Search

This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.

In Nellore beef cattle, studies addressing genetic correlations between ultrasound marbling content and other economically important traits are still incipient. Therefore, this work aimed to estimate heritability and genetic correlations between ultrasound marbling content in the longissimus dorsi muscle (MARB) and growth, reproductive, feed efficiency, and carcass-related traits in a Nellore beef cattle population from Brazil. Phenotypic records of 614,395 Nellore animals were used and included adjusted weight at 210 (W210) and 450 (W450) days of age, adult cow weight (AW), early heifer pregnancy (EH), stayability (STAY), adjusted scrotal circumference at 365 days of age (SC365), ribeye area (REA), subcutaneous backfat thickness (BF), rump fat thickness (RF), and marbling (MARB). The genetic parameters for all traits but EH and STAY were estimated considering a linear animal model, whereas for those two nonlinear traits, a threshold animal model was used. The direct and correlated response to selection for MARB versus the other traits, and the relative efficiency of selection, were also calculated. The heritability estimate for MARB was 0.31 and for the other conventional evaluated traits was low to moderate, with values ranging from 0.14 to 0.41. The genetic correlations between MARB and growth, reproductive, feed efficiency, and carcass-related trait were very low, with values close to zero, with similar correlated responses. The MARB displayed adequate genetic variability to respond to selection and crossbreeding programs looking forward to higher meat quality and differential market standards for the Nellore beef. The selection for growth, reproductive, feed efficiency, and carcass-related traits would not affect MARB in Nellore beef cattle and vice versa. Therefore, this trait should be included as a selection criterion in the Nellore breeding program.

This study aimed to estimate genetic parameters and the prediction ability and bias of the genomic values for residual feed intake (RFI) using genotypic and phenotypic records from 8,354 Nellore animals. The RFI was calculated using a regression equation for each test (RFItest) and for the whole population (RFIpop). An analysis of variance (ANOVA) using the same dataset and number of records was performed to verify the adequacy of the regression equations applied to estimate the RFItest and RFIpop. The (co)variance components were obtained using the single-step genomic best linear unbiased prediction (ssGBLUP) under single and two-trait animal model analyses. The ssGBLUP method was used for the genomic prediction and the cross-validation method as a validation strategy. The prediction ability and bias were estimated to compare the RFItest and RFIpop genomic breeding values (GEBVs). The RFIpop ANOVA showed a higher significance level (p test for the fixed effects. The RFIpop displayed higher additive genetic variance estimated than the RFItest, although the RFIpop and RFItest displayed similar heritabilities. Overall, the RFItest showed higher residual correlations with growth, reproductive and carcass traits, while the RFIpop displayed higher genetic correlations with such traits. The GEBV for the RFItest was slightly biased than that obtained for the RFIpop. The method of calculating the RFI influences the decomposition and estimation of variance components, and genomic prediction. The genetic correlations between RFIpop and RFItest were high, implying that changes in sires ranking and genetic response are expected using one or the other. The application of RFIpop would be more appropriate for genetic evaluation purpose to adjust or correct for non-genetic effects and to decrease the prediction bias.

Made available in DSpace on 2020-12-12T02:06:36Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p

This study aimed to estimate prediction ability and genetic parameters for residual feed intake (RFI) calculated using a regression equation for each test (RFI

Made available in DSpace on 2022-05-01T16:02:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-01-01 The beef fatty acid (FA) profile has the potential to impact human health, and displays polygenic and complex features. This study aimed to identify the transcriptomic FA profile in the longissimus thoracis muscle in Nellore beef cattle finished in feedlot. Forty-four young bulls were sampled to assess the beef FA profile by considering 14 phenotypes and including differentially expressed genes (DEG), co-expressed (COE), and differentially co-expressed genes (DCO) analyses. All samples (n = 44) were used for COE analysis, whereas 30 samples with extreme phenotypes for the beef FA profile were used for DEG and DCO. A total of 912 DEG were identified, and the polyunsaturated (n = 563) and unsaturated ω-3 (n = 346) FA sums groups were the most frequently observed. The COE analyses identified three modules, of which the blue module (n = 1776) was correlated with eight of 14 FA phenotypes. Also, 759 DCO genes were listed, and the oleic acid (n = 358) and monounsaturated fatty acids sum (n = 120) were the most frequent. Furthermore, 243 and 13, 319 and seven, and 173 and 12 gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were enriched respectively for the DEG, COE, and DCO analyses. Combining the results, we highlight the unexplored GIPC2, ASB5, and PPP5C genes in cattle. Besides LIPE and INSIG2 genes in COE modules, the ACSL3, ECI1, DECR2, FITM1, and SDHB genes were signaled in at least two analyses. These findings contribute to understand the genetic mechanisms underlying the beef FA profile in Nellore beef cattle finished in feedlot. School of Agricultural and Veterinary Sciences (FCAV) São Paulo State University (UNESP) School of Veterinary Medicine and Animal Science (FMVZ) University of São Paulo (USP) Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture & Food School of Veterinary Medicine and Animal Science (FMVZ) São Paulo State University (UNESP) School of Agricultural and Veterinary Sciences (FCAV) São Paulo State University (UNESP) School of Veterinary Medicine and Animal Science (FMVZ) São Paulo State University (UNESP)

Made available in DSpace on 2020-12-12T01:51:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The aim of this study was to evaluate the genomic predictions using the single-step genomic best linear unbiased predictor (ssGBLUP) method based on SNPs and haplotype markers associated with beef fatty acids (FAs) profile in Nelore cattle. The data set contained records from 963 Nelore bulls finished in feedlot (±90 days) and slaughtered with approximately 24 months of age. Meat samples from the Longissimus dorsi muscle were taken for FAs profile measurement. FAs were quantified by gas chromatography using a SP-2560 capillary column. Animals were genotyped with the high-density SNP panel (BovineHD BeadChip assay) containing 777,962 markers. SNPs with a minor allele frequency and a call rate lower than 0.05 and 0.90, respectively, monomorphic, located on sex chromosomes, and with unknown position were removed from the data set. After genomic quality control, a total of 469,981 SNPs and 892 samples were available for subsequent analyses. Missing genotypes were imputed and phased using the FImpute software. Haplotype blocks were defined based on linkage disequilibrium using the Haploview software. The model to estimate variance components and genetic parameters and to predict the genomic values included the random genetic additive effects, fixed effects of the contemporary group and the age at slaughter as a linear covariate. Accuracies using the haplotype-based approach ranged from 0.07 to 0.31, and those SNP-based ranged from 0.06 to 0.33. Regression coefficients ranged from 0.07 to 0.74 and from 0.08 to 1.45 using the haplotype- and SNP-based approaches, respectively. Despite the low to moderate accuracies for the genomic values, it is possible to obtain genetic progress trough selection using genomic information based either on SNPs or haplotype markers. The SNP-based approach allows less biased genomic evaluations, and it is more feasible when taking into account the computational and operational cost underlying the haplotypes inference. Faculdade de Ciências Agrárias e Veterinárias Departamento de Zootecnia Universidade Estadual Paulista Júlio de Mesquita Filho UNESP Faculdade de Zootecnia e Engenharia de Alimentos Departamento de Nutrição e Produção Animal Universidade de São Paulo Zoetis Department of Animal Sciences Purdue University Faculdade de Zootecnia e Engenharia de Alimentos Departamento de Medicina Veterinária Universidade de São Paulo Faculdade de Ciências Agrárias e Veterinárias Departamento de Zootecnia Universidade Estadual Paulista Júlio de Mesquita Filho UNESP FAPESP: 2009/16118-5 FAPESP: 2015/25304-8 FAPESP: 2016/24085-3

