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Made available in DSpace on 2022-04-29T08:38:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-01-01 The research article was carried out with the objective of studying the genetic variation on the resilience of buffaloes to negative energy balance—NEB (measured by changes in body weight in early lactation)—as well as investigating genomic regions of interest for this trait. A model of reaction norms was used, considering milk production as the trait to be analyzed and solutions of the contemporary groups to weight changes as environmental gradient. In this methodology, the genetic value of the slope represents the measure of resilience of the animals. After the estimation step, a genome-wide association analysis was performed for the slope of the reaction norms model, to obtain a list of windows and associated genes. The heritability estimates for milk production over the resilience gradient ranged from 0.13 to 0.28, with lower values in the intermediate environmental groups. Regarding the productive resilience of dairy buffalo cows to NEB, the genomic windows with the highest contribution to the genetic variance were detected on chromosomes BBU 1, 2, 3, 4, 9, 12, 19, and 21. A functional analysis of the genes described in the selected windows indicated association with metabolic routes related to growth and immunity of the animals, with an emphasis on the STAT6 gene. The results presented indicate that there is for this trait genetic variation to be used as selection criteria, in addition to genomic regions that can increase the precision of the selection. Instituto Federal de Educação Ciência e Tecnologia Goiano - IFGoiano, Goias Departament of Animal Science Universidade Estadual Paulista “Julio de Mesquita” – UNESP, Jaboticabal Universidade Tecnologica Federal do Paraná – UTFPR, Paraná Animal Genetics and Breeding Unit University of New England Departament of Animal Science Universidade Estadual Paulista “Julio de Mesquita” – UNESP, Jaboticabal

Made available in DSpace on 2021-06-25T11:12:57Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-01 Genomic selection has been widely implemented in many livestock breeding programs, but it remains incipient in buffalo. Therefore, this study aimed to (1) estimate variance components incorporating genomic information in Murrah buffalo; (2) evaluate the performance of genomic prediction for milk-related traits using single- and multitrait random regression models (RRM) and the single-step genomic best linear unbiased prediction approach; and (3) estimate longitudinal SNP effects and candidate genes potentially associated with time-dependent variation in milk, fat, and protein yields, as well as somatic cell score (SCS) in multiple parities. The data used to estimate the genetic parameters consisted of a total of 323,140 test-day records. The average daily heritability estimates were moderate (0.35 ± 0.02 for milk yield, 0.22 ± 0.03 for fat yield, 0.42 ± 0.03 for protein yield, and 0.16 ± 0.03 for SCS). The highest heritability estimates, considering all traits studied, were observed between 20 and 280 d in milk (DIM). The genetic correlation estimates at different DIM among the evaluated traits ranged from −0.10 (156 to 185 DIM for SCS) to 0.61 (36 to 65 DIM for fat yield). In general, direct selection for any of the traits evaluated is expected to result in indirect genetic gains for milk yield, fat yield, and protein yield but also increase SCS at certain lactation stages, which is undesirable. The predicted RRM coefficients were used to derive the genomic estimated breeding values (GEBV) for each time point (from 5 to 305 DIM). In general, the tuning parameters evaluated when constructing the hybrid genomic relationship matrices had a small effect on the GEBV accuracy and a greater effect on the bias estimates. The SNP solutions were back-solved from the GEBV predicted from the Legendre random regression coefficients, which were then used to estimate the longitudinal SNP effects (from 5 to 305 DIM). The daily SNP effect for 3 different lactation stages were performed considering 3 different lactation stages for each trait and parity: from 5 to 70, from 71 to 150, and from 151 to 305 DIM. Important genomic regions related to the analyzed traits and parities that explain more than 0.50% of the total additive genetic variance were selected for further analyses of candidate genes. In general, similar potential candidate genes were found between traits, but our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the traits across parities. These results contribute to a better understanding of the genetic architecture of milk production traits in dairy buffalo and reinforce the relevance of incorporating genomic information to genetically evaluate longitudinal traits in dairy buffalo. Furthermore, the candidate genes identified can be used as target genes in future functional genomics studies. Department of Animal Sciences Purdue University Department of Animal Science College of Agricultural and Veterinary Sciences São Paulo State University (UNESP) Centre for Genetic Improvement of Livestock Department of Animal Biosciences University of Guelph Department of Animal and Avian Science University of Maryland Department of Animal Science College of Agricultural and Veterinary Sciences São Paulo State University (UNESP)

