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The age at first calving has a great economic impact on the beef cattle system and calving at 24 months is an objective of selection for a more efficient herd. However, an age at first calving around 36 months has been observed for Nellore cattle in Brazil. Thus, a genome-wide association study (GWAS) was carried out with 8376 records of age at first calving and 3239 animals genotyped with the GGP-Indicus 35K, which has been developed specifically for Bos taurus indicus. The weighted single-step genomic best linear unbiased prediction method was used, with adjacent SNPs (single nucleotide polymorphisms) in genomic windows of 1.0 Mb. After quality control, 3239 (2161 males and 1078 females) animals genotyped for 30,519 SNPs were used in GWAS analysis. The average and standard deviation of age at first calving were 1041.7 and 140.6 days, respectively. The heritability estimate was 0.10 ± 0.02. The GWAS analysis found seven genomic regions in BTA1, 2, 5, 12, 18, 21, and 24, which explained a total of 11.24% of the additive genetic variance of age at first calving. In these regions were found 62 protein coding genes, and the genes HSD17B2, SERPINA14, SERPINA1, SERPINA5, STAT1, NFATC1, ATP9B, CTDP1, THPO, ECE2, PSMD2, EIF4G1, EIF2B2, DVL3, POLR2H, TMTC2, and GPC6 are possible candidates for age at first birth due their function. Moreover, two molecular functions (“serine-type endopeptidase inhibitor activity” and “negative regulation of endopeptidase activity”) were significant, which depend on several serpin genes. The use of a SNP chip developed especially for Bos taurus indicus allowed to find genomic regions for age at first calving, which are close to QTLs previously reported for other reproduction-related traits. Future studies can reveal the causal variants and their effects on reproductive precocity of Nellore cows.

The domestication of animals has rendered horns less necessary for survival. Moreover, the use of polled and disbudded animals is interesting in order to avoid injuries of animals and handlers, among other advantages. We therefore conducted a comparative economic analysis of different disbudding techniques versus selection for polledness in Nelore cattle, the main beef breed of tropical systems in Brazil. Three scenarios for obtaining animals without horns were simulated and their costs were evaluated: disbudding with hot iron, disbudding with caustic paste, and phenotypic selection for polled animals. Price quotations of the materials were obtained in different states of the country and averaged. An initial frequency of horned animals of 92.16% was obtained based on the records of the Brazilian Association of Zebu Breeders. Selection was found to be the least-cost method. This result differs from intensive production systems of dairy cattle in which disbudding continues to be the least-cost technique. The main explanation is the lack of difference in the price of Nelore semen from polled and horned bulls. Phenotypic selection for polled animals is the least-cost methos and it is in accordance with welfare practices. Care should be taken regarding the intensive use of few polled breeding animals in order to avoid inbreeding depression in other traits.

The measurement of morphometric traits in horses is important for determining breed qualification and is one of the main selection criteria in the species. The development of an index (HPC) that consists of principal components weighted by additive genetic values allows to explore the most relevant relationships using a reduced number of variables that explain the greatest amount of variation in the data. Genome-wide association studies (GWAS) using HPC are a relatively new approach that permits to identify regions related to a set of traits. The aim of this study was to perform GWAS using HPC for 15 linear measurements as the explanatory variable in order to identify associated genomic regions and to elucidate the biological mechanisms linked to this index in Campolina horses. For GWAS, weighted single-step GBLUP was applied to HPC. The eight genomic windows that explained the highest proportion of additive genetic variance were identified. The sum of the additive variance explained by the eight windows was 95.89%. Genes involved in bone and cartilage development were identified (SPRY2, COL9A2, MIR30C, HEYL, BMP8B, LTBP1, FAM98A, and CRIM1). They represent potential positional candidates for the HPC of the linear measurements evaluated. The HPC is an efficient alternative to reduce the 15 usually measured traits in Campolina horses. Moreover, candidate genes inserted in region that explained high additive variance of the HPC were identified and might be fine-mapped for searching putative mutation/markers.

Made available in DSpace on 2022-04-29T08:29:41Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Scrotal circumference (SC) is a commonly used trait related to sexual precocity in bulls. Genome-wide association studies have uncovered a lot of genes related to this trait, however, only those present on autosomes. The inclusion of the second biggest chromosome (BTAX) can improve the knowledge of the genetic architecture of this trait. In this study, we performed a weighted, single-step, genome-wide association study using a 777 k BovineHD BeadChip (IllumHD) to analyze the association between SNPs and SC in Brazilian Nelore cattle. Phenotypes from 79,300 males and 3263 genotypes (2017 from females and 1246 from males)—(39,367 SNPs markers located at ChrX) were used. We identified eight regions on chromosome X that displayed important associations with SC. The results showed that together the genomic windows explained 28.52% of the genetic variance for the examined trait. Genes with potential functions in reproduction and fertility regulation were highlighted as candidates for sexual precocity rates in Nelore cattle (AFF2 and PJA1). Moreover, we found 10 genes that had not previously been identified as being associated with sexual precocity traits in cattle. These findings will further advance our understanding of the genetic architecture, considering mainly the presence of the chromosome X, for indicine cattle reproductive traits, being useful in the context of genomic prediction in beef cattle. Escola de Medicina Veterinária E Zootecnia Universidade Federal da Bahia (UFBA) Departamento de Zootecnia Faculdade de Ciências Agrárias E Veterinárias Universidade Estadual Paulista (Unesp) Departamento de Zootecnia Faculdade de Ciências Agrárias E Veterinárias Universidade Estadual Paulista (Unesp)

Growth data of 77,372 Nelore steers were used to estimate the selection effect on energy requirements considering two beef production systems: cow-calf and slaughter cycles. All the animals had measures from 120 days to 7 years old. The parameters necessary to evaluate the selection effect on energy requirements were obtained by random regression analysis using Legendre polynomials. The models included additive direct and maternal effects, and animal and maternal permanent environmental effects as random terms. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of animal age (cubic regression) were considered random covariables. The coefficients from the model M3353_5 were used to calculate the genetic gains necessary to predict the increase in phenotypes. The selection was simulated for body weight (BW) and weight gain (WG) at different ages and energy requirements were calculated using NRC equations. The cost of feed was calculated for a cow-calf and slaughter cycle of production considering a system of Brachiaria decumbens pasture without supplementation. In slaughter system, the selection for weight of 365 days of age is the best option. In cow-calf systems, the selection W120 is the best choice.

