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Dias MS, Pedrosa VB, Rocha da Cruz VA, Silva MR, Batista Pinto LF. Genome-wide association and functional annotation analysis for the calving interval in Nellore cattle. Theriogenology 2024; 218:214-222. [PMID: 38350227 DOI: 10.1016/j.theriogenology.2024.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/15/2024]
Abstract
Calving interval (CI) measures the number of days between two consecutive calves of the same cow, and previous studies based on phenotype and pedigree data reported low heritability for this trait. However, the genetic architecture of CI in the Nellore breed was not evaluated based on genomic data. Thus, this study aimed to estimate the heritability based on genomic data and carry out a genome-wide association study (GWAS) for CI in the Nellore breed, using 12,599 pedigree records, 5078 CI records, and 3818 animals genotyped with 50k SNPchip panel. Both quality control and GWAS were performed in BLUPF90 family packages, which use the single-step genomic best linear unbiased predictor (ssGBLUP) method. The average CI was 427.6 days, with a standard deviation of 106.9 and a total range of 270-730 days. The heritability estimate was 0.04 ± 0.04. The p-values of GWAS analysis resulted in a genomic inflation factor (lambda) of 1.08. The only significant SNP (rs136725686) at the genome-wide level (p-value = 1.53E-06) was located on BTA13. Other 19 SNPs were significant at the chromosome-wide level, distributed on BTA1, 2, 3, 6, 10, 13, 14, 17, 18, 22, and 26. Functional annotation analysis found thirty-six protein-coding genes, including genes related to cell cycle (RAD21, BCAR3), oocyte function (LHX8, CLPX, UTP23), immune system (TXK, TEC, NFATC2), endocrine function (LRRFIP2, GPR158), estrous cycle (SLC38A7), and female fertility (CCK, LYZL4, TRAK1, FOXP1, STAC). Therefore, CI is a complex trait with small heritability in Nellore cattle, and various biological processes may be involved with the genetic architecture of CI in Nellore cattle.
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Affiliation(s)
- Mayra Silva Dias
- Federal University of Bahia, Animal Science Department, Av. Milton Santos, 500, Ondina, Salvador, BA, 40170-110, Brazil.
| | | | | | - Marcio Ribeiro Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guararapes, SP, 16700-000, Brazil.
| | - Luis Fernando Batista Pinto
- Federal University of Bahia, Animal Science Department, Av. Milton Santos, 500, Ondina, Salvador, BA, 40170-110, Brazil.
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de Souza TC, Pinto LFB, da Cruz VAR, de Oliveira HR, Pedrosa VB, Oliveira GA, Miglior F, Schenkel FS, Brito LF. A comprehensive characterization of longevity and culling reasons in Canadian Holstein cattle based on various systematic factors. Transl Anim Sci 2023; 7:txad102. [PMID: 37841322 PMCID: PMC10576516 DOI: 10.1093/tas/txad102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 10/17/2023] Open
Abstract
The decision of premature culling cows directly impacts the profitability of dairy farms. A comprehensive characterization of the primary causes of culling reasons would greatly improve both management and selection objectives in dairy cattle breeding programs. Therefore, this study aimed to analyze the temporal frequencies of 34 culling reasons in Canadian Holstein cows. After data editing and quality control, records from 3,096,872 cows culled from 9,683 herds spread across Canada were used for the analyses covering the periods from 1996 to 2020. Reproductive issues were the main culling reason accounting for 23.02%, followed by milk production (20.82%), health (20.39%), conformation problems (13.69%), economic factors (13.10%), accidents (5.67%), age-related causes (1.67%), and workability (1.63%). Nearly fifty-eight percent of cows were culled after 47 months of age. The observed frequencies of culling due to economic factors were lower than expected from 1996 to 2014 and higher than expected between 2015 and 2020. Reproduction issues had the highest culling frequencies during fall (24.54%), winter (24.02%), and spring (22.51%), while health issues were the most frequent (22.51%) culling reason in the summer season. Health issues (25.50%) and milk production (27.71%) were the most frequent culling reasons in the provinces of Quebec and Ontario, respectively. Reproductive issues showed the highest frequency across climates based on the Köppen climate classification, except for Csb (Dry-summer subtropical or Mediterranean climate) and Bsk (Middle latitude steppe climate), which correspond to small regions in Canada, where production was the most frequent culling reason (29.42% and 21.56%, respectively). Reproductive and milk performance issues were the two main culling reasons in most ecozones, except in Boreal Shield and Atlantic Marine, where health issues had the highest frequencies (25.12 and 23.75%, respectively). These results will contribute to improving management practices and selective decisions to reduce involuntary culling of Holstein cows.
