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Diaz-Miranda EA, Penitente-Filho JM, Gomez-Leon VE, Lopez CJR, Villadiego FAC, Okano DS, Neto TM, Guimarães SF, Siqueira JB, Guimarães JD. Calving date as a potential predictor for the probability of approval in the first breeding soundness evaluation of Nellore bulls. Reprod Domest Anim 2023; 58:1225-1233. [PMID: 37389473 DOI: 10.1111/rda.14422] [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: 03/22/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023]
Abstract
Beef production systems primarily use natural service (NS) for breeding. However, a significant number of bulls used for NS are subfertile, limiting the profitability of the cow-calf operations. Therefore, producers should select bulls based on breeding soundness evolutions (BSE) to ensure higher pregnancy rates. Several factors can affect the bull ability to pass a BSE. We hypothesize that calving date would be a factor that affects the bull probability of approval at the first BSE. For this purpose, a multivariate logistic regression in a dataset of 14,737 BSEs from young Nellore bulls was used. Correlations between calving date, biometrics, and semen traits were evaluated using Pearson's correlation coefficient. Our results demonstrated that the calving date affected the probability of approval at the first BSE (p < .05). Indeed, the variable that added more information to our model was the calving date, far more than the age group of the bulls according to Akaike's information criterion. Hence, bulls born on day 0 of the calving season have 1.26 more chances to be approved at the first BSE than bulls born 21 days later. This result highlights the importance of getting the dams of future bulls pregnant as soon as possible in the breeding season. In addition, the calving season should be no longer than 47 days to achieve 80% BSE approval in 20-22 months old Nellore bulls. The strongest correlation was with SC, which decreased as the calving date increased. Therefore, the calving date may be used as a predictor of the outcome of the first BSE in young bulls. In that way, the calving date can help seedstock producers to maximize efficiency in making crucial management decisions during the breeding and calving season including nutrition, reproductive, and culling.
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Affiliation(s)
- Edgar Andres Diaz-Miranda
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, Brazil
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, Missouri, USA
| | | | | | | | | | - Denise Silva Okano
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Jeanne Broch Siqueira
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
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2
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Buss CE, Afonso J, de Oliveira PSN, Petrini J, Tizioto PC, Cesar ASM, Gustani-Buss EC, Cardoso TF, Rovadoski GA, da Silva Diniz WJ, de Lima AO, Rocha MIP, Andrade BGN, Wolf JB, Coutinho LL, Mourão GB, de Almeida Regitano LC. Bivariate GWAS reveals pleiotropic regions among feed efficiency and beef quality-related traits in Nelore cattle. Mamm Genome 2023; 34:90-103. [PMID: 36463529 DOI: 10.1007/s00335-022-09969-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/16/2022] [Indexed: 12/07/2022]
Abstract
Feed-efficient cattle selection is among the most leading solutions to reduce cost for beef cattle production. However, technical difficulties in measuring feed efficiency traits had limited the application in livestock. Here, we performed a Bivariate Genome-Wide Association Study (Bi-GWAS) and presented candidate biological mechanisms underlying the association between feed efficiency and meat quality traits in a half-sibling design with 353 Nelore steers derived from 34 unrelated sires. A total of 13 Quantitative Trait Loci (QTL) were found explaining part of the phenotypic variations. An important transcription factor of adipogenesis in cattle, the TAL1 (rs133408775) gene located on BTA3 was associated with intramuscular fat and average daily gain (IMF-ADG), and a region located on BTA20, close to CD180 and MAST4 genes, both related to fat accumulation. We observed a low positive genetic correlation between IMF-ADG (r = 0.30 ± 0.0686), indicating that it may respond to selection in the same direction. Our findings contributed to clarifying the pleiotropic modulation of the complex traits, indicating new QTLs for bovine genetic improvement.
