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Sainz RD, Baldi F, Temp LB, Ribeiro LB. Estimation of genetic parameters for maintenance energy requirements and residual feed intake in Nellore cattle. J Anim Breed Genet 2024. [PMID: 38712720 DOI: 10.1111/jbg.12870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024]
Abstract
We estimated heritabilities and genetic and phenotypic correlation estimates for maintenance energy requirements (NEmR), residual feed intake (RFI), growth, carcass and reproductive indicator traits, using data from 41 feed efficiency trials in Brazil, comprising 4381 males and females. Continuous traits were analysed using a linear animal model and threshold traits were analysed using a threshold animal model. The heritability estimates were low for RFI (0.190) and NEmR (0.193); other heritabilities were mainly moderate (growth and carcass traits) or high (sexual precocity traits). The genetic correlation of RFI with NEmR was high (0.701). The genetic correlations of NEmR were low with carcass and reproductive traits, and moderate with growth traits. Thus, selection to improve weaning weight and female sexual precocity indicator traits would not affect maintenance energy requirement. Genetic selection to reduce maintenance energy requirements is feasible and would also reduce DMI and RFI. Selection to improve RFI can be used to identify animals with lower maintenance energy requirements. Long-term selection to reduce RFI and NEmR would have favourable effects on yearling weight, carcass muscle indicator traits and female sexual precocity. Genetic (co)variance component estimates for NEmR, in conjunction with economic values of selection criteria, may be used to develop novel approaches for genetic selection to improve efficiency of beef production.
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Affiliation(s)
- Roberto D Sainz
- Department of Animal Science, University of California, Davis, California, USA
| | - Fernando Baldi
- Animal Science Department, State University of São Paulo, Jaboticabal, Brazil
| | - Larissa Bordin Temp
- Animal Science Department, State University of São Paulo, Jaboticabal, Brazil
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Benfica LF, Brito LF, do Bem RD, de Oliveira LF, Mulim HA, Braga LG, Cyrillo JNSG, Bonilha SFM, Mercadante MEZ. Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations. Front Genet 2024; 15:1377130. [PMID: 38694873 PMCID: PMC11061390 DOI: 10.3389/fgene.2024.1377130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction: Nellore cattle (Bos taurus indicus) is the main beef cattle breed raised in Brazil. This breed is well adapted to tropical conditions and, more recently, has experienced intensive genetic selection for multiple performance traits. Over the past 43 years, an experimental breeding program has been developed in the Institute of Animal Science (IZ, Sertaozinho, SP, Brazil), which resulted in three differentially-selected lines known as Nellore Control (NeC), Nellore Selection (NeS), and Nellore Traditional (NeT). The primary goal of this selection experiment was to determine the response to selection for yearling weight (YW) and residual feed intake (RFI) on Nellore cattle. The main objectives of this study were to: 1) identify copy number variation (CNVs) in Nellore cattle from three selection lines; 2) identify and characterize CNV regions (CNVR) on these three lines; and 3) perform functional enrichment analyses of the CNVR identified. Results: A total of 14,914 unique CNVs and 1,884 CNVRs were identified when considering all lines as a single population. The CNVRs were non-uniformly distributed across the chromosomes of the three selection lines included in the study. The NeT line had the highest number of CNVRs (n = 1,493), followed by the NeS (n = 823) and NeC (n = 482) lines. The CNVRs covered 23,449,890 bp (0.94%), 40,175,556 bp (1.61%), and 63,212,273 bp (2.54%) of the genome of the NeC, NeS, and NeT lines, respectively. Two CNVRs were commonly identified between the three lines, and six, two, and four exclusive regions were identified for NeC, NeS, and NeT, respectively. All the exclusive regions overlap with important genes, such as SMARCD3, SLC15A1, and MAPK1. Key biological processes associated with the candidate genes were identified, including pathways related to growth and metabolism. Conclusion: This study revealed large variability in CNVs and CNVRs across three Nellore lines differentially selected for YW and RFI. Gene annotation and gene ontology analyses of the exclusive CNVRs to each line revealed specific genes and biological processes involved in the expression of growth and feed efficiency traits. These findings contribute to the understanding of the genetic mechanisms underlying the phenotypic differences among the three Nellore selection lines.