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Affiliation(s)
- Taiana Cortez de Souza
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Hinayah Rojas de Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - Gerson A Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
- Lactanet Canada, Guelph, ON, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
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Alves JS, de Araujo Oliveira CA, Escodro PB, Pinto LFB, Costa RB, de Camargo GMF. Genetic origin of donkeys in Brazil. Trop Anim Health Prod 2022; 54:291. [PMID: 36094617 DOI: 10.1007/s11250-022-03280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION 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. MATERIAL AND METHODS This study aimed to evaluate the variation and origin of maternal lineages of groups of naturalized donkeys in Brazil (Brazilian, Nordestino, and Pêga). RESULTS AND DISCUSSION We detected five mitochondrial haplotypes with 19 polymorphic sites, two of them exclusively found in the Nordestino donkey; this group is in fact more distant from the others. 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, reported here for the first time. CONCLUSION : 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.
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Affiliation(s)
- Jackeline Santos Alves
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Chiara Albano de Araujo Oliveira
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Pierre Barnabé Escodro
- Centro de Engenharias e Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Luis Fernando Batista Pinto
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Raphael Bermal Costa
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Gregório Miguel Ferreira de Camargo
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil.
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Dutra PA, Pinto LFB, Cardoso-Neto BM, Mendes CS, Pinheiro AM, Barbosa LP, de Jesus Pereira TC, de Carvalho GGP. Flaxseed added to the diet of Alpine goats affects the nutrients intake and blood parameters. Trop Anim Health Prod 2022; 54:104. [PMID: 35165796 DOI: 10.1007/s11250-022-03100-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 02/01/2022] [Indexed: 11/27/2022]
Abstract
The flaxseed is a nutraceutical food used as a source of α-linolenic acid, which can bring benefits to the health of mammals. This study was carried out to examine the effect of flaxseed inclusion in the diets on the intake of nutrients, body weight, and blood parameters of Alpine goats. Twenty-one adult females with an initial average weight of 41.06 ± 1.84 kg were used in a completely randomized design, with four experimental treatments (0, 5, 10, and 15% of flaxseed in the total diet) and five replications per treatment. The intake of the dry matter presented a decreasing linear effect (P < 0.001), with a reduction of 53.5% between the control diet (0% of flaxseed) and 15% of flaxseed, but no effect was observed on weight gain (P > 0.05). Inclusion of flaxseed from 0 to 15% linearly decreased the intakes of organic matter, crude protein, non-fibrous carbohydrates, and neutral detergent fiber, but increased the ether extract intake (P < 0.001). Regarding plasma concentration traits, increasing the flaxseed levels from 0 to 15% had linear positive effect on LDL, VLDL, and triglycerides (P < 0.05), but no effect on cholesterol, HDL, glucose, creatinine, and urea (P > 0.05). The inclusion of flaxseed in the diet for 80 days changes the nutrients intake and blood parameters but shows no impact on body weight. However, further studies are required to determine the impact of flaxseed on the goat's health in the long term since there has been an increase in the concentration of triglycerides, LDL, and VLDL.
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Affiliation(s)
- Patrícia Alves Dutra
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Adhemar de Barros Avenue, 500, Ondina, Salvador, Bahia, Zipcode 40170-110, Brazil
| | - Luis Fernando Batista Pinto
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Adhemar de Barros Avenue, 500, Ondina, Salvador, Bahia, Zipcode 40170-110, Brazil
| | - Bianor Matias Cardoso-Neto
- Federal University of Recôncavo of Bahia, 710 Rui Barbosa Street, Cruz das Almas, Bahia, Zipcode 44380-000, Brazil
| | - Claudineia Silva Mendes
- Federal University of Recôncavo of Bahia, 710 Rui Barbosa Street, Cruz das Almas, Bahia, Zipcode 44380-000, Brazil
| | - Alexandre Moraes Pinheiro
- Federal University of Recôncavo of Bahia, 710 Rui Barbosa Street, Cruz das Almas, Bahia, Zipcode 44380-000, Brazil
| | - Larissa Pires Barbosa
- Federal University of Recôncavo of Bahia, 710 Rui Barbosa Street, Cruz das Almas, Bahia, Zipcode 44380-000, Brazil
| | - Taiala Cristina de Jesus Pereira
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Adhemar de Barros Avenue, 500, Ondina, Salvador, Bahia, Zipcode 40170-110, Brazil
| | - Gleidson Giordano Pinto de Carvalho
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Adhemar de Barros Avenue, 500, Ondina, Salvador, Bahia, Zipcode 40170-110, Brazil.