Made available in DSpace on 2022-04-29T08:45:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-11-01 This study aimed to identify structural variations in the form of runs of homozygosity (ROH) and copy number variants (CNVs) in the genome of the Brazilian Senepol cattle and to better explore the potential biological functions of the genes located within such regions. A total of 140 animals were genotyped with the GeneSeek® Genomic Profiler™ Bovine 50 K. Autosomal ROH and CNVs were detected after appropriated quality control. A total of 5,531 ROH were identified, with an average number of 40.37 per animal and an average length of 5.09 Mb. BTA1 had the greatest number of ROH per chromosome (n = 458), while BTA20 displayed the greatest fraction of the chromosome covered with ROH (22.06%). A total of 181 CNVs were identified, with an average length size of 184.67 kb, with values ranging from 26.61 to 334.48 kb. A total of 16 CNV regions (CNVRs) were seen distributed among eleven autosomes, and the largest number of CNVRs (n = 4) was described on BTA12. Autozygosity islands were identified using an outlier approach, and none of them overlapped with CNVRs. Our study revealed that the limited genetic basis together with the narrow number of imported animals to disseminate the breed might have strongly contributed to the low effective population size and the high genomic autozygosity proportion described in this population. The functional enrichment analysis revealed several significant terms (p

Made available in DSpace on 2022-04-29T08:39:28Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-01-01 This study aimed to investigate the prediction ability for growth and maternal traits using different low-density customized SNP arrays selected by informativeness and distribution of markers across the genome employing single-step genomic BLUP (ssGBLUP). Phenotypic records for adjusted weight at 210 and 450 days of age were utilized. A total of 945 animals were genotyped with high-density chip, and 267 individuals born after 2008 were selected as validation population. We evaluated 11 scenarios using five customized density arrays (40 k, 20 k, 10 k, 5 k and 2 k) and the HD array was used as desirable scenario. The GEBV predictions and BIF (Beef Improvement Federation) accuracy were obtained with BLUPF90 family programs. Linear regression was used to evaluate the prediction ability, inflation, and bias of GEBV of each customized array. An overestimation of partial GEBVs in contrast with complete GEBVs and increase of BIF accuracy with the density arrays diminished were observed. For all traits, the prediction ability was higher as the array density increased and it was similar with customized arrays higher than 10 k SNPs. Level of inflation was lower as the density array increased of and was higher for MW210 effect. The bias was susceptible to overestimation of GEBVs when the density customized arrays decreased. These results revealed that the BIF accuracy is sensible to overestimation using low-density customized arrays while the prediction ability with least 10,000 informative SNPs obtained from the Illumina BovineHD BeadChip shows accurate and less biased predictions. Low-density customized arrays under ssGBLUP method could be feasible and cost-effective in genomic selection. Departamento de Zootecnia Faculdade de Ciências Agrarias e Veterinárias Universidade Estadual Paulista (Unesp) Departamento de Medicina Veterinária Faculdade de Zootecnia e Engenharia de Alimentos Universidade de São Paulo (Usp) Departamento de Genética y Mejoramiento Animal Facultad de Veterinaria Universidad de La República Instituto Nacional de Investigación Agropecuaria (INIA) Associação Nacional de Criadores e Pesquisadores (ANCP) Departamento de Zootecnia Faculdade de Ciências Agrarias e Veterinárias Universidade Estadual Paulista (Unesp)

BackgroundPotential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs.ResultsThe systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR ConclusionHere we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.

Made available in DSpace on 2022-04-29T08:32:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-02-01 Gene–gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene–gene interactions using the empirical Hilbert–Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where (Formula presented.) were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ((Formula presented.) < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP–SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products. Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no Instituto de Zootecnia – Centro de Pesquisa em Bovinos de Corte Rodovia Carlos Tonanni, Km94 Faculdade de Zootecnia e Engenharia de Alimentos Núcleo de Apoio à Pesquisa em Melhoramento Animal Biotecnologia e Transgenia Universidade de São Paulo, Rua Duque de Caxias Norte, 225 Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no

This study was conducted to characterize metabolic differences between high feed efficiency (HFE) and low feed efficiency (LFE) chickens to investigate why feed efficient chickens are more susceptible to muscle abnormalities such as wooden breast disease. Gene expression profiles were generated by RNA sequencing of pectoralis major muscle samples from 10 HFE and 13 LFE broiler chickens selected from a modern broiler population. Metabolism-associated differentially expressed genes were identified and interpreted by Ingenuity Pathway Analysis and literature mining. Our RNA-seq data indicate decreased glycolytic capacity, increased fatty acid uptake, mitochondrial oxidation of fatty acids, and several other metabolic alterations in the pectoralis major muscle of HFE chickens. We also quantified glycogen content of the pectoralis major muscle and found that the HFE chickens had a significantly (P ≤ 0.05) lower glycogen content. Collectively, this study indicates extensive metabolic differences in the pectoralis major muscle between HFE and LFE chickens and helps identify metabolic features of susceptibility to muscle disorders in modern broiler chickens.

The aim of this study was to estimate genetic parameters and identify genomic regions associated with carcass traits obtained by ultrasound and visual scores in Nellore cattle. Data from ~66,000 animals from the National Association of Breeders and Researchers (ANCP) were used. The variance components for backfat thickness, rump fat thickness and Longissimus muscle area (LMA) were estimated considering a linear model whereas a threshold model for body structure (BS), finishing precocity (FP) and musculature (MS) traits. The SNP solutions were estimated using the ssGBLUP approach by considering windows of 10 consecutive SNPs. Regions that accounted for more than 1.0% of the additive genetic variance were used. Genes identified within the significant windows, such as FOXA3, AP2S1, FKRP, NPASI and ATP6V1G1, were found to be related with MS, while OMA1 and FFGY with BS and FP traits. The PLTP, TNNC2 and GPAT2 genes were found in the regions associated with LMA, as well as TKT, FNDC5 and CHRND can strongly be related with fat deposition. Gene enrichment analysis revealed processes that might be directly influenced the organism growth and development. These results should help to better understand the genetic and physiological mechanisms regulating growth and body composition, muscle tissue development and subcutaneous fat expression, and this information might be useful for future genomic studies in Nellore cattle.

