell cycle arrest in G0/G1 phase in C2C12. Our results suggest that SKIP plays a negative regulatory role in skeletal muscle development partly by preventing cell proliferation., (Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.)

The functional single polymorphisms identified in the calpastatin (CAST) gene have been related to the rate of meat tenderization and the protein turnover after slaughter, and the Ile199Val polymorphism identified in the coding region of the protein kinase AMP-activated (PRKAG3) gene has been proven to affect ultimate pH in muscle. The aim of the present study was to show the effects of these genetic polymorphisms on the quality traits of Spanish dry-cured ham Jamón Serrano. A tissue sample from 665 crossbreed pigs were genotyped for PRKAG3 Ile199Val, CAST Arg249Lys and CAST Ser638Arg polymorphisms, and a subsample of 120 dry cured hams was selected to perform physico-chemical, rheological, instrumental colour and sensory analyses. Associations between the polymorphisms and several quality traits of dry-cured ham, mainly related to flavour and texture, were found. The genotypes PRKAG3 Ile/Ile, CAST249 Arg/Arg and CAST638 Arg/Arg, and the haplotype CAST 249Arg-638Arg were the most favourable for Jamón Serrano production., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

The ASAP1 gene is located in a QTL region for meat production traits and to access the role of the ASAP1 gene, the association between a SNP in this gene and production traits in beef cattle was studied. For this, about 270 steers of reference families of Nelore breed were used. The investigation of marker effects on the traits was performed using a mixed model under the restricted maximum likelihood method. Novel association of a SNP in the ASAP1 gene and shear force measured at 24 h post mortem (P≤0.0083) was described in this population of Nelore cattle. This polymorphism accounted for 1.13% of the total additive variance and 17.51% of total phenotypic variance of the trait, suggesting that this marker could be used in marker assisted selection., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

The aim of this study was to investigate the effect of the paternal allele (homozygous AA and heterozygous AG) of the IGF-II gene on the fat content, fatty acid composition and sensory characteristics of dry-cured hams and shoulders. The effects were more evident in the subcutaneous fat thickness than in the intramuscular fat (IMF) content, and in the dry-cured hams rather than the dry-cured shoulders. Subcutaneous fat thickness was significantly higher in AG dry-cured hams and shoulders; however, IMF content was only significantly higher in AG dry-cured hams. These effects produce changes in fatty acid composition and sensory characteristics when comparing both batches of each product, but the behavior differed with the type of product. Sensory characteristics were similar in both batches of dry-cured hams in spite of the differences in IMF content. Nevertheless, AG dry-cured shoulders showed higher scores in most of the attributes evaluated, despite the IMF content being similar between batches., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Attributes contributing to differences in beef quality of 206 Hereford steers finished on pasture were assessed. Beef quality traits evaluated were: Warner-Bratzler meat tenderness and muscle and fat color at one and seven days after slaughter and trained sensory panel traits (tenderness, juiciness, flavor, and marbling) at seven days. Molecular markers were CAPN1 316 and an SNP in exon 2 on the leptin gene (E2FB). Average daily live weight gain, ultrasound monthly backfat thickness gain and rib-eye area gain were estimated. Molecular markers effects on meat quality traits were analyzed by mixed models. Association of meat quality with post weaning growth traits was analyzed by canonical correlations. Muscle color and marbling were affected by CAPN1 316 and E2FB and Warner-Bratzler meat tenderness by the former. The results confirm that marker assisted selection for tenderness is advisable only when beef aging is a common practice. The most important sources of variation in tenderness and color of meat remained unaccounted for., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

The aim of the present study, the third in a series of three papers, is to show the effects of PRKAG3 and CAST gene polymorphisms on the quality traits of the Slovenian dry-cured ham "Kraški pršut" and their interaction with ham producers. Significant interaction of polymorphisms with producer in the case of salt content, lipid oxidation (PRKAG3 Ile199Val), proteolysis index (CAST Arg249Lys) and pastiness (CAST Ser638Arg) indicated that genotype manifestation was reliant on the manufacturing practice. PRKAG3 Ile199Val polymorphism affected several physico-chemical, rheological and sensory traits. The Ile/Ile genotype yielded less salty and softer hams, indicating beneficial effects on dry-cured ham quality. The effect of CAST polymorphisms was less pronounced, although the observed associations with pastiness, proteolysis index and several free amino acid concentrations indicate its possible influence on proteolysis, with haplotype CAST 249Arg/638Ser being associated with a higher degree of proteolysis., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Numerous reports have described genetic markers or genomic regions (QTL) associated with pork quality and/or palatability but few validation studies have been reported. Therefore, 156 SNP markers from 45 candidate genes and eight QTL regions were analyzed for association with pork quality and palatability traits from 888 pork loins. Loins were collected at three slaughter facilities and selected to represent a wide range of pork color, pH and marbling. Phenotypic data recorded included objective and subjective measures of color and marbling, purge loss, shear force, and cooking loss. Data were analyzed with SAS PROC MIXED where loin was fit as a random effect. Results indicated some of the markers tested should be useful in industry, while others are not segregating in all populations or linkage disequilibrium between markers and causative genetic variation fluctuates among populations limiting their universal utility. Genes with the largest effects on pork quality were MC4R, IGF2, CAST and PRKAG3., (Published by Elsevier Ltd.)