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Affiliation(s)
- Lorena F. Benfica
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Ricardo D. do Bem
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
| | | | - Henrique A. Mulim
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Larissa G. Braga
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - Sarah F. M. Bonilha
- Beef Cattle Research Center, Institute of Animal Science, Sertaozinho, São Paulo, Brazil
| | - Maria Eugenia Z. Mercadante
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
- Beef Cattle Research Center, Institute of Animal Science, Sertaozinho, São Paulo, Brazil
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Estevam DD, Souza JM, Rey FSB, Martins CL, Stafuzza NB, Espigolan R, Millen DD, Arrigoni MDB. Identification of genomic regions and pathways associated with traits related to rumen acidosis in feedlot Nellore cattle. J Anim Breed Genet 2024. [PMID: 38375946 DOI: 10.1111/jbg.12860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 02/21/2024]
Abstract
There may be an increased risk of metabolic disorders, such as rumen acidosis, in cattle fed high-concentrate diets, particularly those from Bos taurus indicus genotypes, which have shown to be more sensitive to ruminal acidification. Therefore, this study aimed to estimate (co)variance components and identify genomic regions and pathways associated with ruminal acidosis in feedlot Nellore cattle fed high-concentrate diets. It was utilized a dataset containing a total of 642 Nellore bulls that were genotyped from seven feedlot nutrition studies. The GGP Indicus 35k panel was used with the single step genome-wide association study methodology in which the effects of the markers were obtained from the genomic values estimated by the GBLUP model. A bivariate model to estimate genetic correlations between the economically important traits and indicator traits for acidosis was used. The traits evaluated in this study that were nutritionally related to rumen acidosis included average daily gain (ADG), final body weight, time spent eating (TSE), time spent ruminating, rumenitis score (RUM), rumen absorptive surface area (ASA), rumen keratinized layer thickness (KER) and hot carcass weight (HCW). The identified candidate genes were mainly involved in the negative or non-regulation of the apoptotic process, salivary secretion, and transmembrane transport. The genetic correlation between HCW and ASA was low positive (0.27 ± 0.23), and between ADG and ASA was high moderate (0.58 ± 0.59). A positive genetic correlation between RUM and all performance traits was observed, and TSE correlated negatively with HCW (-0.33 ± 0.21), ASA (-0.75 ± 0.48), and KER (-0.40 ± 0.27). The genetic association between economically important traits and indicator traits for acidosis suggested that Nellore cattle may be more sensitive to acidosis in feedlot systems.
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Affiliation(s)
- Daniela D Estevam
- Department of Animal Production, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Johnny M Souza
- Department of Animal Science, College of Technology and Agricultural Sciences, São Paulo State University (UNESP), Dracena, São Paulo, Brazil
| | - Fernando S B Rey
- Department of Animal Science, School of Agricultural and Veterinary Studies, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Cyntia L Martins
- Department of Animal Production, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Nedenia B Stafuzza
- Department of Animal Science, Animal Science Institute (IZ), São Paulo's Agency for Agribusiness Technology (APTA), Sertãozinho, São Paulo, Brazil
| | - Rafael Espigolan
- Department of Animal Science and Biological Sciences (DZCB), Federal University of Santa Maria (UFSM), Palmeira das Missões, Brazil
| | - Danilo D Millen
- Department of Animal Science, College of Technology and Agricultural Sciences, São Paulo State University (UNESP), Dracena, São Paulo, Brazil
| | - Mario D B Arrigoni
- Department of Animal Production, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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Benfica LF, Brito LF, do Bem RD, Mulim HA, Glessner J, Braga LG, Gloria LS, Cyrillo JNSG, Bonilha SFM, Mercadante MEZ. Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle. BMC Genomics 2024; 25:54. [PMID: 38212678 PMCID: PMC10785391 DOI: 10.1186/s12864-024-09976-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Feeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers' profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle (Bos taurus indicus); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated. RESULTS A total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF. CONCLUSIONS A total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.
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Affiliation(s)
- Lorena F Benfica
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA.