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Martins R, Brito LF, Machado PC, Pinto LFB, Silva MR, Schenkel FS, Pedrosa VB. Genome-wide association study and pathway analysis for carcass fatness in Nellore cattle measured by ultrasound. Anim Genet 2021; 52:730-733. [PMID: 34370325 DOI: 10.1111/age.13129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2021] [Indexed: 12/16/2022]
Abstract
Identifying genes or genomic regions influencing carcass-quality traits such as fatness (FTN) is essential to optimize the genetic selection processes in beef cattle. The aim of this study was to identify genomic regions associated with FTN in Nellore cattle as well as to elucidate the metabolic pathways related to the phenotypic expression. Ultrasound-based measurements of FTN were collected in 11 750 animals, with 39 903 animals in the pedigree file. Additionally, 1440 animals were genotyped using the GGP-indicus 35K SNP panel, which contained 33 623 SNPs after quality control. Twenty genes related to FTN were found on 11 chromosomes, explaining 12.96% of the total additive genetic variance. Gene ontology revealed seven genes: NR1L2, PKD2, GSK3β, EXT1, RAD51B, SORCS1 and DPH6, associated with important processes related to FTN. In addition, novel candidate genes (MAATS1, LYPD1, CDK5RAP2, RAD51B, c13H2Oorf96 and TRAPPC11) were detected and could provide further knowledge to uncover genetic regions associated to carcass fatness in beef cattle.
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Affiliation(s)
- R Martins
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - L F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - P C Machado
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - L F B Pinto
- Department of Animal Sciences, Federal University of Bahia, Av. Adhemar de Barros s/n, Ondina, Salvador, BA, 40170-115, Brazil
| | - M R Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guarapes, SP, 16700-000, Brazil
| | - F S Schenkel
- Animal and Poultry Science Department, Centre for Genetic Improvement of Livestock, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - V B Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
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da Silva Magalhães T, Santos EM, de Freitas Júnior JE, Santos SA, dos Santos Pina D, Cirne LGA, Pinto LFB, Mourão GB, dos Santos Soares FD, Leite LC, Ruiz Alba HD, Tosto MSL, de Carvalho GGP. Chitosan and cottonseed processing method association on carcass traits and meat quality of feedlot lambs. PLoS One 2020; 15:e0242822. [PMID: 33227032 PMCID: PMC7682818 DOI: 10.1371/journal.pone.0242822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
The objective of this study was to evaluate the effects of the association of cottonseed processing method with chitosan on carcass traits and meat quality of lambs finished in feedlot. Eighty lambs with an average body weight of 20.6 kg, with 04 months of age, were distributed in a completely randomized design, in a 2 x 2 factorial arrangement. The factors were represented by two cottonseed processing method (whole or ground) and two levels of chitosan (0 and 136 mg/kg BW). The association of cottonseed processing method with chitosan in the lamb diet did not affect (P>0.05) carcasses traits. The pH, color, cooking losses, shear force, and proximate composition of meat were also not affected (P>0.05) by the processing method of cottonseed or its association with chitosan in the lamb diets. There was an increase in palmitoleic (c9-C16:1; P = 0.01) and conjugated linoleic (P = 0.02) fatty acids when ground cottonseed was associated with chitosan. Ground cottonseed associated with chitosan increases the concentration of unsaturated fatty acids in the meat of feedlot lambs.
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Affiliation(s)
| | - Edson Mauro Santos
- Department of Animal Science, Federal University of Paraiba, Areia, Paraíba, Brazil
| | | | | | | | - Luis Gabriel Alves Cirne
- Institute of Biodiversity and Forestry, Federal University of Western Pará, Santarém, Pará, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Laudí Cunha Leite
- Department of Animal Science, Federal University of Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
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Santos Alves J, da Silva Anjos M, Silva Bastos M, Sarmento Martins de Oliveira L, Pereira Pinto Oliveira I, Batista Pinto LF, Albano de Araújo de Oliveira C, Bermal Costa R, Miguel Ferreira de Camargo G. Variability analyses of the maternal lineage of horses and donkeys. Gene 2020; 769:145231. [PMID: 33065240 DOI: 10.1016/j.gene.2020.145231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/24/2020] [Accepted: 10/08/2020] [Indexed: 11/17/2022]
Abstract
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.