The genetic groups of native donkeys in Brazil are characterized by adaptation to the local environment. However, the donkey population in the country is declining, mainly because of agricultural mechanization and transportation that has led to the abandonment and the consequent indiscriminate slaughter of these animals. There are three local genetic groups of distinct geographic and temporal formation. However, analyses of their origin, phylogenetic relationship, and population structure are scarce. Within this context, molecular markers such as the mitochondrial control region (D-loop) are useful for these analyses. This study aimed to evaluate the variation and origin of maternal lineages of groups of naturalized donkeys in Brazil (Brazilian, Nordestino and Pêga). We detected five mitochondrial haplotypes with 18 polymorphic sites, two of them exclusively found in the Nordestino donkey. This group is more distant from the other groups. Phylogenetic analysis indicates maternal contributions of two clades (Nubian and Somali) to the formation of the genetic groups of donkeys, a fact that explains the high diversity, structure and distances of the groups. It was firstly reported here. This analysis contributes production and conservation of native donkey breeds. It also gives clues about the formation of the Iberian breeds from which Brazilian donkeys originated.

Rabbit production is still small in Brazil and organization of its production chain is therefore necessary. The aim of this study was to investigate consumer perceptions of rabbit meat in the country. An online survey was conducted with 2614 participants. The responses were analyzed using the nonparametric Mann-Whitney U test. The survey revealed that the greatest acceptance of rabbit meat occurred in the population of adult men with a higher income and educational level who live in capital cities. Regional differences exist in Brazil. Consumption is more consolidated in the south region. The main limiting factor for rabbit meat consumption is the unavailability of the product. The limited availability of rabbit meat results in low consumption. Producers ensuring a regular supply of rabbit meat and verticalization by the industry are essential. These proposed actions were found to be even more important than demystify the image of the rabbit as a pet.

A2 milk is an easily digestible product since it has only A2 beta-casein. In cattle, the A1 and A2 alleles are found in the population and the A2 milk is produced from A2A2 animals. Little is known about these alleles in other domestic dairy species. The present study aims to analyze sequence of genetic material available on public databases and quantify the animals genotyped. Eight domestic species were analyzed. There is strong evidence that domestic non-bovine species only carry A2 beta-casein. The data reported here for goats already confirm it due to the large number of animals genotyped as well as buffaloes. It means that they naturally produce A2 milk and no selection must be done. Thus, the fact that A2 milk is easier to digest can be used to add value to dairy product of these species. It helps to conquer new markets. It also improves people’s health and breeder profitability.

Grullo is a dun dilution on a black coat that is common in the Campolina horse: an autochthonous Brazilian breed. The aims of this case study were to evaluate inconsistencies in grullo coat color registration and to explain their possible causes. A total of 3,270 grullo Campolina horses were evaluated. To confirm the genetic possibility of having grullo animals, the coat color genotypes of parents were inferred by phenotype and compared with those of progeny. A total of 242 horses that were registered as grullos could not have this coat based on their parents’ information. Possible explanations for incorrect registration are errors of paternity and in coat color identification. We suggest maintaining obligatory paternity testing and enhancing training in coat color identification.

The objective of this work was to distinguish the sexual dimorphism of horses of the Campolina breed, by morphometric measurements, and to classify them according to sex, using discriminating functions. Two-hundred and fifteen horses were measured, and 39 morphometric measurements were evaluated. The analysis of covariance and the discriminant analysis were performed. Males were taller and showed a wider chest, a greater scapular-humeral angle, and a larger neck, both in length and circumference. Females had a larger heart girth, wider hips, and a greater opening of the coxal-ground and femorotibial angles. Regarding classification, circumference measurements (85.58%) were more accurate in sexual differentiation than the linear (83.26%) and angular (73.02%) ones. As to classification error, of the total animals measured, 10 to 20% of the females were categorized as males. In addition, 11 to 38% of the males were categorized as females. It can be concluded that of the 39 morphometric measurements evaluated, 22 are responsible for sexual dimorphism in the Campolina horse breed. Circumference and linear measurements provide a more assertive classification to determine sexual dimorphism. Angular measurements show greater classification errors regarding the gender of the horses. Resumo: O objetivo deste trabalho foi distinguir o dimorfismo sexual de equinos da raça Campolina, por meio de medidas morfométricas, e classificá-los quanto ao sexo, tendo-se utilizado funções discriminantes. Foram mensurados 215 equinos, e avaliadas 39 medidas morfométricas. Realizaram-se análises de covariância e discriminante. Os machos foram mais altos e apresentaram peito mais largo, maior ângulo escapulo-umeral e maior pescoço, tanto em comprimento quanto em perímetro. As fêmeas apresentaram maior perímetro torácico, ancas mais largas e maior abertura dos ângulos coxo-solo e femorotibial. Em relação à classificação, as medidas de perímetros (85,58%) foram mais acuradas na diferenciação sexual do que as lineares (83,26%) e as angulares (73,02%). Quanto ao erro de classificação, do total de animais mensurados, de 10 a 20% das fêmeas foram categorizadas como machos. Além disso, de 11 a 38% dos machos foram categorizados como fêmeas. Conclui-se que, das 39 medidas morfométricas avaliadas, 22 são responsáveis pelo dimorfismo sexual em equinos da raça Campolina. As medidas de perímetros e lineares fornecem classificação mais assertiva para determinar o dimorfismo sexual. As medidas angulares mostram maiores erros de classificação em relação ao sexo dos equinos.