We evaluated a novel frame score system for Nellore cattle raised on pasture (Guimarães et al., 2020 J, Anim. Sci. 98 (Suppl. 4)). Growth traits included age-adjusted weights (kg) at birth (W0), 120 (W120), 210 (W210) and 450 (W450) days of age, and adult weight (AW). Carcass traits (by ultrasound) included ribeye area (REA, cm2), 12th-13th rib backfat (BF, mm), rump fat (RF, mm), and intramuscular fat (IMF, %). Feed efficiency traits included residual feed intake (RFI, kg of DM/d) and DM intake (DMI, kg/d). We applied the previously developed equations (that also include hip height (HH, cm) and age to 12,049 records from the National Association of Breeders and Researchers (ANCP) database:FSmales= -20.35 + 0.1305*REA + 0.2633*BF - 0.5901*RF+ 0.1139*HH + 0.0056*AGEFSfemales = -11.87 + 0.1316*REA - 0.2457*BF - 0.6218*RF + 0.1139*HH + 0.0009507*AGEThe (co)variance components and genetic parameters were estimated using a linear animal model or a threshold animal model depending on the trait. The heritability estimate for frame score was moderate (0.30). Estimated genetic correlations were moderate for growth traits (W0, 0.51; W120, 0.41; W210, 0.35; W450, 0.29; AW, 0.39). Estimated genetic correlations for carcass and efficiency traits ranged from low to high (REA, 0.50; BF, -0.25; RF, -0.84; IMF, -0.15; DMI, 0.29; RFI, 0.10). The estimates support the notion that larger frame animals are heavier, leaner and later maturing, and less feed efficient. The new frame score may be a useful tool for genetic selection of animals that are best suited to their environment.

Made available in DSpace on 2022-04-29T08:31:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-09-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The multiple sire system (MSS) is a common mating scheme in extensive beef production systems. However, MSS does not allow paternity identification and lead to inaccurate genetic predictions. The objective of this study was to investigate the implementation of single-step genomic BLUP (ssGBLUP) in different scenarios of uncertain paternity in the evaluation for 450-day adjusted liveweight (W450) and age at first calving (AFC) in a Nellore cattle population. To estimate the variance components using BLUP and ssGBLUP, the relationship matrix (A) with different proportions of animals with missing sires (MS) (scenarios 0, 25, 50, 75, and 100% of MS) was created. The genotyped animals with MS were randomly chosen, and ten replicates were performed for each scenario and trait. Five groups of animals were evaluated in each scenario: PHE, all animals with phenotypic records in the population; SIR, proven sires; GEN, genotyped animals; YNG, young animals without phenotypes and progeny; and YNGEN, young genotyped animals. The additive genetic variance decreased for both traits as the proportion of MS increased in the population when using the regular REML. When using the ssGBLUP, accuracies ranged from 0.13 to 0.47 for W450 and from 0.10 to 0.25 for AFC. For both traits, the prediction ability of the direct genomic value (DGV) decreased as the percentage of MS increased. These results emphasize that indirect prediction via DGV of young animals is more accurate when the SNP effects are derived from ssGBLUP with a reference population with known sires. The ssGBLUP could be applied in situations of uncertain paternity, especially when selecting young animals. This methodology is shown to be accurate, mainly in scenarios with a high percentage of MS. Grupo de Melhoramento Animal Faculdade de Ciências Agrárias E Veterinárias Universidade Estadual Paulista Júlio de Mesquita Filho Zoetis Faculdade de Medicina Veterinária E Zootecnia Universidade de São Paulo Associação Nacional de Criadores E Pesquisadores (ANCP) Instituto Nacional de Pesquisa Agropecuária (INIA) University of Georgia Grupo de Melhoramento Animal Faculdade de Ciências Agrárias E Veterinárias Universidade Estadual Paulista Júlio de Mesquita Filho FAPESP: 2013/25910-0

Made available in DSpace on 2021-06-25T10:34:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-11-01 The reduction of age at puberty in young bulls is an important issue to reduce the growing phase and promote substantial savings in production cost as well as to reduce the generation interval. This study aims to estimate genetic parameters for age at puberty in males (APM), growth, carcass, and reproductive-related traits in young Nelore bulls. Additionally, the direct and correlated response for growth, reproductive, and carcass traits were also estimated when a selection was applied for APM in such young bulls. APM was determined through evaluations carried out after weaning, using information from andrological clinical examination, ultrasound records, and scrotal circumference measurements. Records from 181,345 Nelore animals born between 2010 to 2017 were used. These animals were calves from 5,257 sires and 50,742 dams, and belonged to 18 farms located in the Midwest, Southeast, Northeast, and North regions of Brazil. The relationship matrix was built using information from 265,813 animals. The covariance components and the genetic parameters for APM, adjusted scrotal circumference at 365 (SC365) and 450 (SC450) days of age, adjusted weight at 210 (W210) and 450 (W450) days of age, age at first calving (AFC), ribeye area (REA), subcutaneous fat thickness (SFT), and rump fat thickness (RFT) were estimated using a linear animal model. A threshold animal model was used for Stayability (STAY) and early heifer pregnancy (PP30) traits. The heritabilities obtained were: 0.30 (APM), 0.33 (SC365), 0.37 (SC450), 0.14 (W210), 0.26 (W450), 0.08 (AFC), 0.29 (PP30), 0.19 (STAY), 0.32 (REA), 0.19 (SFT), and 0.28 (RFT). The genetic correlations estimates between APM and growth, reproductive, and carcass related traits were: -0.39 (SC365), -0.58 (SC450), -0.01 (W210), 0.08 (W450), 0.30 (AFC), -0.24 (PP30), 0.35 (STAY), 0.08 (REA), -0.05 (SFT), and -0.30 (RFT). The APM is a new approach to evaluate early sexual precocity in young bulls, and it would allow better identification of young candidates when compared to those selected based on scrotal circumference measures. Genetic progress is expected for APM in young bulls since it would favor the heifer's sexual precocity together with the dam's longevity without impacting growth and carcass traits. The results of this study encourage the use of male sexual precocity trait assisted by genomic selection to improve the genetic evaluation reliability of young bulls. Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias (FCAV) Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP) Laboratório de Reprodução Animal Faculdade de Medicina Veterinária e Zootecnia (FAMEZ) Universidade Federal de Mato Grosso do Sul (UFMS) Faculdade de Zootecnia e Engenharia de Alimentos Universidade de São Paulo Departamento de Medicina Veterinária PROCRIAR Assistência Veterinária Departamento de Produção Animal Universidade Federal de Goiás Associação Nacional dos Criadores e Pesquisadores (ANCP) Faculdade de Medicina Veterinária e Zootecnia Universidade de São Paulo Departamento de Nutrição e Produção Animal Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias (FCAV) Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP)