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Affiliation(s)
- Jackeline Santos Alves
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, (UFBA), Salvador, BA, Brazil
| | - Marcia da Silva Anjos
- Programa de Pós-Graduação em Biodiversidade e Evolução da UFBA, Salvador, BA, Brazil
| | - Marisa Silva Bastos
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, (UFBA), Salvador, BA, Brazil
| | | | | | | | | | - Raphael Bermal Costa
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, (UFBA), Salvador, BA, Brazil
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Mulim HA, Pinto LFB, Valloto AA, Pedrosa VB. Genotype by environment interaction for somatic cell score in Holstein cattle of southern Brazil via reaction norms. Anim Biosci 2020; 34:499-505. [PMID: 32777892 PMCID: PMC7961275 DOI: 10.5713/ajas.20.0031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/20/2020] [Indexed: 11/27/2022] Open
Abstract
Objective The objective of this study was to evaluate the genetic behavior of a population of Holstein cattle in response to the variation of environmental temperature by analyzing the effects of genotype by environment interaction (GEI) through reaction norms for the somatic cell score (SCS). Methods Data was collected for 67,206 primiparous cows from the database of the Paraná Holstein Breeders Association in Brazil, with the aim of evaluating the temperature effect, considered as an environmental variable, distinguished under six gradients, with the variation range found being 17°C to 19.5°C, over the region. A reaction norm model was adopted utilizing the fourth order under the Legendre polynomials, using the mixed models of analysis by the restricted maximum likelihood method by the WOMBAT software. Additionally, the genetic behavior of the 15 most representative bulls was assessed, in response to the changes in the temperature gradient. Results A mean score of 2.66 and a heritability variation from 0.17 to 0.23 was found in the regional temperature increase. The correlation between the environmental gradients proved to be higher than 0.80. Distinctive genetic behaviors were observed according to the increase in regional temperature, with an observed increase of up to 0.258 in the breeding values of some animals, as well as a reduction in the breeding of up to 0.793, with occasional reclassifications being observed as the temperature increased. Conclusion Non-relevant GEI for SCS were observed in Holstein cattle herds of southern Brazil. Thus, the inclusion of the temperature effect in the model of genetic evaluation of SCS for the southern Brazilian Holstein breed is not required.
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Affiliation(s)
- Henrique Alberto Mulim
- Department of Animal Science, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | | | | | - Victor Breno Pedrosa
- Department of Animal Science, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
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Borges Barbosa AC, De Souza Romano G, Del Solar Velarde JM, Sterman Ferraz JB, Pedrosa VB, Batista Pinto LF. Pedigree analysis of Santa Inês sheep and inbreeding effects on performance traits. REV MEX CIENC PECU 2020. [DOI: 10.22319/rmcp.v11i2.4899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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da Cruz VAR, Alves JS, Bastos MS, Oliveira LSM, Diaz IDPS, Pinto LFB, Costa RB, de Camargo GMF. MC1R gene and coat color in buffaloes. Anim Genet 2020; 51:345-346. [PMID: 31975429 DOI: 10.1111/age.12910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2019] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jackeline Santos Alves
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Marisa Silva Bastos
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | | | | | | | - Raphael Bermal Costa
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
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Gonzalez FAL, Tarouco JU, Lobato JFP, Patino HO, Tarouco AK, Pinto LFB, Pivato M, Feijó FD. Average daily gain rates determine eye muscle area and rump fat depth of beef heifers. Italian Journal of Animal Science 2019. [DOI: 10.1080/1828051x.2018.1466665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | | | | | - Harold Ospina Patino
- Department of Animal Science, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | | | - Mateus Pivato
- Department of Animal Science, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Fernanda Dornelles Feijó
- Department of Animal Science, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Moreira RP, Pinto LFB, Valloto AA, Pedrosa VB. Evaluation of genotype by environment interactions on milk production traits of Holstein cows in southern Brazil. Asian-Australas J Anim Sci 2018; 32:459-466. [PMID: 30056654 PMCID: PMC6409447 DOI: 10.5713/ajas.18.0174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/16/2018] [Indexed: 11/27/2022]
Abstract
Objective This study assessed the possible existence of genotype by environment interactions for milk, fat and protein yields in Holstein cattle raised in one of the most important milk production basins in Brazil. Methods Changes in the genetic parameters and breeding values were evaluated for 57,967 animals from three distinct regions of southern Brazil, divided according to differences in climate. The genotype by environment interaction was determined by genetic correlations between regions, estimated by the restricted maximum likelihood, considering the animal model. Bull rankings were investigated to verify the ratio of coincident selected animals between regions for each trait. Results The estimates of heritability coefficients were similar between two regions, but were lower in the third evaluated area, for all traits. Genetic correlations between regions were high, ranging from 0.91 to 0.99 for milk, fat and protein yields, representing the absence of a genotype by environment interaction for productive traits. The percentage of selection error between regions for the top 10% of animals ranged from 0.88% to 2.07% for milk yield, 0.99% to 2.46% for fat yield and 0.59% to 3.15% for protein yield. Conclusion A slight change in genotype between areas was expected since no significant genotype by environment interactions were identified, facilitating the process of selecting Holstein cattle in southern Brazil.