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
| | - Ricardo D do Bem
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Henrique A Mulim
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
| | - Joseph Glessner
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Larissa G Braga
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Leonardo S Gloria
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
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Silva Neto JB, Mota LFM, Amorim ST, Peripolli E, Brito LF, Magnabosco CU, Baldi F. Genotype-by-environment interactions for feed efficiency traits in Nellore cattle based on bi-trait reaction norm models. Genet Sel Evol 2023; 55:93. [PMID: 38097941 PMCID: PMC10722809 DOI: 10.1186/s12711-023-00867-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Selecting animals for feed efficiency directly impacts the profitability of the beef cattle industry, which contributes to minimizing the environmental footprint of beef production. Genetic and environmental factors influence animal feed efficiency, leading to phenotypic variability when exposed to different environmental conditions (i.e., temperature and nutritional level). Thus, our aim was to assess potential genotype-by-environment (G × E) interactions for dry matter intake (DMI) and residual feed intake (RFI) in Nellore cattle (Bos taurus indicus) based on bi-trait reaction norm models (RN) and evaluate the genetic association between RFI and DMI across different environmental gradient (EG) levels. For this, we used phenotypic information on 12,958 animals (young bulls and heifers) for DMI and RFI recorded during 158 feed efficiency trials. RESULTS The heritability estimates for DMI and RFI across EG ranged from 0.26 to 0.54 and from 0.07 to 0.41, respectively. The average genetic correlations (± standard deviation) across EG for DMI and RFI were 0.83 ± 0.19 and 0.81 ± 0.21, respectively, with the lowest genetic correlation estimates observed between extreme EG levels (low vs. high) i.e. 0.22 for RFI and 0.26 for DMI, indicating the presence of G × E interactions. The genetic correlation between RFI and DMI across EG levels decreased as the EG became more favorable and ranged from 0.79 (lowest EG) to 0.52 (highest EG). Based on the estimated breeding values from extreme EG levels (low vs. high), we observed a moderate Spearman correlation of 0.61 (RFI) and 0.55 (DMI) and a selection coincidence of 53.3% and 40.0% for RFI and DMI, respectively. CONCLUSIONS Our results show evidence of G × E interactions on feed efficiency traits in Nellore cattle, especially in feeding trials with an average daily gain (ADG) that is far from the expected of 1 kg/day, thus increasing reranking of animals.
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Affiliation(s)
- João B Silva Neto
- Department of Animal Science, School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
| | - Lucio F M Mota
- Department of Animal Science, School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Sabrina T Amorim
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Elisa Peripolli
- School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Claudio U Magnabosco
- Embrapa Rice and Beans, GO-462, km12, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | - Fernando Baldi
- Department of Animal Science, School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
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Pagoto JM, Benfica LF, Borges MS, Ligori VA, Canesin RC, Mercadante MEZ, Monteiro FM. Relationship between age, scrotal circumference, postweaning weight and semen quality in Nellore and Caracu bulls: a cross sectional study. Trop Anim Health Prod 2023; 55:397. [PMID: 37934323 DOI: 10.1007/s11250-023-03818-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
The aim of this study was to investigate the relationship between age, scrotal circumference, postweaning weight and semen quality in Nellore and Caracu bulls selected for postweaning weight. Data from the andrological evaluation of 836 bulls born between 2000 and 2019, including 583 Nellore animals (Bos indicus) and 253 Caracu animals (Bos taurus), were used. The bulls were divided into categories of age at the time of assessment: category 1 consisted of animals aged 20 to 23 months (22 ± 0.76 months, 518 ± 94.17 kg), category 2 consisted of animals aged 24 to 35 months (30 ± 4.42 months, 679 ± 137.19 kg), and category 3 consisted of animals ≥ 36 months (60 ± 14.12 months, 907 ± 161.73 kg). The statistical model included the effects of breed, age category, date of semen collection, and breed x age category interaction. Heritability estimates for scrotal circumference at 13 months of age (SC1year) and semen quality traits were obtained for the sample of Nellore animals. Most semen quality traits improved with increasing age in both Nellore and Caracu animals. High heritability was observed for SC1year (0.45), while sperm motility, vigor, turbulence, and major, minor and total sperm defects exhibited low heritability (0.11, 0.019, 0.047, 0.017, 0.017 and 0.019, respectively). Spearman correlations of breeding values for postweaning weight (W378) and SC1year with the semen quality traits were low. Nellore and Caracu bulls have similar semen quality that improves with increasing age. In the Nellore breed, the heritability of SC is high, while semen quality traits exhibit low heritability. Selection for higher postweaning weight does not phenotypically affect the semen quality of bulls at breeding age.