Made available in DSpace on 2022-04-28T19:44:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-10-01 Hair whorl traits can be used as indicators of behavior in horses. However, little is known about the genetic component of this group of traits. The aim of this study was to estimate variance components for hair whorl traits in Quarter Horses. Genetic parameters were estimated for vertical whorl position on the head, number of facial whorls, and number of whorls on both sides of the neck. The heritability estimates ranged from 0.69 to 0.99 and genetic correlations ranged from 0.84 to 0.96. These estimates show that hair whorl traits have a large additive genetic variance and that the phenotype is a good indicator of the genotype. Selection for any of the traits will result in a correlated response for the others. This study contributes to the elucidation and understanding of the genetic basis of the distribution and formation of hair whorls, and encourages future studies investigating the association of these traits with behavior and indirect selection. Escola de Medicina Veterinária e Zootecnia Universidade Federal da Bahia (UFBA) Universidade Estadual Paulista (Unesp) Universidade Estadual Paulista (Unesp)

Simple Summary Whorls have been used to indicate the temperaments of domestic animals; however, little is known about the biological events that drive this association. The present study is the first that aims to find the main genomic regions that influence the whorl traits in livestock, with horses as a model. Genes related to hair follicle growth were found. Interestingly, some of these genes also influence psychiatric diseases and neurological disorders, thus evidencing a consistent biological explanation for the association. Abstract The position and number of hair whorls have been associated with the behavior, temperament, and laterality of horses. The easy observation of whorls assists in the prediction of reactivity, and thus permits the development of better measures of handling, training, mounting, and riding horses. However, little is known about the genetics involved in the formation of hair whorls. Therefore, the aim of this study was to perform a genome-wide association analysis to identify chromosome regions and candidate genes associated with hair whorl traits. Data from 342 Quarter Horses genotyped for approximately 53,000 SNPs were used in an association study using a single-step procedure. The following traits were analyzed: vertical position of hair whorl on the head, number of whorls on the head, and number of whorls on the left and right sides of the neck. The traits had between one and three genomic windows associated. Each of them explained at least 4% of the additive variance. The windows accounted for 20–80% of additive variance for each trait analyzed. Many of the prospected genes are related to hair follicle growth. Some of these genes exert a pleiotropic effect on neurological and behavioral traits. This is the first indication of biological and physiological activity that might explain the association of hair whorls and temperament.

Cow milk might be associated to gastrointestinal disorders and abdominal pain in some people, which are, in part, due to the digestion of A1 beta-casein. Within this context, A2 milk has emerged as an alternative since it only contains A2 beta-casein that does not cause these complications. This milk is produced by cows with the A2A2 genotype. The aim of this study was to investigate the allele and genotype frequencies for the beta-casein gene in Guzerat cattle and to evaluate the feasibility of selection and production of A2 milk. The genotypes of 283 Guzerat cows from 10 herds were analyzed. The frequency of the A2A2 genotype was 0.80 and the frequency of the A2 allele was 0.90. These frequencies are slightly lower than those reported in previous studies involving populations of the same breed, but the number of animals, herein, genotyped was higher. Thus, the estimates are believed to be better and are also equally high. The Guzerat cattle has the potential for A2 milk production since most animals of the herd carry the favorable genotype for A2 milk production. Furthermore, the frequency of the A2A2 genotype can be rapidly increased by marker-assisted selection without compromising genetic variability.

Made available in DSpace on 2021-06-25T11:18:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The objective of this study was to evaluate the accuracy of genomic predictions of growth traits in Nellore cattle. Data from 5064 animals belonging to farms that participate in the Conexão DeltaGen and PAINT breeding programs were used. Genotyping was performed with the Illumina BovineHD BeadChip (777,962 SNPs). After quality control of the genomic data, 412,993 SNPs were used. Deregressed EBVs (DEBVs) were calculated using the estimated breeding values (EBVs) and accuracies of birth weight (BW), weight gain from birth to weaning (GBW), postweaning weight gain (PWG), yearling height (YH), and cow weight (CW) provided by GenSys. Three models were used to estimate marker effects: genomic best linear unbiased prediction (GBLUP), BayesCπ, and improved Bayesian least absolute shrinkage and selection operator (IBLASSO). The prediction ability of genomic estimated breeding value (GEBVs) was estimated by the average Pearson correlation between DEBVs and GEBVs, predicted with the different methodologies in the validation populations. The regression coefficients of DEBVs on GEBVs in the validation population were calculated and used as indicators of prediction bias of GEBV. In general, the Bayesian methods provided slightly more accurate predictions of genomic breeding values than GBLUP. The BayesCπ and IBLASSO were similar for all traits (BW, GBW, PWG, and YH), except for CW. Thus, there does not seem to be a more suitable method for the estimation of SNP effects and genomic breeding values. Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. School of Agricultural and Veterinarian Sciences Sao Paulo State University (UNESP) School of Veterinary and Animal Sciences Universidade Federal da Bahia (UFBA) School of Agricultural and Veterinarian Sciences Sao Paulo State University (UNESP) FAPESP: 2009/16118-5

The information of twin pregnancy frequencies in buffaloes is scarce in the literature. Evidence even indicates that twin pregnancies are not carried to term, but it does not seem to be the case. In this case report, the event of twin pregnancy in buffaloes is reported as well as its frequency. Twin birth is the presence of two or more embryos in a single gestation. Multiple births are uncommon in buffaloes since the species is uniparous. We studied a population of Murrah buffaloes in which slightly more than 13,000 births were observed. In this study, the frequency of occurrence of twin births in Murrah buffaloes was 0.14%. This low incidence impaired the estimation of genetic parameters. Twins can have advantages and disadvantages depending on the production system, which are discussed in this case report.