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Affiliation(s)
- Raphael Patrick Moreira
- Department of Animal Science, Ponta Grossa State University, Ponta Grossa, PR, 84030-900, Brazil
| | | | - Altair Antônio Valloto
- Paraná Holstein Breeders Association - APCBRH, Rua Professor Francisco Dranka, Curitiba, PR, 81200-404, Brazil
| | - Victor Breno Pedrosa
- Department of Animal Science, Ponta Grossa State University, Ponta Grossa, PR, 84030-900, Brazil
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Rovadoscki GA, Pertile SFN, Alvarenga AB, Cesar ASM, Pértille F, Petrini J, Franzo V, Soares WVB, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Lanna DPD, Coutinho LL, Mourão GB. Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Inês sheep. BMC Genomics 2018; 19:375. [PMID: 29783944 PMCID: PMC5963081 DOI: 10.1186/s12864-018-4777-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 05/10/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS Genomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through selection. Twenty-seven genomic regions of 10 adjacent SNPs associated with fatty acids composition were identified on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, and 18, each explaining ≥0.30% of the additive genetic variance. Twenty-three genes supporting the understanding of genetic mechanisms of fat composition in sheep were identified in these regions, such as DGAT2, TRHDE, TPH2, ME1, C6, C7, UBE3D, PARP14, and MRPS30. CONCLUSIONS Estimates of genomic heritabilities and elucidating important genomic regions can contribute to a better understanding of the genetic control of fatty acid deposition and improve the selection strategies to enhance meat quality and health attributes.
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Affiliation(s)
- G A Rovadoscki
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - S F N Pertile
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A B Alvarenga
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A S M Cesar
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - J Petrini
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - V Franzo
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - W V B Soares
- Institute of Zootechny (IZ), Nova Odessa, SP, Brazil
| | - G Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - L F B Pinto
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - G G P Carvalho
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - D P D Lanna
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - G B Mourão
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil.