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Affiliation(s)
- Jaine Martelo Pagoto
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University, Via de Acesso Professor Paulo Donato Castelane - Vila Industrial, Jaboticabal, SP, Brazil
| | - Lorena Ferreira Benfica
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University, Via de Acesso Professor Paulo Donato Castelane - Vila Industrial, Jaboticabal, SP, Brazil
| | - Marcelo Sant'Ana Borges
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University, Via de Acesso Professor Paulo Donato Castelane - Vila Industrial, Jaboticabal, SP, Brazil
| | - Viviane Andrade Ligori
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University, Via de Acesso Professor Paulo Donato Castelane - Vila Industrial, Jaboticabal, SP, Brazil
| | - Roberta Carrilho Canesin
- Beef Cattle Research Center, Institute of Animal Science (IZ), Road Carlos Tonani, 94 - Zona Industrial, Sertãozinho, São Paulo, CEP: 14160-970, Brazil
| | - Maria Eugênia Zerlotti Mercadante
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University, Via de Acesso Professor Paulo Donato Castelane - Vila Industrial, Jaboticabal, SP, Brazil
- Beef Cattle Research Center, Institute of Animal Science (IZ), Road Carlos Tonani, 94 - Zona Industrial, Sertãozinho, São Paulo, CEP: 14160-970, Brazil
| | - Fabio Morato Monteiro
- Department of Pathology, Reproduction and One Health, School of Agricultural and Veterinarian Sciences, São Paulo State University, Via de Acesso Professor Paulo Donato Castelane - Vila Industrial, Jaboticabal, SP, Brazil.
- Beef Cattle Research Center, Institute of Animal Science (IZ), Road Carlos Tonani, 94 - Zona Industrial, Sertãozinho, São Paulo, CEP: 14160-970, Brazil.
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Behren LE, König S, May K. Genomic Selection for Dairy Cattle Behaviour Considering Novel Traits in a Changing Technical Production Environment. Genes (Basel) 2023; 14:1933. [PMID: 37895282 PMCID: PMC10606080 DOI: 10.3390/genes14101933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Cow behaviour is a major factor influencing dairy herd profitability and is an indicator of animal welfare and disease. Behaviour is a complex network of behavioural patterns in response to environmental and social stimuli and human handling. Advances in agricultural technology have led to changes in dairy cow husbandry systems worldwide. Increasing herd sizes, less time availability to take care of the animals and modern technology such as automatic milking systems (AMSs) imply limited human-cow interactions. On the other hand, cow behaviour responses to the technical environment (cow-AMS interactions) simultaneously improve production efficiency and welfare and contribute to simplified "cow handling" and reduced labour time. Automatic milking systems generate objective behaviour traits linked to workability, milkability and health, which can be implemented into genomic selection tools. However, there is insufficient understanding of the genetic mechanisms influencing cow learning and social behaviour, in turn affecting herd management, productivity and welfare. Moreover, physiological and molecular biomarkers such as heart rate, neurotransmitters and hormones might be useful indicators and predictors of cow behaviour. This review gives an overview of published behaviour studies in dairy cows in the context of genetics and genomics and discusses possibilities for breeding approaches to achieve desired behaviour in a technical production environment.