Made available in DSpace on 2021-06-25T11:07:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-02-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The aims of this study were to verify the occurrence of single nucleotide polymorphisms (SNPs) in the JY-1 gene and their association with the in vivo and in vitro production of embryos in Holstein donors. The JY-1 protein is oocyte-specific and has an important regulatory role in folliculogenesis, oocyte maturation, and early embryonic development. Retrospective data of in vivo (n = 572) and in vitro (n = 1068) embryos produced between 2013 and 2015 were obtained from 144 non-lactating, Holstein cows. To identify the polymorphisms, exons 2 and 3 were studied by polymerase chain reaction (PCR) sequencing. The association of SNPs with embryo traits (number of transferable embryos produced in vivo, rate of transferable embryos in vivo, number of embryos produced in vitro, cleavage rate, and embryo rate in vitro) was determined using the GLIMMIX procedure of SAS. Eleven SNPs were detected, located in exon 2, intron 2, and exon 3. The coding genetic variants were non-synonymous, synonymous, and located in untranslated regions. Nine SNPs were associated with at least one in vitro embryo production trait, but none were associated with in vivo embryo production. JY-1 has potential markers that could be used to select donors, and its influence on in vitro embryo production was observed in the present study. Department of Pathology Theriogenology and One Health School of Agricultural and Veterinarian Science São Paulo State University (UNESP) Department of Animal Science School of Agricultural and Veterinarian Science São Paulo State University (UNESP) Clínica Veterinária Samvet São Carlos National Council for Science and Technological Development Department of Pathology Theriogenology and One Health School of Agricultural and Veterinarian Science São Paulo State University (UNESP) Department of Animal Science School of Agricultural and Veterinarian Science São Paulo State University (UNESP) CNPq: 447172/ 2014–0

Made available in DSpace on 2021-06-25T10:48:00Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-02-01 The aim of this study was to evaluate whether there are predictive advantages for breeding values with inclusion of X chromosome genomic markers for reproductive (occurrence of early pregnancy – P16 and age at first calving - AFC) and andrological (scrotal circumference -SC) variables in beef cattle. There were 3263 genotypes of females and males evaluated. There were breeding value estimates for SC, AFC and P16 considering two scenarios: 1) only autosomal markers or 2) autosomal and X chromosome markers. To evaluate effects of inclusion of X chromosome markers on selection, responses to selection were compared including or not including genomic marker information from the X chromosome. There were greater heritability estimates for SC (0.40 and 0.31), AFC (0.11 and 0.09) and P16 (0.43 and 0.38) when analyses included, compared with not including, genomic marker information from the X chromosome. When selection is based on results from analyses that did not include information for the X chromosome, there was about a 7 % lesser mean genomic breeding value for the SC traits for selected animals. For P16, there was an approximate 4% lesser breeding value without inclusion of genomic marker information from the X chromosome, while this inclusion did not have as great an effect on the breeding value for AFC. There was an average predictive correlation of 0.79, 0.98 and 0.84 for SC, AFC and P16, respectively. These estimates indicate inclusion of the X chromosome genomic marker information in the analysis can improve prediction of genomic breeding values, especially for SC. Escola de Medicina Veterinária e Zootecnia Universidade Federal da Bahia (UFBA) Universidade Federal do Oeste da Bahia (UFOB) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp)

Urea-related traits can be used as an indicator of nitrogen (N) utilization and excretion and have a key role in the protein metabolism of ruminants. A genome-wide association study (GWAS) was carried out for plasma urea concentration (PUC) in Santa Ines sheep. PUC was recorded in 229 lambs, which were also genotyped with OvineSNP50K BeadChip. After data quality control, 43,996 variants and 229 PUC records were used in GWAS. The WssGBLUP method was used in GWAS analysis and genome windows of 1.0 Mb were analyzed. Estimate of heritability for PUC was 0.10±0.07. Seven genomic regions in the chromosomes OAR3, OAR6, OAR10, OAR23, and OAR24 explained 12.4% of the additive genetic variance and harbored 95 genes. Some candidate genes (LOC114113767, LOC105612842 in OAR3, CLOCK and NMU in OAR6, KLHL1, and NBEA in OAR10, NDUFV2, RAB31, and RAB12 in OAR23, AZGP1, LAMTOR4, SMURF1, ARPC1A, ARPC1B, LOC101110727, LOC101110202, and CYP3A24 in OAR24) were found. Moreover, five significant (P

The aim of this study was to verify the effect of the inclusion of coat color on the genetic parameter estimation for linear measurements in Campolina horses. Two models (1 and 2) were applied. For model 1, coat color effect was not included as variable of the contemporary group formation; in model 2, it was included. Model 2 presented the best fitting with a Deviance Information Criterion (DIC) of −979,459.020 compared with −1,818,458.572 DIC from model 1. The average of heritability estimates ranged from low to high magnitude (0.15 to 0.53) for model 1 and from moderate to high magnitude for model 2 (0.21 to 0.47). The estimated values varied according to the analyses (models 1 and 2). The highest heritability was found for withers height (0.52), croup height (0.53), and back height (0.51). The genetic correlations ranged from values of moderate to high magnitude for models 1 (0.23 to 0.98) and 2 (0.29 to 0.99), respectively. The finding that genetic variance differed among models 1 and 2 may indicate that genotypes react differently to different coat colors, a fact implying the existence of interaction between these traits and the effect under study. The coat color influence might be explained as a pleiotropic effect of the genes that cause this phenotypic variation and also influence morphometric measures. The inclusion of the coat color effect better estimated the additive genetic variance of morphometric traits in horses. As a consequence, the genetic parameters were also more accurately estimated when it is included in the evaluation model.

