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Bejarano DH, Martínez RA, Rocha JF. Genome-wide association study for growth traits in Blanco Orejinegro and Romosinuano cattle. Trop Anim Health Prod 2023; 55:358. [PMID: 37848724 PMCID: PMC10581918 DOI: 10.1007/s11250-023-03743-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/12/2023] [Indexed: 10/19/2023]
Abstract
Growth traits are economically important characteristics for the genetic improvement of local cattle breeds. Genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to perform a GWAS to identify genomic regions and genes associated to birth weight, weaning weight adjusted for 240 days, 16 months, and 24 months weight in Romosinuano (ROMO) and Blanco Orejinegro (BON) cattle. A single-step genomic-BLUP was implemented using 596 BON and 569 ROMO individuals that were genotyped with an Illumina BovineSNP50 BeadChip. There were 25 regions of interest identified on different chromosomes, with few of them simultaneously associated with two or more growth traits and some were common to both breeds. The gene mapping allowed to find 173 annotations on these regions, from which 49 represent potential candidate genes with known growth-related functions in cattle and other species. Among the regions that were associated with several growth traits, that at 24 - 27 MB of BTA14, has important candidate genes such as LYPLA1, XKR4, TMEM68 and PLAG1. Another region of interest at 0.40-0.77 Mb of BTA23 was identified in both breeds, containing KHDRBS2 as a potential candidate gene influencing body weight. Future studies targeting these regions could provide more knowledge to uncover the genetic architecture underlying growth traits in BON and ROMO cattle. The genomic regions and genes identified in this study could be used to improve the prediction of genetic merit for growth traits in these creole cattle breeds.
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Affiliation(s)
- Diego H Bejarano
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia
| | - Rodrigo A Martínez
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia
| | - Juan F Rocha
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia.
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Mota LF, Carvajal AB, Bernardes PA, Buzanskas ME, Baldi F, Lôbo RB, Munari DP. Integrating genome-wide association study and pathway analysis reveals physiological aspects affecting heifer early calving defined at different ages in Nelore cattle. Genomics 2022; 114:110395. [DOI: 10.1016/j.ygeno.2022.110395] [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] [Received: 10/18/2021] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022]
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Fernandes Júnior GA, Silva DA, Mota LFM, de Melo TP, Fonseca LFS, Silva DBDS, Carvalheiro R, Albuquerque LG. Sustainable Intensification of Beef Production in the Tropics: The Role of Genetically Improving Sexual Precocity of Heifers. Animals (Basel) 2022; 12:174. [PMID: 35049797 DOI: 10.3390/ani12020174] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Tropical pasture-based beef production systems play a vital role in global food security. The importance of promoting sustainable intensification of such systems has been debated worldwide. Demand for beef is growing together with concerns over the impact of its production on the environment. Implementing sustainable livestock intensification programs relies on animal genetic improvement. In tropical areas, the lack of sexual precocity is a bottleneck for cattle efficiency, directly impacting the sustainability of production systems. In the present review we present and discuss the state of the art of genetic evaluation for sexual precocity in Bos indicus beef cattle, covering the definition of measurable traits, genetic parameter estimates, genomic analyses, and a case study of selection for sexual precocity in Nellore breeding programs. Abstract Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.
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Varchaki Portes J, dos Santos Gonçalves Cyrillo JN, El Faro L, Figueiredo Martins Bonilha S, Branco Arnandes RH, de Almeida Teixeira R, Zerlotti Mercadante ME, Talarico Dias L. Genetic parameters for weights from birth to 10 years of age in different beef cow breeds. Anim Prod Sci 2020. [DOI: 10.1071/an18325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Most Brazilian beef breeding programs perform selection for young bodyweight, which will inevitably increase mature weight due to the genetic correlation among weights at different ages.
Aims
The objective of the present study was to estimate genetic parameters for bodyweight from birth to maturity in Gir, Guzerat, Nelore and Caracu cows born between 1981 and 2014 at Centro APTA Bovinos de Corte, Instituto de Zootecnia, Sertãozinho, São Paulo, Brazil.
Methods
The model included the fixed effects of contemporary group (herd and year of birth), month of birth and previous reproductive status (calved = 1, or not calved = 0), the linear and quadratic effects of animal and cow age as covariates, and direct additive genetic, maternal genetic and maternal permanent environmental effects as random effects. The genetic parameters were estimated by univariate analysis of weights adjusted at birth, and at 120, 210, 378, 450 and 550 days of age, and annually from 2 to 10 years. In addition, multivariate analysis was performed considering weights at birth, and at 210 and 550 days, and at 5 years of age for all breeds.
Key results
For the different breeds, the heritability estimates ranged from 0.28 to 0.49 for birthweight, from 0.11 to 0.31 for weaning weight, from 0.25 to 0.43 for yearling weight, and from 0.25 to 0.69 for weights from 2 to 10 years of age. The genetic correlations were high and positive, indicating that selection at any age will affect weights at the other ages.
