RESUMO
Genome-Wide Association Studies (GWAS) are used for identification of quantitate trait loci (QTL) and genes associated with several traits. We aimed to identify genomic regions, genes, and biological processes associated with number of total and viable oocytes, and number of embryos in Gir dairy cattle. A dataset with 17,526 follicular aspirations, including the following traits: number of viable oocytes (VO), number of total oocytes (TO), and number of embryos (EMBR) from 1641 Gir donors was provided by five different stock farms. A genotype file with 2093 animals and 395,524 SNP markers was used to perform a single-step GWAS analysis for each trait. The top 10 windows with the highest percentage of additive genetic variance explained by 100 adjacent SNPs were selected. The genomic regions identified in our work were overlapped with QTLs from QTL database on chromosomes 1, 2, 5, 6, 7, 8, 9, 13, 17, 18, 20, 21, 22, 24, and 29. These QTLs were classified as External, Health, Meat and carcass, Production or Reproduction traits, and about 38% were related to Reproduction. In total, 117 genes were identified, of which 111 were protein-coding genes. Exclusively associations were observed for 42 genes with EMBR, and 1 with TO. Also, 42 genes were in common between VO and TO, 28 between VO and EMBR, and four genes were in common among all traits. In conclusion, great part of the identified genes plays a functional role in initial embryo development or general cell functions. The protein-coding genes ARNT, EGR1, HIF1A, AHR, and PAX2 are good markers for the production of oocytes and embryos in Gir cattle.
Assuntos
Estudo de Associação Genômica Ampla , Oócitos , Animais , Bovinos/genética , Genótipo , Fenótipo , Locos de Características Quantitativas/genética , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
Reactive dairy cows are more susceptible to stress, and this may result in negative effects on milk yield and quality. The aims of this study were to investigate the relationships between temperament traits and concentration of milk cortisol and oxytocin, milk yield, milkability, and milk quality in Holstein-Gyr cows. Temperament traits were assessed in 76 Holstein-Gyr cows in the milking parlor (by scoring milking reactivity and recording the numbers of steps and kicks during pre-milking udder preparation and when fitting the milking cluster) and during handling in the corral (by measuring the time to enter in the squeeze chute, ET and flight speed, FS). Milk samples were collected for milk quality (% fat, % protein, % lactose, and somatic cell count, SCC), and milk cortisol and oxytocin. Milk yield, milking time, and average flow were also measured. The calmer cows during milking management (class 'low') produced milk with higher protein (p = 0.028) content and tendencies for lower fat (p = 0.056) and higher lactose (p = 0.055) contents. Regarding the hormones, the most reactive cows (class 'high') in the milking and handling corral produced milk with higher concentrations of cortisol (p<0.001) and oxytocin (p = 0.023). In addition, the temperament of the animals affected some of the productive measures evaluated. Cows with reactive temperament had lower milk flow and longer milking time than the intermediate ones and had higher fat and a tendency for lower protein percentage in milk compared to cows with intermediate temperaments. Calm and intermediate cows in the handling corral produced more milk and presented better milkability parameters, such as a shorter milking time and greater average milk flow. Our results suggest that the cows' behavioral reactivity can be related to the intensity of their response to stress during handling.
Assuntos
Leite , Ocitocina , Feminino , Bovinos , Animais , Leite/metabolismo , Ocitocina/metabolismo , Lactação/fisiologia , Hidrocortisona/metabolismo , Temperamento , Lactose/metabolismo , Indústria de Laticínios/métodos , Glândulas Mamárias Animais/fisiologiaRESUMO
Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (FROH) and pedigree-based inbreeding (Fped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH1-2Mb: 58.17%), representing ancient inbreeding, ROH2-4Mb (22.74%), ROH4-8Mb (11.34%), ROH8-16Mb (5.51%), and ROH>16Mb (2.24%). Combining our results, we conclude that the increase in general FROH and Fped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with FROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.
Assuntos
Endogamia , Polimorfismo de Nucleotídeo Único , Bovinos/genética , Animais , Homozigoto , Genótipo , OócitosRESUMO
Background: The sequencing and publication of the cattle genome and the identification of single nucleotide polymorphism (SNP) molecular markers have provided new tools for animal genetic evaluation and genomic-enhanced selection. These new tools aim to increase the accuracy and scope of selection while decreasing generation interval. The objective of this study was to evaluate the enhancement of accuracy caused by the use of genomic information (Clarifide® - Pfizer) on genetic evaluation of Brazilian Nellore cattle. Review: The application of genome-wide association studies (GWAS) is recognized as one of the most practical approaches to modern genetic improvement. Genomic selection is perhaps most suited to the improvement of traits with low heritability in zebu cattle. The primary interest in livestock genomics has been to estimate the effects of all the markers on the chip, conduct cross-validation to determine accuracy, and apply the resulting information in GWAS either alone [9] or in combination with bull test and pedigree-based genetic evaluation data. The cost of SNP50K genotyping however limits the commercial application of GWAS based on all the SNPs on the chip. However, reasonable predictability and accuracy can be achieved in GWAS by using an assay that contains an optimally selected predictive subset of markers, as opposed to all the SNPs on the chip. The best way to integrate genomic information into genetic improvement programs is to have it included in traditional genetic evaluations. This approach combines traditional expected progeny differences based on phenotype and pedigree with the genomic breeding values based on the markers. Including the different sources of information into a multiple trait genetic evaluation model, for within breed dairy cattle selection, is working with excellent results. However, given the wide genetic diversity of zebu breeds, the high-density panel used for genomic selection in dairy cattle (Ilumina Bovine SNP50 array) appears insufficient for across-breed genomic predictions and selection in beef cattle. Today there is only one breed-specific targeted SNP panel and genomic predictions developed using animals across the entire population of the Nellore breed (www.pfizersaudeanimal.com), which enables genomically - enhanced selection. Genomic profiles are a way to enhance our current selection tools to achieve more accurate predictions for younger animals. Material and Methods: We analyzed the age at first calving (AFC), accumulated productivity (ACP), stayability (STAY) and heifer pregnancy at 30 months (HP30) in Nellore cattle fitting two different animal models; 1) a traditional single trait model, and 2) a two-trait model where the genomic breeding value or molecular value prediction (MVP) was included as a correlated trait. All mixed model analyses were performed using the statistical software ASREML 3.0. Results: Genetic correlation estimates between AFC, ACP, STAY, HP30 and respective MVPs ranged from 0.29 to 0.46. Results also showed an increase of 56%, 36%, 62% and 19% in estimated accuracy of AFC, ACP, STAY and HP30 when MVP information was included in the animal model. Conclusion: Depending upon the trait, integration of MVP information into genetic evaluation resulted in increased accuracy of 19% to 62% as compared to accuracy from traditional genetic evaluation. GE-EPD will be an effective tool to enable faster genetic improvement through more dependable selection of young animals.