Made available in DSpace on 2021-06-25T10:48:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado da Bahia The aim of this study was to identify SNPs located in mitochondrial DNA that are associated with reproductive traits in beef cows. A total of 1999 Nelore females genotyped with the high-density Illumina BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) were used to study the association of mitochondrial DNA variants with reproductive traits using a single-step procedure. In a preliminary analysis, the present results indicate a small participation of the mitogenome in the expression of reproductive traits in beef cattle. However, possible difficulties related to the biological characteristics of mitochondrial DNA and its inheritance, genotyping, and annotation of the phenotypes studied may also explain the results. Escola de Medicina Veterinária e Zootecnia Universidade Federal da Bahia (UFBA) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp), Jaboticabal Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp), Jaboticabal FAPESP: 2009/16118-5 FAPESP: 2017/10630-2 FAPESP: 2018/20026-8 CNPq: 422799/2016-5 Fundação de Amparo à Pesquisa do Estado da Bahia: BOL2262/2017

BackgroundImputation accuracy among other things depends on the size of the reference panel, the marker’s minor allele frequency (MAF), and the correct placement of variants on the reference genome assembly. Using high-density genotypes of 3938 Nellore cattle from Brazil, we investigated the accuracy of imputation from 50K to 777K SNP density, using map positions determined according to the bovine genome assemblies UMD3.1 and ARS-UCD1.2. We assessed the effect of reference and target panel sizes on the pre-phasing-based imputation quality using ten-fold cross-validation. Further, we compared the reliability of the model-based imputation quality score (Rsq) from Minimac3 to empirical imputation accuracy.ResultsThe overall accuracy of imputation measured as the squared correlation between true and imputed allele dosages (R2dose) was virtually identical using either the UMD3.1 or ARS-UCD1.2 genome assembly. When the size of the reference panel increased from 250 to 2000, R2dose increased from 0.845 to 0.917, and the number of polymorphic markers in the imputed data set increased from 586,701 to 618,660. Advantages in both accuracy and marker density were also observed when larger target panels were imputed, likely resulting from more accurate haplotype inference. Imputation accuracy and the marker density in the imputed data increased from 0.903 to 0.913 and from 593,239 to 595,570 when haplotypes were inferred in 500 and 2900 target animals, respectively. The model-based imputation quality scores from Minimac3 (Rsq) were highly correlated to but systematically higher than empirically estimated accuracies. The correlation between these metrics increased with the size of the reference panel and MAF of imputed variants.ConclusionsAccurate imputation of BovineHD BeadChip markers is possible in Nellore cattle using the new bovine reference genome assembly ARS-UCD1.2. The use of large reference and target panels improves the accuracy of the imputed genotypes and provides genotypes for more markers segregating at low frequency for downstream genomic analyses. The model-based imputation quality score from Minimac3 (Rsq) can be used to detect poorly imputed variants but its reliability depends on the size of the reference panel used and MAF of the imputed variants.

Made available in DSpace on 2021-06-25T10:34:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-11-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Although the second largest chromosome of the genome, the X chromosome is usually excluded from genome-wide association studies (GWAS). Considering the presence and importance of genes on this chromosome that are involved in reproduction, the aim of this study was to evaluate the effect of its inclusion in GWAS on reproductive traits (scrotal circumference [SC], early pregnancy [P16] and age at first calving [AFC]) in a Nelore herd. Genotype data from 3,263 animals with the above-mentioned phenotypes were used. The results showed an increase in the variances explained by the autosomal markers for all traits when the X chromosome was not included. For SC, there was an increase of more than 10% for the windows on chromosomes 2 and 6. For P16, the effect was increased by almost 20% for windows on chromosome 5. The same pattern was found for AFC, with an increase of more than 10% for the most important windows. The results indicate that the noninclusion of the X chromosome can overestimate the effects of autosomes on SC, P16 and AFC not only because of the additive effect of the X chromosome itself but also because of its epistatic effect on autosomal genes. Escola de Medicina Veterinária e Zootecnia Universidade Federal da Bahia (UFBA) Universidade Federal do Oeste da Bahia (UFOB) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) FAPESP: 2009/16118-5

Made available in DSpace on 2021-06-25T10:50:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Fundação de Amparo à Pesquisa do Estado da Bahia Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Beta-casein is a milk protein that has two variants: A1 and A2. Some individuals have difficulties digesting beta-casein A1, which can cause gastrointestinal disorders. A2 milk has emerged as an alternative. This milk only contains beta-casein A2 and is obtained from females carrying the A2A2 genotype of the gene. In cattle, allele and genotype frequencies vary according to breed and marker-assisted selection is performed to obtain A2A2 animals and the consequent production of A2 milk that is easier to digest. This study aimed to evaluate the alleles of beta-casein in buffaloes. A total of 657 buffaloes of four different breeds were genotyped and all animals carried the A2A2 genotype, i.e., allele A1 does not exist in the buffalo species. Thus, all milk products of buffaloes are naturally A2. This result adds value to products derived from buffalo milk. Escola de Medicina Veterinária e Zootecnia Universidade Federal da Bahia (UFBA) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) CNPq: 400227/2016-9

Made available in DSpace on 2021-06-25T10:45:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-01 Principal component analysis (PCA) was applied to evaluate the genetic variability and relationship between 15 morphometric traits in 91,483 Campolina horses, as well as to propose an index based on an aggregate genotype that promotes a particular selection objective. PCA was applied to the genetic (co)variance matrix among variables. After calculation of the principal components, the breeding values were estimated to obtain an index related to the component that explained most of the variation. The first principal component (PC1) accounted for 97.8% of the total additive genetic variance of the traits. PC1 contrasted animals in terms of body size (wither, back and croup heights, body length, and thoracic girth). PC1 traits showed higher heritabilities and positive and high genetic correlations. An index was obtained (HPC1) with the combination of the breeding values of different traits from PC1 which permitted the use of this index as an aggregate genotype to identify the best animals for selection. The second principal component (PC2) was much smaller and grouped traits related to head and neck morphometry, among others. These traits are commonly used for breed qualification, a fact explaining the small variation in this component. An evaluation of the effect of HPC1 on withers height in two-trait analysis was also made which provided positive genetic correlations of moderate to high magnitude (0.73–0.86), indicating that selection for this trait (important in Campolina horses) is accounted for in the index. The use of HCP1 could be considered as an important alternative to selection since it does not consider a single trait but rather a set of variables that capture body proportions. Escola de Medicina e Veterinária e Zootecnia UFBA Universidade Federal da Bahia Departamento de Zootecnia Faculdade de Ciencias Agrarias e Veterinarias UNESP Universidade Estadual Paulista Julio de Mesquita Filho Departamento de Zootecnia Faculdade de Ciencias Agrarias e Veterinarias UNESP Universidade Estadual Paulista Julio de Mesquita Filho