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Affiliation(s)
- Larissa Elisabeth Behren
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390 Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390 Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390 Giessen, Germany
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Kava R, Peripolli E, Brunes LC, Espigolan R, Mendes EDM, da Silva Neto JB, Londoño-Gil M, Sainz RD, Lobo RB, Baldi F. Estimates of genetic and phenotypic parameters for feeding behaviour and feed efficiency-related traits in Nelore cattle. J Anim Breed Genet 2023; 140:264-275. [PMID: 36633154 DOI: 10.1111/jbg.12756] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/23/2022] [Indexed: 01/13/2023]
Abstract
The objective of this study was to obtain (co)variance components, heritability, and genetic and phenotypic correlation estimates for feed efficiency and feed behaviour-related indicator traits. Further, it aimed to predict the direct and correlated responses for feed efficiency traits when selection was applied for feeding behaviour-related traits in Nelore cattle. Phenotypic records (n = 4840) from 125 feed efficiency tests (RFI: Residual feed intake and DMI: Dry matter intake) carried out between 2011 and 2018 were considered in this study. Animals belonged to five farms located in two Brazilian geographical regions (Midwest and Southeast). Animals under similar management and environmental conditions in the feedlot were evaluated when they attained an average of 13.5 ± 4.15 months of age. Feed behaviour-related traits were also obtained, including meal criteria (MC), meal frequency (MF), average meal duration (AMD), meal duration (MD), average consumption per meal (ACM), and consumption rate (CR) through the GrowSafe System® electronic bunk system. The contemporary groups for all traits were composed of farm, management group, feed efficiency test, sex, and birth year. The (co)variance components were estimated using the restricted maximum likelihood method considering a multi-trait (n = 8) animal model. The heritability estimates for RFI (0.23 ± 0.02), DMI (0.31 ± 0.02), MF (0.65 ± 0.02), AMD (0.29 ± 0.02), ACM (0.24 ± 0.02), MD (0.41 ± 0.02), MC (0.48 ± 0.02), and CR (0.42 ± 0.02) were moderate to high. The highest genetic correlation was obtained between CR and MD (-0.91 ± 0.04), MD and AMD (0.73 ± 0.03), CR and AMD (-0.68 ± 0.04), and RFI and DMI (0.81 ± 0.02). The highest phenotypic correlation was between ACM and AMD (0.76 ± 0.02), DMI and MD (0.77 ± 0.02), and DMI and RFI (0.77 ± 0.02). Genetic improvement for feed efficiency and feeding behaviour-related traits is feasible and the results obtained herein provided valuable information regarding the genetic background of Nelore feeding behaviour-related traits. The genetic association between feeding behaviour and feed efficiency-related traits suggested that animals spending less time feeding at a low feeding rate also had lower DMI and higher feed efficiency (RFI), and likely had lower energy maintenance requirements. The relative efficiency of selection showed that feeding behaviour-related traits were not adequate indicator traits to improve RFI and DMI. The DMI might be an effective selection criterion to improve RFI and reduce the herd's maintenance requirements.
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Affiliation(s)
- Rafaela Kava
- Department of Animal Science, São Paulo State University -Júlio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane, Jaboticabal, Brazil
| | - Elisa Peripolli
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
| | | | - Rafael Espigolan
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
| | - Egleu D M Mendes
- Department of Animal Science, Texas A&M University, College Station, Sao Paulo, TX, USA
| | - João Barbosa da Silva Neto
- Department of Animal Science, São Paulo State University -Júlio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane, Jaboticabal, Brazil
| | - Marisol Londoño-Gil
- Department of Animal Science, São Paulo State University -Júlio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane, Jaboticabal, Brazil
| | - Roberto D Sainz
- Department of Animal Science, University of California, Davis, California, USA
| | - Raysildo B Lobo
- National Association of Breeders and Researchers (ANCP), Ribeirão Preto, Brazil
| | - Fernando Baldi
- Department of Animal Science, São Paulo State University -Júlio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane, Jaboticabal, Brazil
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Romanzin A, Florit E, Degano L, Spanghero M. Feeding efficiency and behaviour of growing bulls from the main Italian dual-purpose breeds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2146006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Alberto Romanzin
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Eleonora Florit
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Lorenzo Degano
- National Association of Italian Simmental breeders, Udine, Italy
| | - Mauro Spanghero
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, University of Udine, Udine, Italy
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Bresolin T, Ferreira R, Reyes F, Van Os J, Dórea J. Assessing optimal frequency for image acquisition in computer vision systems developed to monitor feeding behavior of group-housed Holstein heifers. J Dairy Sci 2022; 106:664-675. [DOI: 10.3168/jds.2022-22138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022]
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Cavani L, Brown WE, Parker Gaddis KL, Tempelman RJ, VandeHaar MJ, White HM, Peñagaricano F, Weigel KA. Estimates of genetic parameters for feeding behavior traits and their associations with feed efficiency in Holstein cows. J Dairy Sci 2022; 105:7564-7574. [PMID: 35863925 DOI: 10.3168/jds.2022-22066] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022]