Conclusions
The results suggest the possibility of genetic progress for weights at different ages and the use of the young weights to monitor the mature weight of the animals.
Implications
As the trait most strongly correlated with mature weight was yearling weight, already used as the selection criteria for females in the breeding program of the Instituto de Zootecnia, selection indexes should be derived to keep the mature cow weight constant, since heavier cows could be undesirable for pasture-based Brazilian production systems.
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Ferreira FR, de Araujo Neto FR, Borges HB, Aspilcueta-Borquis RR, Hurtado-Lugo NA, de Oliveira HN, de Albuquerque LG, Tonhati H. Random regression models to estimate genetic parameters for weights in Murrah buffaloes. Anim Sci J 2016; 88:1212-1219. [PMID: 28004872 DOI: 10.1111/asj.12758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 07/05/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 12/01/2022]
Abstract
This article reports genetic analysis of the weight at different ages of Murrah water buffaloes, using random regression models (RRM). Models ranging from third to sixth order polynomial were used to describe direct genetic and animal permanent environmental effects. Contemporary group was included as a fixed effect, and a cubic polynomial was used to model the mean curve of the population. The residual was modeled considering a log-linear function. Two models were selected for study of genetic parameters. The first model included third and sixth order polynomials for direct genetic and animal permanent environmental effects (M36). The second model included sixth order polynomials for all random effects (M66). The estimates of heritability varied from 0.16 + 0.04 (44 days) to 0.38 + 0.04 (568 days) for model M36 and from 0.16 + 0.05 (33 days) to 0.42 + 0.05 (600 days) for model M66. Regarding estimates of the correlation for all effects, the magnitude tended to decline with the increase of the time span between measurements. These results indicate that the species has potential for genetic selection based on weight at different ages, since we found favorable genetic variability within the herd, with selection likely to be more efficient at ages near 600 days.
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Affiliation(s)
| | | | | | | | | | | | | | - Humberto Tonhati
- Universidade Estadual Paulista Júlio de Mesquita, Jaboticabal, São Paulo, Brazil
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Raidan FSS, Santos DCC, Moraes MM, Araújo AEM, Ventura HT, Bergmann JAG, Turra EM, Toral FLB. Selection of performance-tested young bulls and indirect responses in commercial beef cattle herds on pasture and in feedlots. Genet Sel Evol 2016; 48:85. [PMID: 27829375 PMCID: PMC5103466 DOI: 10.1186/s12711-016-0265-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Central testing is used to select young bulls which are likely to contribute to increased net income of the commercial beef cattle herd. We present genetic parameters for growth and reproductive traits on performance-tested young bulls and commercial animals that are raised on pasture and in feedlots. METHODS Records on young bulls and heifers in performance tests or commercial herds were used. Genetic parameters for growth and reproductive traits were estimated. Correlated responses for commercial animals when selection was applied on performance-tested young bulls were computed. RESULTS The 90% highest posterior density (HPD90) intervals for heritabilities of final weight (FW), average daily gain (ADG) and scrotal circumference (SC) ranged from 0.41 to 0.49, 0.23 to 0.30 and 0.47 to 0.57, respectively, for performance-tested young bulls on pasture, from 0.45 to 0.60, 0.20 to 0.32 and 0.56 to 0.70, respectively, for performance-tested young bulls in feedlots, from 0.29 to 0.33, 0.14 to 0.18 and 0.35 to 0.45, respectively, for commercial animals on pasture, and from 0.24 to 0.44, 0.13 to 0.24 and 0.35 to 0.57 respectively, for commercial animals in feedlots. The HPD90 intervals for genetic correlations of FW, ADG and SC in performance-tested young bulls on pasture (feedlots) with FW, ADG and SC in commercial animals on pasture (feedlots) ranged from 0.86 to 0.96 (0.83 to 0.94), 0.78 to 0.90 (0.40 to 0.79) and from 0.92 to 0.97 (0.50 to 0.83), respectively. Age at first calving was genetically related to ADG (HPD90 interval = -0.48 to -0.06) and SC (HPD90 interval = -0.41 to -0.05) for performance-tested young bulls on pasture, however it was not related to ADG (HPD90 interval = -0.29 to 0.10) and SC (HPD90 interval = -0.35 to 0.13) for performance-tested young bulls in feedlots. CONCLUSIONS Heritabilities for growth and SC are higher for performance-tested young bulls than for commercial animals. Evaluating and selecting for increased growth and SC on performance-tested young bulls is efficient to improve growth, SC and age at first calving in commercial animals. Evaluating and selecting performance-tested young bulls is more efficient for young bulls on pasture than in feedlots.