Made available in DSpace on 2018-12-11T17:08:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-02-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The aim of this study was to determine the extent (r2) of linkage disequilibrium (LD) in the genome of Nellore cattle, and to examine associations between single nucleotide polymorphisms (SNP) and age at first calving (AFC) and early pregnancy (EP) using a panel of high-density SNPs and data from 1182 Nellore females. A total of 13 contemporary groups (CG) were used consisting of farm, season, and year of birth. For genome-wide association analysis, SNPs with a minor allele frequency (MAF)

Carcass traits measured after slaughter are economically relevant traits in beef cattle. In general, the slaughter house payment system is based on HCW. Ribeye area (REA) is associated with the amount of the meat in the carcass, and a minimum of backfat thickness (BFT) is necessary to protect the carcass during cooling. The aim of this study was to identify potential genomic regions harboring candidate genes affecting those traits in Nellore cattle. The data set used in the present study consisted of 1,756 Nellore males with phenotype records. A subset of 1,604 animals had both genotypic and phenotypic information. Genotypes were generated based on a panel with 777,962 SNPs from the Illumina Bovine HD chip. The SNP effects were calculated based on the genomic breeding values obtained by using the single-step GBLUP approach and a genomic matrix re-weighting procedure. The proportion of the variance explained by moving windows of 100 consecutive SNPs was used to assess potential genomic regions harboring genes with major effects on each trait. The top 10 non-overlapping SNP-windows explained 8.72%, 11.38%, and 9.31% of the genetic variance for REA, BFT, and HCW, respectively. These windows are located on chromosomes 5, 7, 8, 10, 12, 20, and 29 for REA; chromosomes 6, 8, 10, 13, 16, 17, 18, and 24 for BFT; and chromosomes 4, 6, 7, 8, 14, 16, 17, and 21 for HCW. For REA, there were identified genes ( and ) involved in the cell cycle biological process which affects many aspects of animal growth and development. The and genes, both from AA transporter family, was also associated with REA. The AA transporters are essential for cell growth and proliferation, acting as carriers of tissue nutrient supplies. Various genes identified for BFT (, , , , , and ) have been associated with lipid metabolism in different mammal species. One of the most promising genes identified for HCW was the . There is evidence, in the literature, that this gene is located in putative QTL affecting carcass weight in beef cattle. Our results showed several genomic regions containing plausible candidate genes that may be associated with carcass traits in Nellore cattle. Besides contributing to a better understanding of the genetic control of carcass traits, the identified genes can also be helpful for further functional genomic studies.

Made available in DSpace on 2019-10-05T08:00:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-02-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The objective of this study was to assess the accuracy of genomic predictions for female reproductive traits in Nellore cattle. A total of 1853 genotyped cows and 305,348 SNPs were used for genomic selection analyses. GBLUP, BAYESC pi, and IBLASSO were applied to estimate SNP effects. The pseudo-phenotypes used as dependent variables were: observed phenotype (PHEN), adjusted phenotype (CPHEN), estimated breeding value (EBV), and deregressed estimated breeding value (DEBV). Predictive abilities were assessed by the average correlation between CPHEN and genomic estimated breeding value (GEBV) and by the average correlation between DEBV and GEBV in the validation population. Regression coefficients of pseudo phenotypes on GEBV in the validation population were indicators of prediction bias in GEBV. BAYESC pi showed higher predictive ability to estimate SNP effects and GEBV for all traits. (C) 2018 Elsevier Inc. All rights reserved. Sao Paulo State Univ, Via Acesso Prof Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, Brazil Univ Fed Bahia, Ave Adhemar de Barros 500, BR-40170110 Salvador, BA, Brazil Sao Paulo State Univ, Via Acesso Prof Paulo Donato Castellane S-N, BR-14884900 Jaboticabal, Brazil FAPESP: :2009/16118-5

Made available in DSpace on 2019-10-06T16:11:40Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-02-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Sex chromosomes are generally excluded from genomic analyses, although X chromosome is the second largest chromosome and harbors many genes. The objective of this study was to evaluate the effect of X chromosome by identifying its regions associated with reproductive traits in Nelore cows through a genome-wide association and by estimating its linkage disequilibrium. Phenotypic data of 76,845 and 76,700 animals were used for pregnancy at 16 months and age at first calving, respectively, as well as genotypic data of 1,999 females. Linkage disequilibrium was estimated for X chromosome and for autosomes 1 and 2, due to similar size of chromosomes. Single-step method was used for association analysis and some genes with known role in reproduction were reported for both traits, such as KLHL4 which is associated with development of the female reproductive system, and PCDH11X which is associated with the onset of primary ovarian insufficiency. Moreover, some genes were associated with both traits, indicating a pleiotropic effect. However, contribution of the windows in X-chromosome is very small when compared to autosomes: an unexpected fact. The results revealed higher linkage disequilibrium on the X chromosome (0.2248 ± 0.17) compared to the other chromosomes (0.1965 ± 0.14 and 0.1967 ± 0.14 for autosomes 1 and 2, respectively), indicating low recombination rates. Universidade Federal do Oeste da Bahia (UFOB) Escola de Medicina Veterinária e Zootecnia Universidade Federal da Bahia (UFBA) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp) FAPESP: 2009/16118-5 CNPq: 310443/2017-2 CNPq: 422799/2016-5