Made available in DSpace on 2021-06-26T08:03:36Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-06-09 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The objectives of this study were to provide the buffalo research community with an updated SNP map for the Axiom Buffalo Genotyping (ABG) array with genomic positions for SNP currently unmapped and to map all cattle QTL from the CattleQTLdb onto the buffalo reference assembly. To update the ABG array map, all SNP probe sequences from the ABG array were re-aligned against the UOA_WB_1 assembly. With the new map, the number of mapped markers increased by approximately 10% and went from 106 778 to 116 708, which reduced the average marker spacing by approximately 2 kb. A comparison of results between signatures of autozygosity study using the ABG and the new map showed that, when the additional markers were used there was an increase in the autozygosity peaks and additional peaks in BBU5 and BBU11 could be identified. After sequence alignment and quality control, 64 650 (UMD3.1) and 76 530 (ARS_UCD1.2) cattle QTL were mapped onto the buffalo genome. The mapping of the bovine QTL database onto the buffalo genome should be useful for genome-wide association studies in buffalo and, given the high homology between the two species, the positions of cattle QTL on the buffalo genome can serve as a stepping stone towards a water buffalo QTL database. Sao Paulo State Univ, Dept Anim Sci, BR-14884900 Jaboticabal, Brazil Michigan State Univ, Genet & Genome Sci Program, E Lansing, MI 48823 USA Univ Guelph, Dept Anim Biosci, Guelph, ON N1G 2W1, Canada Univ Maryland, Dept Anim Sci, College Pk, MD 20740 USA Michigan State Univ, Dept Anim Sci, E Lansing, MI 48823 USA Sao Paulo State Univ, Dept Anim Sci, BR-14884900 Jaboticabal, Brazil FAPESP: 2016/21213-0 FAPESP: 2017/10542-6 FAPESP: 2018/25725-1

Made available in DSpace on 2020-12-11T01:40:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-11-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Growth traits are important for the profitability of buffalo breeding systems, since in general, these animals are raised both for meat and milk. In this study, the single-step genomic BLUP method was employed to prospect the genomic regions' associated with weight at standard ages of 100, 210, 365, and 550 days in a buffalo population, aiming to identify genes with stronger expression for those characteristics. We found 6, 1, 2, and 5 SNPs significantly associated (p value < 10(-5)) with weight at 100, 210, 365, and 550 days of age, respectively, where those SNPs respectively explained 0.164, 0.040, 0.044, and 0.213% of the additive variance of each trait. SNP AX-85099682 (BBU24) was significant for weight at 100, 210, and 365 days, indicating the existence of a possible QTL affecting the initial growth rate of buffaloes. All told, eight genes (CBLB, TRNAG-UCC, GADD45B, LOC112583811, MGAT4C, KCNMA1, SLC5A2, and TGFB1I1) were identified as candidates for the growth traits of buffaloes. However, molecular and gene expression studies are necessary to validate these genes for subsequent use in programs for genetic improvement of the species. Inst Fed Goiano, Campus Rio Verde, Rio Verde, Brazil Univ Maryland, College Pk, MD 20742 USA Univ Estadual Paulista, Campus Jaboticabal, Jaboticabal, SP, Brazil Fundacao Univ Fed Grande Dourados, Dourados, MS, Brazil Univ Estadual Paulista, Campus Jaboticabal, Jaboticabal, SP, Brazil CNPq: 420202/2016-1 FAPESP: 2016/21213-0

