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Bovine spongiform encephalopathy (BSE) is a transmissible progressive neurodegenerative disease characterized by the accumulation of a pathological isoform (PrpSC) of the cellular prion protein (PrpC) in the brain of cattle. Two insertion/deletion polymorphisms in the PRNP gene (23bp in the promoter and 12bp in intron 1) have been associated with resistance or susceptibility to the disease. The aim of this study was to analyze the distribution of these polymorphisms in 214 healthy bovines belonging to four different breed groups (Aberdeen Angus, Aberdeen Angus x Hereford, Holstein Friesian and Uruguayan Creole cattle). DNA samples were amplified by end-point PCR. A high frequency of the alleles and haplotype associated with susceptibility to BSE (del12 and del23, and del12-del23, respectively) were found in the Aberdeen Angus, Aberdeen Angus x Hereford and Holstein Friesian animals. At the same time, the Uruguayan Creole cattle presented a higher frequency of the alleles and haplotype associated with resistance to BSE (ins12 and ins23, and ins12-ins23, respectively). These data could indicate a greater genetic resistance of the Uruguayan Creole cattle to BSE compared to other analyzed breeds, reinforcing its value as a zoogenetic resource.

A encefalopatia espongiforme bovina (EEB) é uma doença neurodegenerativa progressiva transmissível dos bovinos, caracterizada pelo acúmulo no cérebro de uma isoforma patológica (PrpSC) da proteína priônica celular (PrpC). Dois polimorfismos de inserção/deleção no gene PRNP (23bp no promotor e 12bp no íntron 1) foram associados à resistência ou suscetibilidade à doença. O objetivo deste trabalho foi analisar a distribuição desses polimorfismos em 214 bovinos sadios, pertencentes a quatro diferentes grupos raciais (Aberdeen Angus, Aberdeen Angus x Hereford, Holstein Friesian e Crioulo Uruguaio). As amostras de DNA foram amplificadas por PCR de tempo final. Uma alta frequência dos alelos e haplótipos associados à suscetibilidade à BSE (del12 e del23 e del12-del23, respectivamente) foram encontrados nos animais Aberdeen Angus, Aberdeen Angus x Hereford e Holstein Friesian, enquanto o gado Crioulo Uruguaio apresentou maior frequência dos alelos e haplótipos associados à resistência à BSE (ins12 e ins23 e ins12-ins23, respectivamente). Esses dados podem indicar uma maior resistência genética do gado Crioulo Uruguaio à BSE em comparação com as outras raças analisadas, reforçando seu valor como recurso zoogenético.

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Several ocular pathologies in cattle, such as ocular squamous cell carcinoma and infectious keratoconjunctivitis, have been associated with low pigmentation of the eyelids. The main objective of this study was to analyze the transcriptome of eyelid skin in Hereford cattle using strand-specific RNA sequencing technology to characterize and identify long noncoding RNAs (lncRNAs). We compared the expression of lncRNAs between pigmented and unpigmented eyelids and analyzed the interaction of lncRNAs and putative target genes to reveal the genetic basis underlying eyelid pigmentation in cattle. We predicted 4,937 putative lncRNAs mapped to the bovine reference genome, enriching the catalog of lncRNAs in Bos taurus. We found 27 differentially expressed lncRNAs between pigmented and unpigmented eyelids, suggesting their involvement in eyelid pigmentation. In addition, we revealed potential links between some significant differentially expressed lncRNAs and target mRNAs involved in the immune response and pigmentation. Overall, this study expands the catalog of lncRNAs in cattle and contributes to a better understanding of the biology of eyelid pigmentation.

RESUMO

Ocular squamous cell carcinoma and infectious keratoconjunctivitis are common ocular pathologies in Hereford cattle with considerable economic impact. Both pathologies have been associated with low eyelid pigmentation, and thus, genetic selection for higher eyelid pigmentation could reduce their incidence. The objective of the present study was to reveal the genetic basis of eyelid pigmentation in Hereford cattle. The analysis included a single-step genome-wide association study (ssGWAS) and a subsequent gene-set analysis in order to identify individual genes, genetic mechanisms, and biological pathways implicated in this trait. Data consisted of eyelid pigmentation records in 1,165 Hereford bulls and steers, visually assessed in five categories between 0% and 100%. Genotypic data for 774,660 single-nucleotide polymorphism markers were available for 886 animals with pigmentation records. Pedigree information of three generations of ancestors of animals with phenotype was considered in this study, with a total of 4,929 animals. Our analyses revealed that eyelid pigmentation is a moderately heritable trait, with heritability estimates around 0.41. The ssGWAS identified at least eight regions, located on BTA1, BTA3, BTA5, BTA14, BTA16, BTA18, BTA19, and BTA24, associated with eyelid pigmentation. These regions harbor genes that are directly implicated in melanocyte biology and skin pigmentation, such as ADCY8, PLD1, KITLG, and PRKCA. The gene-set analysis revealed several functional terms closely related to melanogenesis, such as positive regulation of melanocyte differentiation and regulation of ERK1 and ERK2 cascade. Overall, our findings provide evidence that eyelid pigmentation is a heritable trait influenced by many loci. Indeed, the ssGWAS detected several candidate genes that are directly implicated in melanocyte biology, including melanogenesis. This study contributes to a better understanding of the genetic and biological basis of eyelid pigmentation and presents novel information that could aid to design breeding strategies for reducing the incidence of ocular pathologies in cattle. Additional research on the genetic link between eyelid pigmentation and ocular pathologies is needed.