Made available in DSpace on 2020-12-10T19:45:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) National Institute of Agricultural research (INIA) of Uruguay The objective of this study was to evaluate the effect of nutritional management during rearing and finishing phases on beef fatty acid composition, and carcass and beef quality traits of Hereford cattle. The study used 240 castrated male calves weaned at 8 months of age, and with an average weight of 170 +/- 17 kg. After weaning, the experiment was divided in to three phases in a 4 x 2 factorial design: a 93-day winter period with four treatment groups (on pasture or in feedlot and at high or low feeding levels); a 196-day compensatory-growth phase on pasture; and a finishing phase either on pasture or in feedlot. Animals were slaughtered when each group attained a mean liveweight of 500 kg. The winter growth x finishing management interaction significantly affected hot carcass weight (P = 0.0029). There was no differences observed for feedlot-finished steers, but for pasture-finished steers, those pasture-reared had higher hot carcass weight (kg) than those feedlot-reared (low pasture 256.30 +/- 1.60, high pasture 253.72 +/- 1.60, low feedlot 249.85 +/- 1.66, high feedlot 247.60 +/- 1.62). Feedlot-finished steers showed higher (P < 0.05) mean values than pasture-finished steers for ribeye area (55.61 +/- 0.69 cm(2) vs 53.18 cm(2)), backfat thickness (8.62 +/- 0.32 mm vs 6.21 mm), marbling score (237.97 +/- 13.06 vs 171.70) and final pH (5.53 +/- 0.02 vs 5.48). Additionally, feedlot-finished steers raised in feedlot during the winter-growth period displayed the heaviest hindquarter cuts. Meat from pasture-finished steers had lower (P < 0.05) shear-force values than from feedlot-finished cattle (2.95 +/- 0.18 vs 3.66 +/- 0.17 kg), and when reared on either high or low pasture during winter-growth, they showed the highest (P < 0.05) conjugated linoleic acid (cis-9, trans-11) and n-3 polyunsaturated fatty acid concentrations. In conclusion, growing and finishing cattle on pasture improved the carcass yield of retail cuts because of low fat concentration, and improved the nutritional and health value of the beef fatty acid profile. Univ Sao Paulo, Fac Zootecnia & Engn Alimentos, BR-13635900 Pirassununga, SP, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Zootecnia, BR-14884900 Jaboticabal, SP, Brazil INIA, Estn Expt Estanzuela, Colonia 70000, Uruguay Conselho Nacl Desenvolvimento Cient & Tecnol, BR-71605001 Brasilia, DF, Brazil Inst Nacl Ciencia & Tecnol Ciencia Anim, BR-36570000 Vicosa, MG, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Zootecnia, BR-14884900 Jaboticabal, SP, Brazil FAPESP: 2016/22022-4 FAPESP: 2011/21241-0

The aim of this study was to assess the distribution of runs of homozygosity (ROH) and autozygosity islands in the composite Montana Tropical® beef cattle to explore hotspot regions which could better characterize the different biological types within the composite breed. Montana animals (n = 1,436) were genotyped with the GGP-LD BeadChip (~30,000 markers). ROH was identified in every individual using the plink v1.90 software. Medium and long ROH prevailed in the genome, which accounted for approximately 74% of all ROH detected. On an average, 2.0% of the genome was within ROH, agreeing with the pedigree-based inbreeding coefficient. The Montana cattle with a higher proportion of productive breed types showed the highest number of autozygosity islands (n = 17), followed by those with a higher proportion of breeds adapted to tropical environments (n = 15). Enriched terms (p

Frame score systems developed for Bos taurus breeds do not translate well for Bos indicus breeds, as these tend to be taller. We evaluated a novel frame score system for Nellore cattle raised on pasture [Guimaraes et al., 2020 J, Anim. Sci. 98 (Suppl. 4)]. Traits included adjusted scrotal circumference (cm) at 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC, d), early heifer pregnancy (EHP, % calving as two-year-olds), stayability (STAY, % of cows remaining in the herd over 76 months of age, calving at least three times), and accumulated productivity (AP, kg of calf weaned per cow per year). In this study, we applied the previously developed equations (that also include hip height (HH, cm) and age to 12,049 records from the National Association of Breeders and Researchers (ANCP) database:FSmales= -20.35 + 0.1305*REA + 0.2633*BF - 0.5901*RF + 0.1139*HH + 0.0056*AGEFSfemales = -11.87 + 0.1316*REA - 0.2457*BF - 0.6218*RF + 0.1139*HH + 0.0009507*AGEThe (co)variance components and genetic parameters were estimated using a linear animal model or a threshold animal model depending on the trait. The heritability estimate for frame score was moderate (0.30). Estimated genetic correlations for reproductive traits were low to moderate (SC365, 0.06; SC450, 0.04; AFC, 0.18; EHP, -0.24; STAY, 0.06; AP, 0.25). The estimates support the notion that larger frame animals are later maturing but have greater lifetime productivity. The new frame score may be a useful tool for genetic selection of animals that are best suited to their environment.

Summary This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (FROH) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (FPED). The better results of FROH suggest that FROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.

The aim of this study was to assess the distribution of runs of homozygosity (ROH) and autozygosity islands in the composite Montana Tropical

The objective of this study was to investigate the application of BLUP and single step genomic BLUP (ssGBLUP) models in different scenarios of paternity uncertainty with different strategies of scaling the G matrix to match the A22 matrix, using simulated data for beef cattle. Genotypes, pedigree, and phenotypes for age at first calving (AFC) and weight at 550 days (W550) were simulated using heritabilities based on real data (0.12 for AFC and 0.34 for W550). Paternity uncertainty scenarios using 0, 25, 50, 75, and 100% of multiple sires (MS) were studied. The simulated genome had a total length of 2,333 cM, containing 735,293 biallelic markers and 7,000 QTLs randomly distributed over the 29 BTA. It was assumed that QTLs explained 100% of the genetic variance. For QTL, the amount of alleles per loci randomly ranged from two to four. The BLUP model that considers phenotypic and pedigree data, and the ssGBLUP model that combines phenotypic, pedigree and genomic information were used for genetic evaluations. Four ways of scaling the mean of the genomic matrix (G) to match to the mean of the pedigree relationship matrix among genotyped animals (A22) were tested. Accuracy, bias, and inflation were investigated for five groups of animals: ALL = all animals; BULL = only bulls; GEN = genotyped animals; FEM = females; and YOUNG = young males. With the BLUP model, the accuracies of genetic evaluations decreased for both traits as the proportion of unknown sires in the population increased. The EBV accuracy reduction was higher for GEN and YOUNG groups. By analyzing the scenarios for YOUNG (from 0 to 100% of MS), the decrease was 87.8 and 86% for AFC and W550, respectively. When applying the ssGBLUP model, the accuracies of genetic evaluation also decreased as the MS in the pedigree for both traits increased. However, the accuracy reduction was less than those observed for BLUP model. Using the same comparison (scenario 0 to 100% of MS), the accuracies reductions were 38 and 44.6% for AFC and W550, respectively. There were no differences between the strategies for scaling the G matrix for ALL, BULL, and FEM groups under the different scenarios with missing pedigree. These results pointed out that the uninformative part of the A22 matrix and genotyped animals with paternity uncertainty did not influence the scaling of G matrix. On the basis of the results, it is important to have a G matrix in the same scale of the A22 matrix, especially for the evaluation of young animals in situations with missing pedigree information. In these situations, the ssGBLUP model is an appropriate alternative to obtain a more reliable and less biased estimate of breeding values, especially for young animals with few or no phenotypic records. For accurate and unbiased genomic predictions with ssGBLUP, it is necessary to assure that the G matrix is compatible with the A22 matrix, even in situations with paternity uncertainty. Made available in DSpace on 2017-12-21T23:28:05Z (GMT). No. of bitstreams: 1 ApplicationofsinglestepgenomicBLUPunderdifferentuncertainpaternityscenariosusingsimulateddata..pdf: 782402 bytes, checksum: ec6960b2579b83b77b9aca6119ae98c8 (MD5) Previous issue date: 2017-12-21