Abstract
Residual feed intake (RFI) is commonly used to measure feed efficiency but individual intake recording systems are needed. Feeding behavior may be used as an indicator trait for feed efficiency using less expensive precision livestock farming technologies. Our goal was to estimate genetic parameters for feeding behavior and the genetic correlations with feed efficiency in Holstein cows. Data consisted of 75,877 daily feeding behavior records of 1,328 mid-lactation Holstein cows in 31 experiments conducted from 2009 to 2020 with an automated intake recording system. Feeding behavior traits included number of feeder visits per day, number of meals per day, duration of each feeder visit, duration of each meal, total duration of feeder visits, intake per visit, intake per meal [kg of dry matter (DM)], feeding rate per visit, and feeding rate per meal (kg of DM per min). The meal criterion was estimated as 26.4 min, which means that any pair of feeder visits separated by less than 26.4 min were considered part of the same meal. The statistical model included lactation and days in milk as fixed effects, and experiment-treatment, animal, and permanent environment as random effects. Genetic parameters for feeding behavior traits were estimated using daily records and weekly averages. Estimates of heritability for daily feeding behavior traits ranged from 0.09 ± 0.02 (number of meals; mean ± standard error) to 0.23 ± 0.03 (feeding rate per meal), with repeatability estimates ranging from 0.23 ± 0.01 (number of meals) to 0.52 ± 0.02 (number of feeder visits). Estimates of heritability for weekly averages of feeding behavior traits ranged from 0.19 ± 0.04 (number of meals) to 0.32 ± 0.04 (feeding rate per visit), with repeatability estimates ranging from 0.46 ± 0.02 (duration of each meal) to 0.62 ± 0.02 (feeding rate per visit and per meal). Most of the feeding behavior measures were strongly genetically correlated, showing that with more visits or meals per day, cows spend less time in each feeder visit or meal with lower intake per visit or meal. Weekly averages for feeding behavior traits were analyzed jointly with RFI and its components. Number of meals was genetically correlated with milk energy (0.48), metabolic body weight (-0.27), and RFI (0.19). Duration of each feeder visit and meal were genetically correlated with milk energy (0.43 and 0.44, respectively). Total duration of feeder visits per day was genetically correlated with DM intake (0.29), milk energy (0.62), metabolic body weight (-0.37), and RFI (0.20). Intake per visit and meal were genetically correlated with DM intake (0.63 and 0.87), milk energy (0.47 and 0.69), metabolic body weight (0.47 and 0.68), and RFI (0.31 and 0.65). Feeding rate was genetically correlated with DM intake (0.69), metabolic body weight (0.67), RFI (0.47), and milk energy (0.21). We conclude that measures of feeding behavior could be useful indicators of dairy cow feed efficiency, and individual cows that eat at a slower rate may be more feed efficient.
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Affiliation(s)
- Ligia Cavani
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison 53706.
| | - William E Brown
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison 53706
| | | | - Robert J Tempelman
- Department of Animal Science, Michigan State University, East Lansing 48824
| | | | - Heather M White
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison 53706
| | | | - Kent A Weigel
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison 53706
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Mota LFM, Santos SWB, Júnior GAF, Bresolin T, Mercadante MEZ, Silva JAV, Cyrillo JNSG, Monteiro FM, Carvalheiro R, Albuquerque LG. Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits. BMC Genomics 2022; 23:424. [PMID: 35672696 PMCID: PMC9172108 DOI: 10.1186/s12864-022-08671-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/03/2022] [Indexed: 11/28/2022] Open
Abstract
Background Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI). The FE-related traits and genomic information belong to two breeding programs that perform the FE test at different ages: post-weaning (1,024 animals IZ population) and post-yearling (918 animals for the QLT population). Results The meta-analyze MTwGWAS identified 14 genomic regions (-log10(p -value) > 5) regions mapped on BTA 1, 2, 3, 4, 7, 8, 11, 14, 15, 18, 21, and 29. These regions explained a large proportion of the total genetic variance for FE-related traits across-population ranging from 20% (FCR) to 36% (DMI) in the IZ population and from 22% (RFI) to 28% (ADG) in the QLT population. Relevant candidate genes within these regions (LIPE, LPL, IGF1R, IGF1, IGFBP5, IGF2, INS, INSR, LEPR, LEPROT, POMC, NPY, AGRP, TGFB1, GHSR, JAK1, LYN, MOS, PLAG1, CHCD7, LCAT, and PLA2G15) highlighted that the physiological mechanisms related to neuropeptides and the metabolic signals controlling the body's energy balance are responsible for leading to greater feed efficiency. Integrated meta-analysis results and functional pathway enrichment analysis highlighted the major effect of biological functions linked to energy, lipid metabolism, and hormone signaling that mediates the effects of peptide signals in the hypothalamus and whole-body energy homeostasis affecting the genetic control of FE-related traits in Nellore cattle. Conclusions Genes and pathways associated with common signals for feed efficiency-related traits provide better knowledge about regions with biological relevance in physiological mechanisms associated with differences in energy metabolism and hypothalamus signaling. These pleiotropic regions would support the selection for feed efficiency-related traits, incorporating and pondering causal variations assigning prior weights in genomic selection approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08671-w.