Made available in DSpace on 2021-06-25T11:56:34Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-04-16 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) The study's objective was to compare the genomic prediction ability methods for the traits milk yield, milk composition and somatic cell count of Saanen Brazilian goats. Nine hundred forty goats, genotyped with an Axiom_OviCap (Caprine) panel, Affimetrix customized array with 62,557 single nucleotide polymorphisms (SNPs), were used for the genomic selection analyses. The genomic methods studied to estimate the effects of SNPs and direct genomic values (DGV) were as follows: (a) genomic BLUP (GBLUP), (b) Bayes C pi and (c) Bayesian Lasso (BLASSO). Estimated breeding values (EBV) and deregressed estimated breeding values (dEBV) were used as response variables for the genomic predictions. The prediction ability was assessed by Pearson's correlation between DGV and response variables (EBV and dEBV). Regression coefficients of the response variables on the DGV were obtained to verify if the genomic predictions were biased. In addition, the mean square error of prediction (MSE) was used as a measure of verification of model fit to the data. The means of prediction accuracy, when EBV was used as a response variable, were 0.68, 0.68 and 0.67 for GBLUP, Bayes C pi and BLASSO, respectively. With dEBV, the mean prediction accuracy was 0.50 for all models. The averages of the EBV regression coefficients on DGV were 1.08 for all models (GBLUP, Bayes C pi and BLASSO), higher than those obtained for the regression coefficient of dEBV on DGV, which presented values of 1.05, 1.05 and 1.08 for GBLUP, Bayes C pi and BLASSO, respectively. None of the methods stood out in terms of prediction ability; however, the GBLUP method was the most appropriate for estimating the DGV, in a slightly more reliable and less biased way, besides presenting the lowest computational cost. In the context of the present study, EBV was the preferred response variables considering the genomic prediction accuracy despite dEBV also presented lower bias. Univ Fed Ceara, Dept Anim Sci, Fortaleza, Ceara, Brazil Sao Paulo State Univ Julio de Mesquita Filho, Fac Agr & Vet Sci Jaboticabal, Anim Sci Dept 1, Jaboticabal, Brazil Brazilian Agr Res Corp EMBRAPA, Embrapa Caprinos & Ovinos, Estr Sobral Groairas, Sobral, Brazil Natl Council Sci & Technol Dev CNPq, Lago Sul, Brazil Sao Paulo State Univ Julio de Mesquita Filho, Fac Agr & Vet Sci Jaboticabal, Anim Sci Dept 1, Jaboticabal, Brazil

Made available in DSpace on 2021-06-25T11:07:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-11-05 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Considering the importance of the diseases affecting the productive performance of animals in the dairy industry worldwide, it is necessary to implement tools that help to control and limit the occurrence of such diseases. As the increased somatic cell counts (SCC) are a direct expression of the inflammatory process, they are candidates to become the usual parameter for assessing udder health regarding milk quality and for monitoring mastitis incidences. Toll-Like Receptors are membrane proteins that play a key role in immunity, recognizing pathogens and, subsequently, activating immune responses. The present study was conducted to identify single nucleotide polymorphisms in the TLR4 gene of buffaloes and to analyze its associations with somatic cell counts. DNA samples of 120 Murrah buffaloes were used. The whole coding region of the TLR4 gene was amplified by polymerase chain reaction reactions and sequenced for polymorphism scanning. A total of 13 polymorphisms were identified for the sequenced regions of the TLR4, most of which are in the coding region. The association with the somatic cell score was highly significant (p < 0.001) for all identified polymorphisms of TLR4 gene (g.54621T>A, g.54429G>T, g.54407T>A, g.46616C>A, g.46613T>G, g.46612A>G, g.46611C>A, g.46609T>G, g.46541C>G, g.46526C>A, g.46516T>C, g.46376C>T, g.46372T>C). Therefore, it is suggested that the markers of the TLR4 gene can be used as molecular markers for mastitis resistance in buffaloes, due to their association with somatic cell counts. Department of Animal Science School of Agricultural and Veterinarian Science São Paulo State University (UNESP) Department of Animal Biosciences Centre for Genetic Improvement of Livestock University of Guelph Facultad de Ciências Agrárias Universidad Francisco de Paula Santander Department of Animal and Avian Sciences University of Maryland Escola de Medicina Veterinária e Zootecnia Universidade Federal da Bahia Department of Animal Science School of Agricultural and Veterinarian Science São Paulo State University (UNESP)