SUMMARY The objective of this study was to evaluate the effect of the genotype-environment interaction (GEI) for scrotal circumference traits measured at different ages, 365 (SC365), 450 (SC450) and 550 (SC550) days of age, and age at first calving (AFC) for Nellore animals raised in different regions of Brazil. For the evaluation, the herds were grouped in the following regions of the country: North, Southeast and Central-west, using information from 26,619, 28,730, 14,476, 15,397 for the traits SC365, SC450, SC550 and AFC respectively. Genetic parameters, as well as the assessment of GEI were performed using Bayesian inference, using the programs of the BLUPF90. The estimated heritabilities were: 0.465 ± 0.021, 0.500 ± 0.022, 0.492 ± 0.026, 0.117 ± 0.017 for SC365, SC450, SC550 and AFC respectively. The results obtained in the analysis, indicated that this interaction was not significant for SC at different ages (genetic correlation, rg> 0.8). For AFC, significant effect of GEI was observed for combinations involving the Northern region (rg0,8). No entanto, para a IPP foi evidenciado efeito significativo da IGA para as combinações envolvendo a região Norte (rg< 0,8), indicando que esta interação é significativa devendo ser considerada pelos diferentes programas de avaliação genética da raça,para os animais criados nesta região.

Equid breeds originating from the Iberian Peninsula and North Africa are believed to have genetically contributed to the formation of breeds and ecotypes from Brazil. The country has numerous breeds and ecotypes of horses and donkeys but there are no extensive studies on maternal genetic diversity and their origins. This study reports the results of the first genetic analysis of all horse and donkey breeds/ecotypes from Brazil based on sequences of the mitochondrial DNA control region (D-loop) whose main objective was to characterize the genetic variation in these animals. These analyses will contribute to the understanding of the current population structure and diversity of breeds/ecotypes of horses and donkeys raised in the Brazil. We analyzed 310 D-loop sequences representing 41 breeds/ecotypes of Equus caballus and Equus asinus, including 14 native horse breeds/ecotypes, 3 native donkey breeds/ecotypes and 24 cosmopolite horse breeds. The results revealed that the breeds are well structured genetically and that they comprise different groups. A total of 80 and 14 haplotypes were identified for horses and donkeys, respectively. Most of the horse mtDNA haplotypes were shared by many breeds, whereas donkey mtDNA haplotypes seemed to be more group-especif. Some groups presented a low intrabreed distance and/or a low haplotype/nucleotide diversity such as Lavradeiro, Crioulo, Piquira and Percheron horses and Brazilian donkey. Thus, specific actions must be designed for each population. The different levels of genetic diversity provided important information for conservation resource management of adapted groups as well as for mating orientation of breed associations. Some autochthonous ecotypes require attention because of their low genetic variability.

Made available in DSpace on 2020-12-12T01:13:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-02-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) White markings are very common in several horse breeds. These patterns are used for breed characterization, for the identification of animals (records) and might be associated with anomalies such as skin problems and deafness. The aim of the study was to perform genome-wide association analysis to identify genomic regions associated with the presence of white markings on the head and legs of Quarter Horses. The horses were from racing lineage and raised in Brazil. Records of 342 individuals and genotypes of 360 animals, genotyped for 63k, were used in a genome-wide association study, using the single-step procedure. Traits under analyses were presence of white markings on the head, forelegs, and hind legs. Few genomic regions influencing the traits were identified. Only one region containing the MC1R gene has been reported previously. The remaining genomic regions were detected for the first time in the present study. Within the genomic windows, some candidate genes were pointed out: ZEB2, KYNU, SLC36A1, STX12, MAP3K6, and GJB2. Markings in horses are characterized by genetic heterogeneity. It means that different genes can give origin to the same phenotype depending on the population. Candidate genes were, herein, described. It will permit future fine mapping studies in Quarter Horses in order to identify their causal mutations and also the development of molecular markers. Universidade Federal da Bahia (UFBA) Universidade Federal Rural do Rio de Janeiro (UFRRJ) Universidade Estadual Paulista (Unesp) Universidade Estadual Paulista (Unesp) FAPESP: 2014/20207-1

ContextCow milk is consumed in many countries. However, its consumption can be associated with gastrointestinal disorders in humans. The genetic profile of β-casein is one of the factors responsible for these disorders and the A1 variant is a causal agent. The β-casein A1 leads to the formation of bioactive peptides, which trigger intestinal reactions. The same is not observed for the A2 allele. A2 milk is obtained from cows with the A2A2 genotype. The identification of breeds and selection of animals for A2 milk production is important for public health and animal production. The Sindhi cattle (Bos taurus indicus) possesses characteristics such as adaptation to hot climate, resistance to parasites and utilisation of low-quality forage that are important for rearing in the tropics. AimsThe objective of the present study was to genotype the single-nucleotide polymorphism (SNP) that forms A1 and A2 alleles of the β-casein in Sindhi cattle. MethodsIn total, 348 Sindhi animals were used. DNA was extracted from hair follicles and submitted to PCR-sequencing for genotyping. Key resultsAllele frequency for A2 was 0.94 and for A1 it was 0.06. Genotype frequencies were 0.90 (A2A2), 0.09 (A1A2) and 0.01 (A1A1). The frequency of the A2A2 genotype in Sindhi cattle was similar to or higher than those found in zebu breeds and higher than those reported for specialised taurine breeds. ConclusionsThis high frequency of the A2A2 genotype indicates a genetic potential of the breed for A2 milk production and easy, assisted selection (if that is the intention). ImplicationsThis information gives importance to the breed and permits to add value to dairy product derived from it. It may increase producer’s income through producing and marketing A2 milk.