Proline-rich nuclear receptor coactivator (PNRC)1 is a member of a new family of nuclear receptor coactivators capable of potentiating the transcriptional activity of nuclear receptors. The objective was to investigate the relationship between PNRC1 genotypes of single nucleotide polymorphism (SNP) and reproductive traits in ducks. Brown Tsaiya ducks (N = 305) from two lines, a control line with no selection and the selected line, were used. Polymerase chain reaction-single strand polymorphism and DNA sequencing were done to screen polymorphisms of the PNRC1 gene. A novel SNP (G98T) in 3'-untranslated region of the PNRC1 gene was identified and resulted in two genotypes, GG and GT. The frequencies of genotype GG and allele G were higher in both lines investigated. Regarding egg weight at first egg (EWFE), based on SNP trait association analysis, ducks with the GG genotype had a 4.48 g per egg greater egg weight at first egg when compared with ducks of the GT genotype in the control line (P < 0.05). In addition, this SNP was associated with the hatchability rate (HR) in the selected line; ducks with the GT genotype had a 6.70% higher hatchability rate than those with the GG genotype (P < 0.05). Therefore, we inferred that the PNRC1 gene could be a candidate locus or linked to a major gene that influenced egg weight-related and hatchability traits in Tsaiya ducks. Further investigations on additional duck populations with larger sample sizes are needed to confirm these results., (Copyright © 2012 Elsevier Inc. All rights reserved.)

The Wnt signaling pathway plays a crucial role during embryogenesis in vertebrates. In this study, 124 SNP in 31 Wnt signaling pathway genes were selected to genotype 764 individuals in an F(2) resource population by reciprocally crossing Silkie fowls and Cornish broilers, and 102 SNP were polymorphic. Pairwise linkage disequilibrium among the SNP within each gene was calculated. Haplotypes were reconstructed from the SNP in strong linkage disequilibrium. The associations of SNP and haplotypes with carcass traits were analyzed respectively, and the SNP contributions to phenotypic variance were estimated. The present study showed that 58 SNP in 24 genes and 8 haplotype blocks within 7 genes were significantly (P < 0.05) associated with at least one carcass trait. Fourteen SNP (among the 58 SNP) explained >2% phenotypic variance, 12 of which had significantly (P < 0.01) additive or dominant effects. Furthermore, both rs15865526 (Wnt9A) and rs14066777 (MAPK9) as well as their corresponding haplotype blocks were significantly associated with shank circumference and wing weight, respectively. In addition, 5 muscle-weight-related SNP explained >7% phenotypic variance, which was much higher than those of others. It was found that the Wnt signaling pathway was strongly associated with chicken carcass traits, and 7 genes were particularly important, namely RHOA and CHP for breast muscle weight, Wnt3A for breast muscle weight percentage over carcass weight, RAC1 for thigh weight percentage and thigh muscle weight percentage over carcass weight, Wnt11 for thigh weight percentage over carcass weight, Wnt9A for shank length, and MAPK9 for shank circumference. It is evident that Wnt signaling plays a major role in regulating carcass characteristics important for production traits in chickens.

Bone morphogenetic protein 5 (BMP5) gene was suggested to be a potential positional candidate gene for fatness trait QTLs on SSC7. Here by comparative sequencing of BMP5 gene in Meishan (MS) and Large White (LW) pigs, one SNP *131C>T in 3' un-translated region was detected. Association analysis results in 322 LW×MS F(2) pigs showed that CC pigs had thinner back fatness and heavier ham than TC (P<0.05 or P<0.1), and had a higher fat percentage and a lower lean meat percentage (P<0.1) than TT. Moreover, this C/T transition was predicted to alter BMP5 interaction with let-7c and miR-184 by using RNA22 and RNAhybrid. The negative expression of BMP5 gene with let-7c and miR-184 detected from miRNAs overexpression in swine fibroblast, indicating these 2 miRNAs might participate in the translational inhibition of BMP5 gene. Overall, SNP *131C>T might be a good marker for fatness traits., (Copyright © 2010. Published by Elsevier Ltd.)