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Affiliation(s)
- Fernanda S S Raidan
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.,School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Dalinne C C Santos
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Mariana M Moraes
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Andresa E M Araújo
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Henrique T Ventura
- Associação Brasileira dos Criadores de Zebu, Uberaba, MG, 38022-330, Brazil
| | - José A G Bergmann
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Eduardo M Turra
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Fabio L B Toral
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
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Grossi DDA, Grupioni NV, Buzanskas ME, de Paz CCP, Regitano LCA, de Alencar MM, Schenkel FS, Munari DP. Allele substitution effects of IGF1, GH and PIT1 markers on estimated breeding values for weight and reproduction traits in Canchim beef cattle. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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de Rezende Neves HH, Polin dos Reis F, Motta Paterno F, Rocha Guarini A, Carvalheiro R, da Silva LR, de Oliveira JA, Aidar de Queiroz S. Herd-of-origin effect on the post-weaning performance of centrally tested Nellore beef cattle. Trop Anim Health Prod 2014; 46:1235-41. [PMID: 25015182 DOI: 10.1007/s11250-014-0633-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
Abstract
The objective of a performance test station is to evaluate the performance of potential breeding bulls earlier in order to decrease the generation interval and increase genetic gain as well. This study evaluates the herd-of-origin influence on end-of-test weight (ETW), average daily weight gain during testing (ADG), average daily weight gain during the adjustment period (ADGadj), rib eye area (REA), marbling (MARB), subcutaneous fat thickness (SFT), conformation (C), early finishing (EF), muscling (M), navel (N) and temperament (T) scores, and scrotal circumference (SC) of Nellore cattle that underwent a performance test. We evaluated 664 animals that participated in the performance tests conducted at the Center for Performance CRV Lagoa between 2007 and 2012. Components of variance for each trait were estimated by an animal model (model 1), using the restricted maximum likelihood method. An alternative animal model (model 2) included, in addition to the fixed effects present in S1, the non-correlated random effect of herd-year (HY). A significant HY effect was observed on ETW, REA, SFT, ADGadj, C, and Cw (p < 0.05). The estimated heritability of all traits decreased when the HY effect was included in the model; also, the bull rank, in deciles, changed significantly for traits ETW, REA, SFT, and C. The adjustment period did not completely remove the environmental effect of herd of origin on ETW, REA, SFT, and C. It is recommended that the herd-of-origin effect should be included in the statistical models used to predict the breeding values of the participants of these performance tests.
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Buzanskas ME, Grossi DA, Ventura RV, Schenkel FS, Sargolzaei M, Meirelles SLC, Mokry FB, Higa RH, Mudadu MA, da Silva MVGB, Niciura SCM, Júnior RAAT, Alencar MM, Regitano LCA, Munari DP. Genome-wide association for growth traits in Canchim beef cattle. PLoS One 2014; 9:e94802. [PMID: 24733441 PMCID: PMC3986245 DOI: 10.1371/journal.pone.0094802] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 11/19/2013] [Accepted: 03/20/2014] [Indexed: 12/01/2022] Open
Abstract
Studies are being conducted on the applicability of genomic data to improve the accuracy of the selection process in livestock, and genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to identify genomic regions and genes that play roles in birth weight (BW), weaning weight adjusted for 210 days of age (WW), and long-yearling weight adjusted for 420 days of age (LYW) in Canchim cattle. GWAS were performed by means of the Generalized Quasi-Likelihood Score (GQLS) method using genotypes from the BovineHD BeadChip and estimated breeding values for BW, WW, and LYW. Data consisted of 285 animals from the Canchim breed and 114 from the MA genetic group (derived from crossings between Charolais sires and ½ Canchim + ½ Zebu dams). After applying a false discovery rate correction at a 10% significance level, a total of 4, 12, and 10 SNPs were significantly associated with BW, WW, and LYW, respectively. These SNPs were surveyed to their corresponding genes or to surrounding genes within a distance of 250 kb. The genes DPP6 (dipeptidyl-peptidase 6) and CLEC3B (C-type lectin domain family 3 member B) were highlighted, considering its functions on the development of the brain and skeletal system, respectively. The GQLS method identified regions on chromosome associated with birth weight, weaning weight, and long-yearling weight in Canchim and MA animals. New candidate regions for body weight traits were detected and some of them have interesting biological functions, of which most have not been previously reported. The observation of QTL reports for body weight traits, covering areas surrounding the genes (SNPs) herein identified provides more evidence for these associations. Future studies targeting these areas could provide further knowledge to uncover the genetic architecture underlying growth traits in Canchim cattle.
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Affiliation(s)
- Marcos E. Buzanskas
- Departamento de Ciências Exatas, UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Daniela A. Grossi
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, Ontario, Canada
| | - Ricardo V. Ventura
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, Ontario, Canada
- Beef Improvement Opportunities (BIO), Guelph, Ontario, Canada
| | - Flávio S. Schenkel
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, Ontario, Canada
- The Semex Alliance, Guelph, Ontario, Canada
| | - Sarah L. C. Meirelles
- Department of Animal Science, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Fabiana B. Mokry
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, Brazil
| | - Roberto H. Higa
- Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
| | | | | | | | | | | | | | - Danísio P. Munari
- Departamento de Ciências Exatas, UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
- * E-mail:
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