Made available in DSpace on 2018-12-11T17:16:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-07-01 The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) with birth weight, weight gain from birth to weaning and from weaning to yearling, yearling height and cow weight in Nelore cattle. Data from 5064 animals participating in the DeltaGen and PAINT breeding programs were used. The animals were genotyped with a panel of 777 962 SNPs (Illumina BovineHD BeadChip) and 412 993 SNPs remained after quality control analysis of the genomic data. A genome-wide association study was performed using a single-step methodology. The analyses were processed with the BLUPF90 family of programs. When applied to a genome-wide association studies, the single-step GBLUP methodology is an iterative process that estimates weights for the SNPs. The weights of SNPs were included in all analyses by iteratively applying the single-step GBLUP methodology and repeated twice so that the effect of the SNP and the effect of the animal were recalculated in order to increase the weight of SNPs with large effects and to reduce the weight of those with small effects. The genome-wide association results are reported based on the proportion of variance explained by windows of 50 adjacent SNPs. Considering the two iterations, only windows with an additive genetic variance >1.5% were presented in the results. Associations were observed with birth weight on BTA 14, with weight gain from birth to weaning on BTA 5 and 29, with weight gain from weaning to yearling on BTA 11, and with yearling height on BTA 8, showing the genes TMEM68 (transmembrane protein 8B) associated with birth weight and yearling height, XKR4 (XK, Kell blood group complex subunit-related family, member 4) associated with birth weight, NPR2 (natriuretic peptide receptor B) associated with yearling height, and REG3G (regenerating islet-derived 3-gamma) associated with weight gain from weaning to yearling. These genes play an important role in feed intake, weight gain and the regulation of skeletal growth. Departamento de Zootecnia Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Escola de Medicina Veterinária e Zootecnia Universidade Federal da Bahia (UFBA) Departamento de Zootecnia Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias

Made available in DSpace on 2018-12-11T17:35:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Reproductive traits are of the utmost importance for any livestock farming, but are difficult to measure and to interpret since they are influenced by various factors. The objective of this study was to detect associations between known polymorphisms in candidate genes related to sexual precocity in Nellore heifers, which could be used in breeding programs. Records of 1,689 precocious and non-precocious heifers from farms participating in the Conexão Delta G breeding program were analyzed. A subset of single nucleotide polymorphisms (SNP) located in the region of the candidate genes at a distance of up to 5 kb from the boundaries of each gene, were selected from the panel of 777,000 SNPs of the High-Density Bovine SNP BeadChip. Linear mixed models were used for statistical analysis of early heifer pregnancy, relating the trait with isolated SNPs or with haplotype groups. The model included the contemporary group (year and month of birth) as fixed effect and parent of the animal (sire effect) as random effect. The fastPHASE® and GenomeStudio® were used for reconstruction of the haplotypes and for analysis of linkage disequilibrium based on r2 statistics. A total of 125 candidate genes and 2,024 SNPs forming haplotypes were analyzed. Statistical analysis after Bonferroni correction showed that nine haplotypes exerted a significant effect (p

The aim of this study was to evaluate the morphometric measurements of stallion and mares show-winning and nonwinning Campolina breed with batida and picada gaits. A total of 167 horses (74 stallions and 93 mares), consisting of 102 batida and 65 picada gait animals, were used. Among these horses, 96 were awarded and 71 were not. Twenty linear, seven angular, and 11 girth measurements were taken. Results from the judging sessions were collected, and awards were observed in both sexes and both gaits. A descriptive statistical analysis and an analysis of variance were performed using the MEANS statement and generalized linear model procedures of SAS software. For both sexes and gait types, most size measurements (height and length) were smaller in the winning animals. Results suggested that, based on the judges' assessments, the breed is targeting the breeding strategies toward a reduction in animal size because champions are becoming a standard for breeders and technicians and are more often used in reproduction.

We evaluated the genetic association of growth traits [weight adjusted to 205 days of age (W205), 365 days of age (W365), and 550 days of age (W550); weight gain between 205 days of age and 365 days of age (WG1) and between 365 days of age and 550 days of age (WG2)] and reproductive traits [age at first calving (AFC); first calving interval (FCI)] with stayability in the herd (STAY), using Bayesian inference in linear and threshold models. We defined STAY as the probability of a cow calving three or more times before the age of 76 months, given that she had calved at least once. We assigned binary codes (0, failure; 1, success) to each female. We used a sire model for analysis and formed different contemporary groups for the investigated traits. We analyzed the results by applying a two-trait sire model that included STAY (threshold trait) and linear traits (W205, W365, W550, WG1, WG2, AFC, and FCI). We used Gibbs sampling to estimate variance components and heritabilities. In all the analyses, we found that the mean heritability estimates for STAY were of moderate magnitude (0.20-0.25). The mean heritabilities for W205, W365, W550, WG1, WG2, AFC, and FCI were 0.20, 0.23, 0.39, 0.08, 0.14, 0.12, and 0.11, respectively. We observed wide variation in the posterior distributions of genetic correlations; however, with the exception of those obtained for the reproductive traits, the mean estimates were of low magnitude. Selection for WG2 can results in favorable correlated response in STAY.

Made available in DSpace on 2018-12-11T17:32:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-06-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Stayability, which can be defined as the probability of a cow calving at a certain age when given the opportunity, is an important reproductive trait in beef cattle because it is directly related to herd profitability. The objective of this study was to estimate genetic parameters and to identify possible genomic regions associated with the phenotypic expression of stayability in Nellore cows. The variance components were estimated by Bayesian inference using a threshold animal model that included the systematic effects of contemporary group and sexual precocity and the random effects of animal and residual. The SNP effects were estimated by the single-step genomic BLUP method using information of 2,838 animals (2,020 females and 930 sires) genotyped with the Illumina High-Density BeadChip Array (San Diego, CA, USA). The variance explained by windows formed by 200 consecutive SNPs was used to identify genomic regions of largest effect on the expression of stayability. The heritability was 0.11 ± 0.01 when A matrix (pedigree) was used and 0.14 ± 0.01 when H matrix (relationship matrix that combines pedigree information and SNP data) was used. A total of 147 candidate genes for stayability were identified on chromosomes 1, 2, 5, 6, 9 and 20 and on the X chromosome. New candidate regions for stayability were detected, most of them related to reproductive, immunological and central nervous system functions. Faculdade de Ciências Agrárias e Veterinárias UNESP Escola de Medicina Veterinária e Zootecnia UFBA CNPq Fellowship Faculdade de Ciências Agrárias e Veterinárias UNESP