Made available in DSpace on 2019-10-06T16:51:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-11-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The aim of the present study was to compare the predictive ability of SNP-BLUP model using different pseudo-phenotypes such as phenotype adjusted for fixed effects, estimated breeding value, and genomic estimated breeding value, using simulated and real data for beef FA profile of Nelore cattle finished in feedlot. A pedigree with phenotypes and genotypes of 10,000 animals were simulated, considering 50% of multiple sires in the pedigree. Regarding to phenotypes, two traits were simulated, one with high heritability (0.58), another with low heritability (0.13). Ten replicates were performed for each trait and results were averaged among replicates. A historical population was created from generation zero to 2020, with a constant size of 2000 animals (from generation zero to 1000) to produce different levels of linkage disequilibrium (LD). Therefore, there was a gradual reduction in the number of animals (from 2000 to 600), producing a “bottleneck effect” and consequently, genetic drift and LD starting in the generation 1001 to 2020. A total of 335,000 markers (with MAF greater or equal to 0.02) and 1000 QTL were randomly selected from the last generation of the historical population to generate genotypic data for the test population. The phenotypes were computed as the sum of the QTL effects and an error term sampled from a normal distribution with zero mean and variance equal to 0.88. For simulated data, 4000 animals of the generations 7, 8, and 9 (with genotype and phenotype) were used as training population, and 1000 animals of the last generation (10) were used as validation population. A total of 937 Nelore bulls with phenotype for fatty acid profiles (Sum of saturated, monounsaturated, omega 3, omega 6, ratio of polyunsaturated and saturated and polyunsaturated fatty acid profile) were genotyped using the Illumina BovineHD BeadChip (Illumina, San Diego, CA) with 777,962 SNP. To compare the accuracy and bias of direct genomic value (DGV) for different pseudo-phenotypes, the correlation between true breeding value (TBV) or DGV with pseudo-phenotypes and linear regression coefficient of the pseudo-phenotypes on TBV for simulated data or DGV for real data, respectively. For simulated data, the correlations between DGV and TBV for high heritability traits were higher than obtained with low heritability traits. For simulated and real data, the prediction ability was higher for GEBV than for Yc and EBV. For simulated data, the regression coefficient estimates (b (Yc,DGV) ), were on average lower than 1 for high and low heritability traits, being inflated. The results were more biased for Yc and EBV than for GEBV. For real data, the GEBV displayed less biased results compared to Yc and EBV for SFA, MUFA, n-3, n-6, and PUFA/SFA. Despite the less biased results for PUFA using the EBV as pseudo-phenotype, the b (Yi,DGV estimates obtained for the different pseudo-phenotypes (Yc, EBV and GEBV) were very close. Genomic information can assist in improving beef fatty acid profile in Zebu cattle, since the use of genomic information yielded genomic values for fatty acid profile with accuracies ranging from low to moderate. Considering both simulated and real data, the ssGBLUP model is an appropriate alternative to obtain more reliable and less biased GEBVs as pseudo-phenotype in situations of missing pedigree, due to high proportion of multiple sires, being more adequate than EBV and Yc to predict direct genomic value for beef fatty acid profile. Faculdade de Ciências Agrárias e Veterinárias UNESP Faculdade de Medicina Veterinária e Zootecnia USP Faculdade de Zootecnia e Engenharia de Alimentos USP Instituto Nacional de Investigación Agropecuaria Faculdade de Ciências Agrárias e Veterinárias UNESP FAPESP: 2009/16118-5 FAPESP: 2011/2141-0

The aim of this study was to estimate genetic parameters for different precocious calving criteria and their relationship with reproductive, growth, carcass and feed efficiency in Nellore cattle using the single-step genomic BLUP. The reproductive traits used were probability of precocious calving (PPC) at 24 (PPC24), 26 (PPC26), 28 (PPC28) and 30 (PPC30) months of age, stayability (STAY) and scrotal circumference at 455 days of age (SC455). Growth traits such as weights at 240 (W240) and 455 (W455) days of age and adult weight (AW) were used. Rib eye area (REA), subcutaneous fat thickness (SFT), rump fat thickness (RFT) and residual feed intake (RFI) were included in the analyses. The estimation of genetic parameters was performed using a bi-trait threshold model including genomic information in a single-step approach. Heritability for PPC traits was moderate to high (0.29-0.56) with highest estimates for PPC24 (0.56) and PPC26 (0.50). Genetic correlation estimates between PPC and STAY weakened as a function of calving age. Correlation with SC455, growth and carcass traits were low (0.25-0.31; -0.22 to 0.04; -0.09 to 0.18, respectively), the same occurs with RFI (-0.09 to 0.08), this suggests independence between female sexual precocity and feed efficiency traits. The results of this study encourage the use of PPC traits in Nellore cattle because the selection for such trait would not have a negative impact on reproductive, growth, carcass and feed efficiency indicator traits. Stayability for sexual precocious heifers (PPC24 and PPC26) must be redefined to avoid incorrectly phenotype assignment.