Made available in DSpace on 2021-06-25T16:33:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-10-05 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) In Brazil, water buffaloes have been used to produce milk for mozzarella cheese production. Consequently, the main selection criterion applied for the buffalo genetic improvement is the estimated mozzarella yield as a function of milk, fat and protein production. However, given the importance of reproductive traits in production systems, this study aimed to use techniques for identifying genomic regions that affect the age at first calving (AFC) and first calving interval (FCI) in buffalo cows and to select candidate genes for the identification of QTL and gene expression studies. The single-step GBLUP method was used for the identification of genomic regions. Windows of 1 Mb containing single-nucleotide polymorphisms were constructed and the 10 windows that explained the greatest proportion of genetic variance were considered candidate regions for each trait. Genes present into the selected windows were identified using the UOA_WB_1 assembly as the reference, and their ontology was defined with the Panther tool. Candidate regions for both traits were identified on BBU 3, 12, 21 and 22; for AFC, candidates were detected on BBU 6, 7, 8, 9 and 15 and for first calving interval on BBU 4, 14 and 19. This study identified regions with great contribution to the additive genetic variance of age at first calving and first calving interval in the population of buffalo cows studied. The ROCK2, PMVK, ADCY2, MAP2K6, BMP10 and GFPT1 genes are main candidates for reproductive traits in water dairy buffaloes, and these results may have future applications in animal breeding programs or in gene expression studies of the species. Inst Fed Goiano, Campus Rio Verde,Km1,Zip Code 66, BR-75901970 Rio Verde, Go, Brazil Univ Estadual Paulista, Jaboticabal, Brazil Univ Maryland, College Pk, MD 20742 USA Univ Fed Tecnol Parana UFTPR, Dois Vizinhos, Brazil Univ Estadual Paulista, Jaboticabal, Brazil CNPq: 420202/2016-1 FAPESP: 2016/21213-0

Made available in DSpace on 2021-06-25T11:08:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-02-01 Characterization of autozygosity is relevant to monitor genetic diversity and manage inbreeding levels in breeding programs. Identification of autozygosity hotspots can unravel genomic regions targeted by selection for economically important traits and can help identify candidate genes for selection. In this study, we estimated the inbreeding levels of a Brazilian population of Murrah buffalo undergoing selection for milk production traits, particularly milk yield. We also studied the distribution of runs of homozygosity (ROH) islands and identified putative genes and quantitative trait loci (QTL) under selection. We genotyped 422 Murrah buffalo for 51,611 SNP; 350 of these had ROH longer than 10 Mb, indicating the occurrence of inbreeding in the last 5 generations. The mean length of the ROH per animal was 4.28 ± 1.85 Mb. Inbreeding coefficients were calculated from the genomic relationship matrix, the pedigree, and the ROH, with estimates varying between 0.242 and 0.035. Inbreeding estimates from the pedigree had a low correlation with the genomic estimates, and estimates from the genomic relationship matrix were much higher than those from the pedigree or the ROH. Signatures of selection were identified in 6 genomic regions, located on chromosomes 1, 2, 3, 5, 16, and 18, encompassing a total of 190 genes and 174 QTL. Many of the genes (e.g., APRT and ACSF3) and QTL identified are related to milk production traits, such as milk yield, milk fat yield and percentage, and milk protein yield and percentage. Other genes are associated with reproduction and immune response traits as well as morphological aspects of the buffalo species. Inbreeding levels in this population are still low but are increasing due to selection and should be managed to avoid future losses due to inbreeding depression. The proximity of genes linked to milk production traits with genes associated with reproduction and immune system traits suggests the need to include these latter genes in the breeding program to avoid negatively affecting them due to selection for production traits. Department of Animal Science São Paulo State University (UNESP) Department of Animal Science University of Maryland College of Agricultural Sciences Federal University of Grande Dourados (UFGD) Goiano Federal Institute Campus Rio Verde Department of Animal Science Michigan State University Department of Animal Science São Paulo State University (UNESP)