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Affiliation(s)
- Lucio F M Mota
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil.
| | - Samuel W B Santos
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Tiago Bresolin
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Maria E Z Mercadante
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil.,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil
| | - Josineudson A V Silva
- National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil.,School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu - SP, 18618-681, Brazil
| | - Joslaine N S G Cyrillo
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil
| | - Fábio M Monteiro
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil.,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil. .,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil.
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Kelly DN, Sleator RD, Murphy CP, Conroy SB, Berry DP. Genetic variability in the feeding behavior of crossbred growing cattle and associations with performance and feed efficiency. J Anim Sci 2021; 99:6407711. [PMID: 34673943 PMCID: PMC8679004 DOI: 10.1093/jas/skab303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/19/2021] [Indexed: 11/26/2022] Open
Abstract
The objectives of the present study were to estimate genetic parameters for
several feeding behavior traits in growing cattle, as well as the genetic
associations among and between feeding behavior and both performance and feed
efficiency traits. An additional objective was to investigate the use of feeding
behavior traits as predictors of genetic merit for feed intake. Feed intake and
live-weight data on 6,088 growing cattle were used of which 4,672 had ultrasound
data and 1,548 had feeding behavior data. Feeding behavior traits were defined
based on individual feed events or meal events (where individual feed events
were grouped into meals). Univariate and bivariate animal linear mixed models
were used to estimate (co)variance components. Heritability estimates (±
SE) for the feeding behavior traits ranged from 0.19 ± 0.08 for meals per
day to 0.61 ± 0.10 for feeding time per day. The coefficient of genetic
variation per trait varied from 5% for meals per day to 22% for the duration of
each feed event. Genetically heavier cattle, those with a higher daily energy
intake (MEI), or those that grew faster had a faster feeding rate, as well as a
greater energy intake per feed event and per meal. Better daily feed efficiency
(i.e., lower residual energy intake) was genetically associated with both a
shorter feeding time per day and shorter meal time per day. In a validation
population of 321 steers and heifers, the ability of estimated breeding values
(EBV) for MEI to predict (adjusted) phenotypic MEI was demonstrated; EBVs for
MEI were estimated using multi-trait models with different sets of predictor
traits such as liveweight and/or feeding behaviors. The correlation (± SE)
between phenotypic MEI and EBV for MEI marginally improved (P < 0.001) from
0.64 ± 0.03 to 0.68 ± 0.03 when feeding behavior phenotypes from the
validation population were included in a genetic evaluation that already
included phenotypic mid-test metabolic live-weight from the validation
population. This is one of the largest studies demonstrating that significant
exploitable genetic variation exists in the feeding behavior of young crossbred
growing cattle; such feeding behavior traits are also genetically correlated
with several performance and feed efficiency metrics. Nonetheless, there was
only a marginal benefit to the inclusion of time-related feeding behavior
phenotypes in a genetic evaluation for MEI to improve the precision of the EBVs
for this trait.