Made available in DSpace on 2018-12-11T17:17:17Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-09 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Background: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). Results: ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1-2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from -0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. Conclusions: Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. UNESP Univ Estadual Paulista Júlio de Mesquita Filho Faculdade de Ciências Agrárias e Veterinárias Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Faculdade de Ciências Agrárias e Veterinárias Departamento de Ciências Exatas Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ) Universidade Federal de Santa Catarina Centro de Ciências Agrárias Departamento de Zootecnia e Desenvolvimento Rural Embrapa Gado de Leite Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos Beef Improvement Opportunities University of Guelph Centre for Genetic Improvement of Livestock, ABScBG UNESP Univ Estadual Paulista Júlio de Mesquita Filho Faculdade de Ciências Agrárias e Veterinárias Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Faculdade de Ciências Agrárias e Veterinárias Departamento de Ciências Exatas

Made available in DSpace on 2018-12-11T17:16:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The aim of the present study was to analyze the distribution of CNV regions (CNVRs) as well as to address hypothesis about the natural/artificial selection process in Nellore cattle. A total of 399,361 CNVs were identified, using the PennCNV algorithm, in 3794 Nellore cattle (Bos taurus indicus) genotyped with the Bovine HD BeadChip array. The default quality control was applied and 2902 samples and 195,873 CNVs remained. The medium CNV length size was 54,744 bp with a maximum of 870,000 bp and a minimum of 3000 bp. The CNVRs were generated by overlapping the 195,873 identified CNVs using the CNVRuler program. There was a higher incidence of CNVRs on BTA19 (24.26%), BTA23 (18.68%), and BTA25 (18.05%). The chromosomes that showed a lower incidence of CNVR were BTA29 (1.63%), BTA13 (9.72%), and BTA8 (9.72%). According to the type, 38.5%, 28.5% and 33.0% of the CNVRs were characterized as insertion, deletion and mixed (insertion and deletion in the same region), respectively. The 9805 CNVR estimated in the present study covered approximately 13.05% of the cattle genome (UMD_3.1, 2,649,685,063 bp) and overlapped with 5495 genes. These genes have functions described as involved in biological processes that might be related to the environmental adaptation of the subspecies to tropical areas, such as regulation of vasodilatation, immune system response, hair follicle morphogenesis, among others. This study confirms the existence of large structural variations in the Nellore cattle genome and contributes to understanding the differences between cattle subspecies. Besides, it can also work as a guideline for future studies in which structural variations are present. Department of Animal Science State University of São Paulo FCAV – UNESP, Via de acesso Prof. Paulo Donato Castellane Universidade Federal da Bahia (UFBA) Departamento de Zootecnia Department of Animal Science University of São Paulo University of São Paulo Faculdade de Medicina Veterinária e Zootecnia Department of Nutrition and Animal Production Department of Animal Science State University of São Paulo FCAV – UNESP, Via de acesso Prof. Paulo Donato Castellane FAPESP: #2009/16118-5 FAPESP: #2011/21241-0

Made available in DSpace on 2018-12-11T17:36:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-05-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The aim of this study was to analyze the association between the copy number variation regions (CNVRs) and fatty acid profile phenotypes for saturated (SFA), monosaturated (MUFA), polyunsaturated (PUFA), ω6 and ω3 fatty acids, PUFA/SFA and ω6/ω3 ratios, as well as for their sums, in Nellore cattle (Bos primigenius indicus). A total of 963 males were finished in feedlot and slaughtered with approximately 2 years of age. Animals were genotyped with the BovineHD BeadChip (Illumina Inc., San Diego, CA, USA). The copy number variation (CNV) detection was performed using the PennCNV algorithm. Log R ratio (LRR) and allele B frequency (BAF) were used to estimate the CNVs. The association analyses were done using the CNVRuler software and applying a logistic regression model. The phenotype was adjusted using a linear model considering the fixed effects of contemporary group and the animal age at slaughter. The fatty acid profile was analyzed on samples of longissimus thoracis muscle using gas chromatography with a 100-m capillary column. For the association analysis, the adjusted phenotypic values were considered for the traits, while the data was adjusted for the effects of the farm and year of birth, management groups at birth, weaning, and superannuation. A total of 186 CNVRs were significant for SFA (43), MUFA (42), PUFA (66), and omega fatty acid (35) groups, totaling 278 known genes. On the basis of the results, several genes were associated with several fatty acids of different saturations. Olfactory receptor genes were associated with C12:0, C14:0, and C18:0 fatty acids. The SAMD8 and BSCL2 genes, both related to lipid metabolic process, were associated with C12:0. The RAPGEF6 gene was found to be associated with C18:2 cis-9 cis-12 n-6, and its function is related to regulation of GTPase activity. Among the results, we highlighted the olfactory receptor activity (GO:0004984), G-protein-coupled receptor activity (GO:0004930), potassium:proton antiporter activity (GO:0015386), sodium:proton antiporter activity (GO:0015385), and odorant-binding (GO:0005549) molecular functions. A large number of genes associated with fatty acid profile within the CNVRs were identified in this study. These findings must contribute to better elucidate the genetic mechanism underlying the fatty acid profile of intramuscular fat in Nellore cattle. Faculdade de Ciências Agrárias e Veterinárias UNESP Faculdade de Medicina Veterinária e Zootecnia USP Faculdade de Ciências Agrárias e Veterinárias UNESP FAPESP: 2009/16118-5 FAPESP: 2011/2141-0 FAPESP: 2013/11853-4

Made available in DSpace on 2019-10-04T12:31:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-10-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) This study was carried out to estimate the heritability and genetic correlations between adjusted weights at 210 (W210) and 450 (W450) days of age, scrotal circumference adjusted at 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), probability of precocious calving (PPC), stayability (STAY), ribeye area (REA), subcutaneous backfat thickness (BF), and rump fat (RF) traits. The covariance components and genetic parameters for all traits but PPC and STAY were estimated considering a linear animal model, for the remaining traits a threshold animal model was used. The single-step genomic BLUP (ssGBLUP) procedure was used for all traits, and the correlation estimates were obtained by two-traits analysis. The heritability estimated by single-trait analysis were 0.21 +/- 0.01, 0.43 +/- 0.01, 0.47 +/- 0.02, 0.52 +/- 0.02, 0.11 +/- 0.01, 0.12 (0.07-0.16), 0.37 (0.26-0.38), 0.33 +/- 0.02, 0.17 +/- 0.01 and 0.33 +/- 0.02 for W210, W450, SC365, SC450, AFC, PPC, STAY, REA, BF and RF, respectively. Growth traits (W210 and W450) showed high (0.95) genetic correlation with one another, moderate (0.30 to 0.66) with REA and scrotal circumferences, and low (0.07 to 0.20) with female reproductive traits (AFC, PPC, and STAY) and fat carcass indicator traits (BF and RF). Female reproductive traits displayed moderate (0.29 to 0.52) genetic correlations with male reproductive traits, and varied from low to moderate (0.02 to 0.35) with carcass traits. Additionally, carcass traits exhibited low to moderate (0.02 to 0.48) genetic correlations with all traits, except for the genetic correlation between BF and RF (0.73). Hence, higher genetic gains by direct selection would be obtained for W450, SC365, SC450, STAY, REA, and RF. Selection to increase growth traits might increase carcass yield and scrotal circumference, and it would not affect carcass fat content, precocity, and cow longevity indicator traits. The results of this study encourage the use of PPC in Nelore cattle since the selection for such trait would improve the productivity and longevity of the cows. The inclusion of carcass quality indicator traits such as BF or RF in selection indices would increase the genetic gain for carcass grade, but it will require further studies to estimate the economic value of these traits. Univ Estadual Paulista, Dept Zootecnia, Jaboticabal, Brazil Univ Nacl La Plata, Dept Prod Anim, La Plata, Buenos Aires, Argentina Assoc Nacl Criadores & Pesquisadores, Ribeirao Preto, Brazil Brazilian Agr Res Corp, Brasilia, DF, Brazil Zoetis Genet, Kalamazoo, MI USA Univ Sao Paulo, Fac Med Vet & Zootecnia, Dept Nutr & Prod Anim, Pirassununga, Brazil Univ Sao Paulo, Fac Med Ribeirao Preto, Ribeirao Preto, Brazil Univ Wisconsin, Dept Anim Sci, Madison, WI 53706 USA Univ Estadual Paulista, Dept Zootecnia, Jaboticabal, Brazil FAPESP: 2016/22751-6

Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p

Made available in DSpace on 2018-11-26T17:44:35Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) The aim of the present study was to estimate covariance components and genetic parameters for beef fatty acid (FA) composition of intramuscular fat in the longissimus thoracis muscle in Nelore bulls finished in feedlot. Twenty-two FAs were selected. The heritability estimates for individual FAs ranged from 0.01 to 0.35. The heritability estimates for myristic (0.25 +/- 0.09), palmitic (0.18 +/- 0.07), oleic (0.28 +/- 0.09), linoleic (0.16 +/- 0.06) and alpha-linolenic (0.35 +/- 0.10) FAs were moderate. Stearic, elaidic, palmitoleic, vaccenic, conjugated linoleic acid, docosahexanoic, eicosatrienoic and arachidonic FAs had heritability estimates below 0.15. The genetic-correlation estimates between the individual saturated FAs (SFAs) were low and negative between myristic and stearic FAs (-0.22 +/- 0.84), moderate between palmitic and myristic FAs (0.58 +/- 0.56) and negative between palmitic and stearic FAs (-0.69 +/- 0.45). The genetic correlations between the individual long-chain polyunsaturated FAs (PUFAs) were positive and moderate (>0.30). However, the genetic-correlation estimates between long-chain PUFAs and alpha-linolenic acid were low (

Made available in DSpace on 2019-10-04T12:32:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-11-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with maternal related traits in Santa Ines sheep breed adapted to tropical climate. Phenotypic records for maternal efficiency (ME), metabolic maternal efficiency (MME), twin lambing (TL), adult weight (AW), metabolic adult weight (MAW), and body condition score (BCS) from 1333 ewes from Santa Ines breed were used. A total of 576 animals were genotyped with the Ovine SNP12k BeadChip (Illumina, Inc.), that contains 12,785 bialleleic SNP markers. The variance components were estimated using a single trait animal model by single step genomic BLUP procedure. For AW, MAW, BCS, ME, MME and TL the mean values were 50.30 (+/- 9.76), 19.2 (+/- 2.33), 2.76 (+/- 0.72), 34.6 (+/- 15.95), 91.8 (+/- 42.52), and 1.27 (+/- 0.44), respectively. The heritabilities estimated were moderate for AW (0.32) and MAW (0.33) and low for BCS (0.04), ME (0.07), MME (0.08), and TL (0.10). A total of 7, 8, 13, 16, 19, and 09 candidate regions for ME, MME, TL, AW, MAW and BCS traits were identified, respectively. AW and MAW had a total of 15 regions in common, while AW and BCS had a common region on chromosome 21. ME and MME had six candidate regions in common, and TL had no common regions with any other features. The maternal indicator traits have genetic variability to respond to selection in Santa Ines breed, and it would be expected higher genetic gain for ewe adult weight when compared to the others studied traits. Several candidate regions related to growth, reproduction, lactation and enviromental adaptability were identified in this study. These candidate regions would give support to identify and select animals with higher maternal efficiency and fitness, and consequently, increase the productivity of Santa Ines sheep. Moreover, the results of this study should help to understand the genetic and physiologic mechanism associated with maternal related traits in Santa Ines breed. Univ Fed Santa Catarina, Dept Zootecnia & Desenvolvimento Rural, Rodovia Admar Gonzaga 1346, BR-88034000 Florianopolis, SC, Brazil Univ Estadual Paulista, Dept Zootecnia, Fac Ciencias Agr & Vet, Via Acesso Prof Paulo Donato Castellane S-no, BR-14884900 Jaboticabal, SP, Brazil Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Crta Coruna,Km 7,5, Madrid 28040, Spain INIA, Ruta 50 Km 12, Colonia, Uruguay Univ Sao Paulo, Fac Zootecnia & Engn Alimentos, Nucleo Apoio Pesquisa Melhoramento Anim Biotecnol, Rua Duque de Caxias Norte 225, BR-13635900 Pirassununga, SP, Brazil Univ Estadual Paulista, Dept Zootecnia, Fac Ciencias Agr & Vet, Via Acesso Prof Paulo Donato Castellane S-no, BR-14884900 Jaboticabal, SP, Brazil FAPESP: 2010/05516-7 FAPESP: 2011/00396-6 FAPESP: 2014/07566-2

Made available in DSpace on 2018-11-28T03:37:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-02-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The objective of this study was to estimate the genetic-quantitative relationships between the beef fatty acid profile with the carcass and meat traits of Nellore cattle. A total of 1826 bulls finished in feedlot conditions and slaughtered at 24 months of age on average were used. The following carcass and meat traits were analysed: subcutaneous fat thickness (BF), shear force (SF) and total intramuscular fat (IMF). The fatty acid (FA) profile of the Longissimus thoracis samples was determined. Twenty-five FAs (18 individuals and seven groups of FAs) were selected due to their importance for human health. The animals were genotyped with the BovineHD BeadChip and, after quality control for single nucleotide polymorphisms (SNPs), only 470,007 SNPs from 1556 samples remained. The model included the random genetic additive direct effect, the fixed effect of the contemporary group and the animal's slaughter age as a covariable. The (co)variances and genetic parameters were estimated using the REML method, considering an animal model (single-step GBLUP). A total of 25 multi-trait analyses, with four traits, were performed considering SF, BF and IMF plus each individual FA. The heritability estimates for individual saturated fatty acids (SFA) varied from 0.06 to 0.65, for monounsaturated fatty acids (MUFA) it varied from 0.02 to 0.14 and for polyunsaturated fatty acids (PUFA) it ranged from 0.05 to 0.68. The heritability estimates for Omega 3, Omega 6, SFA, MUFA and PUFA sum were low to moderate, varying from 0.09 to 0.20. The carcass and meat traits, SF (0.06) and IMF (0.07), had low heritability estimates, while BF (0.17) was moderate. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with BF were 0.04, 0.64 and -0.41, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with SF were 0.29, -0.06 and -0.04, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with IMF were 0.24, 0.90 and -0.67, respectively. The selection to improve meat tenderness in Nellore cattle should not change the fatty acid composition in beef, so it is possible to improve this attribute without affecting the nutritional beef quality in zebu breeds. However, selection for increased deposition of subcutaneous fat thickness and especially the percentage of intramuscular fat should lead to changes in the fat composition, highlighting a genetic antagonism between meat nutritional value and acceptability by the consumer. Sao Paulo State Univ, Fac Agr & Vet Sci, Dept Anim Sci, Jaboticabal, SP, Brazil Univ Sao Paulo, Sch Vet Med & Anim Sci, Dept Anim Sci, Pirassununga, SP, Brazil Univ Sao Paulo, Fac Anim Sci & Food Engn, Dept Anim Sci, Pirassununga, SP, Brazil Univ Sao Paulo, Fac Anim Sci & Food Engn, Dept Food Engn, Pirassununga, SP, Brazil CNPq, Natl Counsel Technol & Sci Dev, Brasilia, DF, Brazil INIA, Natl Agr Res Inst, Las Brujas 90200, Uruguay Sao Paulo State Univ, Fac Agr & Vet Sci, Dept Anim Sci, Jaboticabal, SP, Brazil FAPESP: 2009/16118-5 FAPESP: 2011/21241-0 FAPESP: 2012/23979-0