Low eyelid pigmentation is considered as a predisposing factor associated with common ocular pathologies in cattle, such as ocular squamous cell carcinoma and infectious keratoconjunctivitis, with considerable economic impact. The aim of our study was to investigate the genetic basis of eyelid pigmentation in Hereford cattle. The analysis included estimation of genetic parameters, a genome-wide association study, and a subsequent gene-set analysis to identify individual genes, genetic mechanisms, and biological pathways implicated in eyelid pigmentation. Our results indicate that eyelid pigmentation is a complex trait, with a moderate heritability around 0.41, and affected by multiple loci, including genes related to melanocyte biology, melanogenesis, skin pigmentation, and development of melanoma. Evidence that biological processes such as melanocyte development and melanocyte differentiation explain part of the observed variation in eyelid pigmentation were also found. Overall, this study provides a better understanding of the genetics underlying eyelid pigmentation in Hereford. Our findings could contribute to point out breeding strategies for reducing the incidence of ocular pathologies in cattle.

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Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed phenotypic differences in histochemical and metabolic parameters related to meat quality among different muscles. In this study, we sequenced by RNA-Seq the whole transcriptome of nine lamb muscles: Semimembranosus (SM), Semitendinosus (ST), Cranial gluteobiceps, Gluteus medius (GM), Rectus femoris, Supraspinatus (SS), Longissimus lumborum (LL), Adductor and Psoas major. Significant gene expression differences were detected between almost all pairwise comparisons, being more pronounced between SS and ST, SM and LL, and ST and GM. These differences can be explained in terms of ATPase and glycolytic activities, muscle fiber typing and oxidative score, clustering muscles as fast glycolytic, intermediate or slow oxidative. ST showed up-regulation of gene pathways related to carbohydrate metabolism, energy generation and protein turnover as expected from a fast white muscle. SS showed myosin isoforms typical of slow muscles and high expression of genes related to calcium homeostasis and vascularization. SM, LL and GM showed in general intermediate gene expression patterns. Several novel transcripts were detected, mostly related to muscle contraction and structure, oxidative metabolism, lipid metabolism and protein phosphorylation. Expression profiles were consistent with previous histochemical and metabolic characterization of these muscles. Up-regulation of ion transport genes may account for significant differences in water holding capacity. High expression of genes related to cell adhesion, cytoskeleton organization, extracellular matrix components and protein phosphorylation may be related to meat yellowness and lower tenderness scores. Differential expression of genes related to glycolytic activity and lactic acid generation among fast, intermediate and slow muscles may explain the detected final meat pH differences. These results reveal new candidate genes associated with lamb meat quality, and give a deeper insight into the genetic architecture of these complex traits.

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The ancestors of Uruguayan Creole cattle were introduced by the Spanish conquerors in the XVII century, following which the population grew extensively and became semi-feral before the introduction of selected breeds. Today the Uruguayan Creole cattle genetic reserve consists of 575 animals. We used the tetra primer amplification refractory mutation system polymerase chain reaction (ARMS-PCR) to analyze the kappa-casein, beta-casein, alphaS1-casein and alpha-lactoalbumin gene polymorphisms and restriction fragment length polymorphism PCR (RFLP-PCR) for the beta-lactoglobulin and the acylCoA:diacyl glycerol acyltransferase 1 (DGAT1) genes. The kappa-casein and beta-lactoglobulin genes presented very similar A and B allele frequencies, while the alphas1-casein and alpha-lactoalbumin gene B alleles showed much higher frequencies than the corresponding A alleles. The beta-casein B allele was not found in the population sampled. There was a very high frequency of the DGAT1 gene A allele which is associated with low milk fat content and high milk yield. All loci were in Hardy-Weinberg equilibrium and the level of heterozygosity agreed with the high genetic diversity observed in a previous analysis of this population. Preservation of the allelic richness observed in the Uruguayan Creole cattle should be considered for future dairy management and livestock genetic improvement. The results also emphasize the value of the tetra primers ARMS-PCR technique as a rapid, easy and economical way of genotyping cattle breeds for milk gene single nucleotide polymorphisms.

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The Uruguayan Creole cattle genetic reserve consists of a herd of about 600 animals (bulls, cows and calves) located in an indigenous habitat of 650 hectares. In a previous study, a random sample from this herd showed high heterozygosity and a Hardy-Weinberg equilibrium for markers of major genes related to milk production. To study its genetic diversity we genotyped a sample of bulls (N = 19 out of 23 for the whole herd) using the PCR reaction with a set of 17 microsatellite markers. Between two and seven different alleles were identified per microsatellite in a total of 73 alleles. The expected mean heterozygosity (He) per locus was between 0.465 and 0.801, except for microsatellite HEL13 which gave a He value of 0.288. The expected mean heterozygosity was 0.623 and the polymorphic information content (PIC) was between 0.266 for HEL13 and 0.794 for CSSM66. The genetic diversity found in polymorphic markers in the breeding bulls of this Creole cattle population supports previous genetic analyses using major production genes and indicate that further studies should be carried out on this population to provide data of interest to cattle production.

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