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Affiliation(s)
- David N Kelly
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.,Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Co. Cork, Ireland
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Co. Cork, Ireland
| | - Craig P Murphy
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Co. Cork, Ireland
| | - Stephen B Conroy
- Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Co. Cork, Ireland
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
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Zhang X, Li G, Li F, Zhang D, Yuan L, Zhao Y, Zhang Y, Li X, Song Q, Wang W. Effect of feed efficiency on growth performance, body composition, and fat deposition in growing Hu lambs. Anim Biotechnol 2021; 34:183-198. [PMID: 34346280 DOI: 10.1080/10495398.2021.1951747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The present study aimed to investigate the relationship between growth performance, body composition, and fat deposition factors, and feed efficiency in growing lambs. We measured average daily feed intake (ADFI) and body weight (BW) from 653 Hu sheep that were fed a pellet diet. The residual feed intake (RFI) not significantly genetic and phenotypic correlated with the metabolic body weight (MBW) and average daily gain (ADG), but it was significantly genetic and phenotypic correlated with ADFI and the feed conversion ratio (FCR) (p < 0.01). However, the FCR was significantly associated with growth traits (p < 0.01). With the same ADG, body fat deposition was greater in animals with low feed efficiency compared with high feed efficiency. Therefore, excessive fat deposition can affect the feed efficiency of the body, and organ weight and gut-weight have a greater impact on the feed efficiency of lambs. The reticulum stomach and jejunum of lambs with a low RFI were smaller compared with that in the high RFI, indicating that lambs with a low RFI have less intake and a higher absorption rate. Small organs, such as the liver, of lambs with high FE might be associated with low energy expenditure and slow metabolism. This study provides a new perspective to study the biological processes responsible for feed efficiency variation in lambs.
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Affiliation(s)
- Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Guoze Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lvfeng Yuan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Romanzin A, Degano L, Vicario D, Spanghero M. Feeding efficiency and behavior of young Simmental bulls selected for high growth capacity: Comparison of bulls with high vs. low residual feed intake. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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de Paula Freitas A, Santana Júnior ML, Schenkel FS, Mercadante MEZ, Cyrillo JNDSG, de Paz CCP. Different selection practices affect the environmental sensitivity of beef cattle. PLoS One 2021; 16:e0248186. [PMID: 33798231 PMCID: PMC8018670 DOI: 10.1371/journal.pone.0248186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/19/2021] [Indexed: 11/23/2022] Open
Abstract
The objective of the present study was to evaluate the effects of different selection practices on the environmental sensitivity of reproductive and growth traits in males and females of three Nellore selection lines [control (NeC), selection (NeS), and traditional (NeT) lines]. Moreover, genetic trends for the intercept and slope were estimated for each line, and the possible reranking of sires was examined. A total of 8,757 records of selection weight (SW), 3,331 records of scrotal circumference (SC), and 2,311 records of days to first calving (DFC) from Nellore cattle born between 1981 and 2017 were analyzed. (Co)variance components and genetic parameters of all traits were estimated using a reaction norm model with Gibbs sampler. In all cattle lines, the mean heritability of the studied traits ranged from 0.39 to 0.75 for SW in both males and females, from 0.46 to 0.68 for SC, and from 0.06 to 0.57 for DFC along with the environmental descriptor. In all cattle lines, the genetic correlation coefficients between the intercept and slope ranged from 0.03 to 0.81 for SW, from -0.14 to 0.39 for SC, and from -0.87 to -0.42 for DFC. Genetic trends for the slope and proportion of plastic genotypes indicated that the NeS line was more responsive to environmental changes, whereas the NeC and NeT lines tended to respond more modestly. Reranking of sires was observed for all traits, specifically in the NeC and NeT lines, because of the weak correlation between the opposite extreme environments. In the NeS line, reranking of sires was observed for DFC alone. Our results indicate that the effects of genotype-environment interaction are important and should be considered in genetic evaluations of Nellore cattle. Moreover, different selection practices affected the environmental sensitivity of the Nellore selection lines tested in this study.
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Affiliation(s)
- Anielly de Paula Freitas
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mário Luiz Santana Júnior
- Advanced Beef Cattle Research Center, Animal Science Institute/APTA/SAA, Sertãozinho, São Paulo, Brazil
| | - Flavio Schramm Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Claudia Cristina Paro de Paz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Advanced Beef Cattle Research Center, Animal Science Institute/APTA/SAA, Sertãozinho, São Paulo, Brazil
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