Made available in DSpace on 2018-11-26T17:12:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-11-25 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Background: Fatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique. Results: Differential expression analyses between animals with extreme phenotype for fatty acid composition showed a total of 13 differentially expressed genes for myristic (C14:0), 35 for palmitic (C16:0), 187 for stearic (C18:0), 371 for oleic (C18:1, cis-9), 24 for conjugated linoleic (C18:2 cis-9, trans11, CLA), 89 for linoleic (C18:2 cis-9,12 n6), and 110 genes for a-linolenic (C18:3 n3) fatty acids. For the respective sums of the individual fatty acids, 51 differentially expressed genes for saturated fatty acids (SFA), 336 for monounsaturated (MUFA), 131 for polyunsaturated (PUFA), 92 for PUFA/SFA ratio, 55 for omega 3, 627 for omega 6, and 22 for omega 6/omega 3 ratio were identified. Functional annotation analyses identified several genes associated with fatty acid metabolism, such as those involved in intra and extra-cellular transport of fatty acid synthesis precursors in intramuscular fat of longissimus thoracis muscle. Some of them must be highlighted, such as: ACSM3 and ACSS1 genes, which work as a precursor in fatty acid synthesis; DGAT2 gene that acts in the deposition of saturated fat in the adipose tissue; GPP and LPL genes that support the synthesis of insulin, stimulating both the glucose synthesis and the amino acids entry into the cells; and the BDH1 gene, which is responsible for the synthesis and degradation of ketone bodies used in the synthesis of ATP. Conclusion: Several genes related to lipid metabolism and fatty acid composition were identified. These findings must contribute to the elucidation of the genetic basis to improve Nellore meat quality traits, with emphasis on human health. Additionally, it can also contribute to improve the knowledge of fatty acid biosynthesis and the selection of animals with better nutritional quality. Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Zootecnia, BR-14884900 Jaboticabal, SP, Brazil Conselho Nacl Desenvolvimento Cient & Tecnol, BR-71605001 Lago Sul, DF, Brazil Univ Sao Paulo, Fac Med Vet & Zootecnia, Dept Nutr & Prod Anim, BR-13635900 Pirassununga, SP, Brazil Univ Sao Paulo, Dept Zootecnia, BR-13418900 Piracicaba, SP, Brazil Univ Sao Paulo, Fac Zootecnia & Engn Alimentos, Dept Zootecnia, BR-13635900 Pirassununga, SP, Brazil Clemson Univ, Anim & Vet Sci Dept, Clemson, SC 29634 USA Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Zootecnia, BR-14884900 Jaboticabal, SP, Brazil FAPESP: 2011/2141-0 FAPESP: 2009/16118-5 FAPESP: 2012/15098-3

Sao Paulo State Univ UNESP, Sch Agr & Veterinarian Sci FCAV, Dept Anim Sci, Jaboticabal, Brazil

Made available in DSpace on 2018-11-26T17:51:51Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 The objective of the present study was to evaluate the effect of nutritional management treatments during the rearing period on the performance and carcass traits of Hereford steers finished either on pasture or in feedlot. Two hundred and forty male Hereford calves, weaned at 8 months of age with an average weight of 170 +/- 17 kg, were used. After weaning, four nutritional treatments were imposed on the calves so as to obtain different daily liveweight gains (LWGs, kg/day) during the first winter (winter-growth phase). The nutritional management groups were high LWG in feedlot (HF), low LWG in feedlot (LF), high LWG on pasture (HP) and low LWG on pasture (LP). Finishing phase began when each group reached a mean liveweight (LW) of 350 +/- 28 kg. During this phase, one half of the HF, LF, HP and LP animals were finished on pasture and the other half in feedlot. The animals were slaughtered when each group attained a mean LW of 500 kg. The carcass traits ribeye area (cm(2)) and backfat thickness (mm) were measured by ultrasonography. Liveweight, LWG and ultrasonography records were analysed by repeated-measures analysis. DM intake as a percentage of LW and feed conversion ratio (FCR; kg DM/kg LW) during feedlot were analysed by ANOVA. Least-square means for LWGs of pasture-finished animals were 0.807, 0.799, 0.819c and 0.782 kg/day for HF, LF, HP and LP respectively. Least-square means for LWG of feedlot-finished animals were 1.569, 1.554, 1.484 and 1.431 kg/day for HF, LF, HP and LP respectively. Least-square means for FCR in feedlot were 7.12, 7.20, 7.97 and 8.92 for HF, LF, HP and LP respectively. Hot carcass weight had a similar trend as did LWG. Feedlot-finished animals attained heavier hot carcass weights once they received a better nutritional management during the first winter. The growth-group management did not affect (P > 0.05) dressing percentage. The carcasses of feedlot-finished animals showed higher (P < 0.05) dressing percentages than did carcasses of pasture-finished animals. Nutritional feeding management during the first winter had permanent effects on growth, carcass and FCR traits; however, the prevalence of these effects depended on the feeding system during the finishing phase. On the basis of the results obtained in the study, it is recommended that animals receive an adequate nutritional management during the first winter so as to maximise their future performance, especially for intensive beef-cattle growing-finishing systems. However, if the animals have been subjected to restriction during early growth, they should be finished under pasture conditions. Univ Estadual Paulista, FCAV, Dept Zootecnia, BR-14884900 Jaboticabal, Brazil INIA, Colonia 70000, Uruguay Univ Sao Paulo, Dept Nutr & Prod Anim, BR-13635900 Pirassununga, Brazil Univ Estadual Paulista, FCAV, Dept Zootecnia, BR-14884900 Jaboticabal, Brazil