Made available in DSpace on 2019-10-04T23:10:43Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-10-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) This study compared the expression profile of the candidate genes, CSF3 and LPO, by investigating the immune response mechanisms involved in the phenotype of resistance and susceptibility to mastitis of healthy and infected buffaloes. The Granulocyte Colony Stimulating Factor 3 (CSF3) and Lactoperoxidase (LPO) genes expression profiles were determined in 24 milk samples from buffaloes with (N = 12) and without (N = 12) mastitis, using the quantitative real-time PCR (qRT-PCR) technique. CSF3 and LPO expressions were 5.14 (P = 0.001) and 2.41 (P = 0.097) times higher in animals with mastitis compared to healthy animals, respectively, evidencing a trend toward different expressions of this gene in the studied groups. Our finding suggests that LPO and CSF3 genes are an important defense mechanism against mastitis in dairy buffaloes, and may be putative genes for selecting healthier animals in buffalo breeding programs. Sao Paulo State Univ, Fac Agr & Vet Sci, Dept Anim Sci, Via Acesso Prof Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, SP, Brazil Sao Paulo State Univ, Fac Agr & Vet Sci, Dept Anim Sci, Via Acesso Prof Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, SP, Brazil FAPESP: 2014/25309-7

Made available in DSpace on 2018-12-11T16:51:50Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-04-01 The aim of this work was to identify genomic regions and genes in association with the navel length, coat and scrotal circumference traits of Canchim breed of cattle, using genome-wide association studies (GWAS). Imputed data from single nucleotide polymorphism type markers were used, with accuracy greater than 95%. The analyses of genome-wide association were conducted by the Bayes B method, implemented in the GenSel program. Non-overlapping windows that explained at least 0.19% of the additive genetic variance were considered as significant, this value corresponds five times the expected for 1 Mb size windows. GWAS indicated 31 regions in association with navel length, one coat region, and four SC-related regions. In these regions, 4 quantitative loci (QTLs) related to navel length and 5 with SC were identified, as for the coat, the QTLs detected did not present previously described relation with this trait. Among the candidate genes in the associated regions, 7 genes were cited in previous studies, with biological functions related to navel length, one for coat and three for SC. The candidate genes TMEM176A and TMEM176AB, which are orthologous in humans, are in association with navel's trait and compose the Androgen Induced 1 cluster. The identification of genes and QTLs, with a function related to the studied traits, previously described in the literature, reinforces the evidence that the found regions are associated with navel length, coat and SC. This information may contribute to the understanding of the genetic architecture involved with of these traits, to guiding genetic validation studies, gene introgression and contribute to include information concerning molecular markers in genetic evaluation of animal improvement programs. Federal University of Dourados (UFGD) Embrapa Beef Cattle Federal University of Mato Grosso do Sul (UFMS) Embrapa Southeast Livestock Brazilian Association of Canchim Cattle Breeders (ABCCAN) São Paulo State University (UNESP) São Paulo State University (UNESP)

Nuclear abnormalities (micronuclei and meta-nuclear changes) have been used as biomarkers to identify cell damages. As children are more vulnerable to the adverse effects of pollution when compared to adults, assessing genetic damage caused by environmental influences is of great interest. As such, the objective was to determine metanuclear (karyolysis, pycnosis, karyorrhexis, binucleated cells, chromosome bridges and micronuclei) in cells from the oral mucosa of children associated with the school environment, gender, exposure to cigarette smoke and vehicular traffic. Analyses of nuclear abnormalities were performed in exfoliated buccal cells of children from two public schools located in Dourados - MS. The data were analyzed through Kruskal-Wallis test considering a significance level of 5% (p .05). The results showed that children exposed to cigarette smoke presented higher levels of nuclear abnormalities than children who were not usually exposed to this type of mutagenic and genotoxic agent, suggesting that such contaminants are related to clastogenic and aneugenic effects on DNA. Moreover, female children had higher amounts of nuclear abnormalities when compared to male children. With regards to the school environment, the study results indicated statistical differences in of term chromosomal abnormalities for schools A and B. Thus, it was possible to determine that children exposed to cigarette smoke are susceptible to further genetic damage than unexposed children, and female children may be more susceptible to genotoxic and mutagenic agents. This study contributes to the current knowledge on the mutagenic characteristics of human cells, supporting the adoption of preventive Public Health measures.