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Carvalho CVD, Almeida EC, Pinto LFB, Bittencourt TCC, Costa RB. Geoclimatic evaluation of the Northeast Region of Brazil and its suitability for breeding beef cattle. JABB 2018. [DOI: 10.31893/2318-1265jabb.v6n1p14-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Carvalho CVD, Almeida EC, Pinto LFB, Bittencourt TCC, Costa RB. Geoclimatic evaluation of the Northeast Region of Brazil and its suitability for breeding beef cattle. JABB 2018. [DOI: 10.31893/2318-1265/2318-1265jabb.v6n1p14-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gomes RC, Silva SL, Carvalho ME, Rezende FM, Pinto LFB, Santana MHA, Stella TR, Meirelles FV, Rossi Júnior P, Leme PR, Ferraz JBS. Protein synthesis and degradation gene SNPs related to feed intake, feed efficiency, growth, and ultrasound carcass traits in Nellore cattle. Genet Mol Res 2013; 12:2923-36. [PMID: 24065648 DOI: 10.4238/2013.august.12.8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We looked for possible associations of SNPs in genes related to protein turnover, with growth, feed efficiency and carcass traits in feedlot Nellore cattle. Purebred Nellore bulls and steers (N = 290; 378 ± 42 kg body weight, 23 months ± 42 days old) were evaluated for daily feed intake, body weight gain (BWG), gross feed efficiency, feed conversion ratio, partial efficiency of growth, residual feed intake (RFI), ultrasound backfat, rump fat, and ribeye area. Genotypes were obtained for SNPs in the growth hormone receptor (GHR-1 and GHR-2); calpain (CAPN4751); calpastatin (UoGCAST); ubiquitin-conjugating enzyme 2I (UBE2I-1 and UBE2I-2); R3H domain containing 1 (R3HDM1-1, -2, -3, and -4), ring finger protein 19 (RNF19); proteasome 26S subunit, non-ATPase, 13 (PSMD13); ribosomal protein, large, P2 (RPLP2); and isoleucine-tRNA synthetase 2, mitochondrial (IARS2) genes. Allelic substitution, additive and dominant effects were tested and molecular breeding values were computed. CAPN4751, GHR-1 and -2, IARS2, R3HDM1-4, and UoGCAST were found to be normally segregating polymorphisms. Additive and dominance effects were observed on BWG, feed efficiency and carcass traits, although dominant effects predominated. Significant allelic substitution effects were observed for CAPN4751, GHR-1 and -2, and UoGCAST on BWG, gross feed efficiency, RFI, and carcass traits, under single- or multiple-marker analyses. Correlations between molecular breeding values and phenotypes were low, excepted for RFI, based on allelic substitution estimates obtained by stepwise linear regression. We conclude that SNPs in genes related to protein turnover are related to economically important traits in Nellore cattle.
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Affiliation(s)
- R C Gomes
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brasil
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Nones K, Ledur MC, Zanella EL, Klein C, Pinto LFB, Moura ASAMT, Ruy DC, Baron EE, Ambo M, Campos RLR, Boschiero C, Burt DW, Coutinho LL. Quantitative trait loci associated with chemical composition of the chicken carcass. Anim Genet 2012; 43:570-6. [PMID: 22497237 DOI: 10.1111/j.1365-2052.2012.02321.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2011] [Indexed: 11/29/2022]
Abstract
Major objectives of the poultry industry are to increase meat production and to reduce carcass fatness, mainly abdominal fat. Information on growth performance and carcass composition are important for the selection of leaner meat chickens. To enhance our understanding of the genetic architecture underlying the chemical composition of chicken carcasses, an F(2) population developed from a broiler × layer cross was used to map quantitative trait loci (QTL) affecting protein, fat, water and ash contents in chicken carcasses. Two genetic models were applied in the QTL analysis: the line-cross and the half-sib models, both using the regression interval mapping method. Six significant and five suggestive QTL were mapped in the line-cross analysis, and four significant and six suggestive QTL were mapped in the half-sib analysis. A total of eleven QTL were mapped for fat (ether extract), five for protein, four for ash and one for water contents in the carcass using both analyses. No study to date has reported QTL for carcass chemical composition in chickens. Some QTL mapped here for carcass fat content match, as expected, QTL regions previously associated with abdominal fat in the same or in different populations, and novel QTL for protein, ash and water contents in the carcass are presented here. The results described here also reinforce the need for fine mapping and to perform multi-trait analyses to better understand the genetic architecture of these traits.
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Affiliation(s)
- K Nones
- Departamento de Zootecnia, USP/ESALQ, C.P. 09, Piracicaba, SP, 13418-900, Brazil
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Pinto LFB, Ferraz JBS, Pedrosa VB, Eler JP, Meirelles FV, Bonin MN, Rezende FM, Carvalho ME, Cucco DC, Silva RCG. Single nucleotide polymorphisms in CAPN and leptin genes associated with meat color and tenderness in Nellore cattle. Genet Mol Res 2011; 10:2057-64. [PMID: 21968622 DOI: 10.4238/vol10-3gmr1263] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We analyzed single nucleotide polymorphisms in calpain, leptin, leptin receptor, and growth hormone receptor genes and their association with color, drip and cooking losses of longissimus muscle at 7, 14 and 21 days postmortem in 638 purebred Nellore bulls slaughtered between 22 and 26 months of age. Meat samples were vacuum-packed and aged at 4°C. The single nucleotide polymorphisms T945M, GHR2, E2FB, and CAPN4751 were evaluated. All genotypic classes were observed; however, the T/T genotype of T945M and E2FB was found at a low frequency. A significant association of E2FB with drip loss (a measure of water-holding capacity) was detected at seven days of meat aging. CAPN4751 had an additive effect on red and yellow color intensities. The T allele of CAPN4751 was found to be positively associated with improved meat color, but not with meat tenderness, differing from a previous report indicating that it is associated with meat tenderness. We conclude that the potential for use of CAPN4751 as a marker for these meat quality traits requires further research.
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Affiliation(s)
- L F B Pinto
- Departamento de Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, Salvador, BA, Brasil
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Ferraz JBS, Pinto LFB, Meirelles FV, Eler JP, de Rezende FM, Oliveira ECM, Almeida HB, Woodward B, Nkrumah D. Association of single nucleotide polymorphisms with carcass traits in Nellore cattle. Genet Mol Res 2009; 8:1360-6. [PMID: 19937580 DOI: 10.4238/vol8-4gmr650] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The association between two single nucleotide polymorphisms (SNPs), T945M and UCP1SNP1, with hot carcass weight (HCW, kg, N = 618), longissimus dorsi muscle area (REA, cm(2), N = 633), and backfat thickness (BF, mm, N = 625), measured in Nellore cattle in Brazil, was evaluated. Likelihood ratio tests were used to evaluate reduced (fixed effects of general mean, contemporary group, yearling weight, age at slaughter, and random effect of infinitesimal genetic value) and full model (reduced model effects plus quantitative trait locus effects). Additive and dominance effects were tested for each SNP. Genotypic and gene frequencies were also obtained for the SNPs and a descriptive phenotype analysis was made. Mean values for HCW, REA and BF were equal to 288.13 +/- 0.55 kg, 73.14 +/- 0.27 cm(2), and 4.28 +/- 0.07 mm, respectively; the coefficients of variation were 4.74, 9.24, and 42.43%, respectively. Gene frequencies for T945M and UCP1SNP1 were f(C) = 0.89, f(T) = 0.11, f(C) = 0.81, and f(G) = 0.19. The SNP T945M had a genotypic frequency of only three animals for TT genotype. Additive effects were observed for T945M on REA and BF, while UCP1SNP1 affected HCW and BF. Based on the significant additive effects of the SNPs and the gene frequencies that we found, we can expect genetic gains with marker assisted selection.
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Affiliation(s)
- J B S Ferraz
- Departamento de Ciências Básicas, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brasil.
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Affiliation(s)
- D C Cucco
- Departamento de Ciências Básicas, Grupo de Melhoramento Animal e Biotecnologia, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil.
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Ambo M, Moura ASAMT, Ledur MC, Pinto LFB, Baron EE, Ruy DC, Nones K, Campos RLR, Boschiero C, Burt DW, Coutinho LL. Quantitative trait loci for performance traits in a broiler x layer cross. Anim Genet 2008; 40:200-8. [PMID: 19170675 DOI: 10.1111/j.1365-2052.2008.01824.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
An F(2) resource population, derived from a broiler x layer cross, was used to map quantitative trait loci (QTL) for body weights at days 1, 35 and 41, weight gain, feed intake, feed efficiency from 35 to 41 days and intestinal length. Up to 577 F(2) chickens were genotyped with 103 genetic markers covering 21 linkage groups. A preliminary QTL mapping report using this same population focused exclusively on GGA1. Regression methods were applied to line-cross and half-sib models for QTL interval mapping. Under the line-cross model, eight QTL were detected for body weight at 35 days (GGA2, 3 and 4), body weight at 41 days (GGA2, 3, 4 and 10) and intestine length (GGA4). Under the half-sib model, using sire as common parent, five QTL were detected for body weight at day 1 (GGA3 and 18), body weight at 35 days (GGA2 and 3) and body weight at 41 days (GGA3). When dam was used as common parent, seven QTL were mapped for body weight at day 1 (GGA2), body weight at day 35 (GGA2, 3 and 4) and body weight at day 41 (GGA2, 3 and 4). Growth differences in chicken lines appear to be controlled by a chronological change in a limited number of chromosomal regions.
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Affiliation(s)
- M Ambo
- Animal Biotechnology Laboratory, Department of Animal Science, ESALQ-USP, Av. Pádua Dias 11, Piracicaba, SP 13418-900, Brazil
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