Made available in DSpace on 2018-11-29T13:28:33Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-05-02 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Background: This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results: Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (F-ST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions: The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight. Sao Paulo State Univ, Fac Agr & Vet Sci, Dept Anim Sci, Jaboticabal, SP, Brazil Natl Counsel Technol & Sci Dev CNPq, Brasilia, DF, Brazil Univ Goettingen, Dept Anim Sci, Anim Breeding & Genet Grp, Gottingen, Germany Bavarian State Res Ctr Agr, Inst Anim Breeding, Grub, Germany APTA Beef Cattle Ctr, Inst Anim Sci, Sertaozinho, SP, Brazil Sao Paulo State Univ, Fac Agr & Vet Sci, Dept Anim Sci, Jaboticabal, SP, Brazil FAPESP: 2009/16118-5 : 2012/24600-4 : 2014/13445-3

The aim of this study was to evaluate a genome wide association study (GWAS) approach to identify single nucleotide polymorphisms (SNPs) associated with fertility traits (early puberty) in Nellore cattle (Bos indicus). Fifty-five Nellore cows were selected from a herd monitored for early puberty onset (positive pregnancy at 18 months of age). Extremes of this phenotype were selected; 30 and 25 individuals were pregnant and non-pregnant, respectively, at that age. DNA samples were genotyped using a high-density SNP chip (>777.000 SNP). GWAS using a case-control strategy highlighted a number of significant markers based on their proximity with the Bonferroni correction line. Results indicated that chromosomes 5, 6, 9, 10, and 22 were associated with the traits of interest. The most significant SNPs on these chromosomes were rs133039577, rs110013280, rs134702839, rs109551605, and rs41639155. Candidate genes, as well as quantitative trait loci (QTL) previously reported in the Ensembl and Cattle QTLdb databases, were further investigated. Analysis of the regions close to the SNP on chromosomes 9 and 10 revealed that four QTL had been previously classified under the reproduction category. In conclusion, we have identified SNPs in close proximity to genes associated with reproductive traits. Moreover, U6 spliceosomal RNA was present on three different chromosomes, which is possibly associated with age at first calving, suggesting that it might be a strong candidate for future studies.

Made available in DSpace on 2018-12-11T17:22:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-08-01 Zebu cattle (Bos taurus indicus) are highly adapted to tropical regions. However, females reach puberty after taurine heifers, which affects the economic efficiency of beef cattle breeding in the tropical regions. The aims of this study were to establish associations between the haplotype alleles of the bovine genome and age at first calving (AFC) in the Nelore cattle, and to identify the genes and quantitative trait loci (QTL) related to this phenotype. A total of 2,273 Nelore cattle (995 males and 1,278 females) genotyped using the Illumina BovineHD BeadChip were used in the current study. The association analysis included females with valid first calving records as well as open heifers. Linkage disequilibrium (LD) analysis among the markers was performed using blocks of 5, 10, and 15 markers, which were determined by sliding windows shifting one marker at a time. Then, the haplotype block size to be used in the association study was chosen based on the highest r2 average among the SNPs in the block. The five HapAlleles most strongly associated with the trait (top five) were considered as significant associations. The results of the analysis revealed four genomic regions related to AFC, which overlapped with 20 QTL of the reproductive traits reported previously. Furthermore, there were 19 genes related to reproduction in those regions. In conclusion, the use of haplotypes allowed the detection of chromosomal regions associated with AFC in Nelore cattle, and provided the basis for elucidating the mechanisms underlying this trait. Faculdade de Ciências Biológicas e Ambientais Universidade Federal da Grande Dourados UFGD Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP Departamento de Medicina Veterinária Preventiva e Reprodução Animal Faculdade de Ciências Agrárias e Veterinárias UNESP Departamento de Apoio Produção e Saúde Animal Faculdade de Medicina Veterinária de Araçatuba UNESP GenSys Consultores Associados S/S Ltda International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP Departamento de Medicina Veterinária Preventiva e Reprodução Animal Faculdade de Ciências Agrárias e Veterinárias UNESP Departamento de Apoio Produção e Saúde Animal Faculdade de Medicina Veterinária de Araçatuba UNESP