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Affiliation(s)
- Carlos Eduardo Buss
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Mindflow Genomics, Leuven, Flanders, Belgium
| | - Juliana Afonso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Priscila S N de Oliveira
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Emanuele Cristina Gustani-Buss
- Mindflow Genomics, Leuven, Flanders, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
| | - Tainã Figueiredo Cardoso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Gregori A Rovadoski
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Division of Medical Genetics, Department of Genomics Science, University of Washington, Seattle, WA, USA
| | | | - Bruno Gabriel Nascimento Andrade
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
- Department of Computer Science, Munster Technological University/MTU, Cork, Ireland
| | - Jason B Wolf
- Department of Biology & Biochemistry, Milner Centre for Evolution Bath, University of Bath, Bath, BA2 7AY, UK
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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Alves AAC, da Costa RM, Fonseca LFS, Carvalheiro R, Ventura RV, Rosa GJDM, Albuquerque LG. A Random Forest-Based Genome-Wide Scan Reveals Fertility-Related Candidate Genes and Potential Inter-Chromosomal Epistatic Regions Associated With Age at First Calving in Nellore Cattle. Front Genet 2022; 13:834724. [PMID: 35692843 PMCID: PMC9178659 DOI: 10.3389/fgene.2022.834724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
This study aimed to perform a genome-wide association analysis (GWAS) using the Random Forest (RF) approach for scanning candidate genes for age at first calving (AFC) in Nellore cattle. Additionally, potential epistatic effects were investigated using linear mixed models with pairwise interactions between all markers with high importance scores within the tree ensemble non-linear structure. Data from Nellore cattle were used, including records of animals born between 1984 and 2015 and raised in commercial herds located in different regions of Brazil. The estimated breeding values (EBV) were computed and used as the response variable in the genomic analyses. After quality control, the remaining number of animals and SNPs considered were 3,174 and 360,130, respectively. Five independent RF analyses were carried out, considering different initialization seeds. The importance score of each SNP was averaged across the independent RF analyses to rank the markers according to their predictive relevance. A total of 117 SNPs associated with AFC were identified, which spanned 10 autosomes (2, 3, 5, 10, 11, 17, 18, 21, 24, and 25). In total, 23 non-overlapping genomic regions embedded 262 candidate genes for AFC. Enrichment analysis and previous evidence in the literature revealed that many candidate genes annotated close to the lead SNPs have key roles in fertility, including embryo pre-implantation and development, embryonic viability, male germinal cell maturation, and pheromone recognition. Furthermore, some genomic regions previously associated with fertility and growth traits in Nellore cattle were also detected in the present study, reinforcing the effectiveness of RF for pre-screening candidate regions associated with complex traits. Complementary analyses revealed that many SNPs top-ranked in the RF-based GWAS did not present a strong marginal linear effect but are potentially involved in epistatic hotspots between genomic regions in different autosomes, remarkably in the BTAs 3, 5, 11, and 21. The reported results are expected to enhance the understanding of genetic mechanisms involved in the biological regulation of AFC in this cattle breed.
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Affiliation(s)
- Anderson Antonio Carvalho Alves
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, Brazil
| | - Rebeka Magalhães da Costa
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, Brazil
| | - Larissa Fernanda Simielli Fonseca
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, Brazil
| | - Roberto Carvalheiro
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasília, Brazil
| | - Ricardo Vieira Ventura
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
| | | | - Lucia Galvão Albuquerque
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasília, Brazil
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Ferreira CER, Campos GS, Schmidt PI, Sollero BP, Goularte KL, Corcini CD, Gasperin BG, Lucia T, Boligon AA, Cardoso FF. Genome-wide association and genomic prediction for scrotal circumference in Hereford and Braford bulls. Theriogenology 2021; 172:268-280. [PMID: 34303226 DOI: 10.1016/j.theriogenology.2021.07.007] [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: 08/14/2020] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/19/2022]
Abstract
Scrotal circumference (SC) is widely used as a selection criterion for bulls in breeding programs, since it is easily assessed and correlated with several desirable reproductive traits. The objectives of this study were: to perform a genome-wide association study (GWAS) to identify genomic regions associated with SC adjusted for age (SCa) and for both age and weight (SCaw); to select Tag SNPs from GWAS to construct low-density panel for genomic prediction; and to compare the prediction accuracy of the SC through different methods for Braford and Hereford bulls from the same genetic breeding program. Data of SC from 18,172 bulls (30.4 ± 3.7 cm) and of genotypes from 131 sires and 3,545 animals were used. From GWAS, the top 1% of 1-Mb windows were observed on chromosome (BTA) 2, 20, 7, 8, 15, 3, 16, 27, 6 and 8 for SCa and on BTA 8, 15, 16, 21, 19, 2, 6, 5 and 10 for SCaw, representing 17.4% and 18.8% of the additive genetic variance of SCa and SCaw, respectively. The MeSH analysis was able to translate genomic information providing biological meanings of more specific gene functions related to the SCa and SCaw. The genomic enhancement methods, especially single step GBLUP, that combined phenotype and pedigree data with direct genomic values generated gains in accuracy in relation to pedigree BLUP, suggesting that genomic predictions should be applied to improve genetic gain and to narrow the generation interval compared to traditional methods. The proposed Tag-SNP panels may be useful for lower-cost commercial genomic prediction applications in the future, when the number of bulls in the reference population increases for SC in Hereford and Braford breeds.
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Affiliation(s)
- Carlos E R Ferreira
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
| | - Gabriel S Campos
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Patricia I Schmidt
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo, Jaboticabal, SP, Brazil
| | | | - Karina L Goularte
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Carine D Corcini
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Bernardo G Gasperin
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Thomaz Lucia
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Arione A Boligon
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Fernando F Cardoso
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Embrapa Pecuária Sul, Bagé, RS, Brazil
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5
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Miszura AA, Ferraz MVC, Cardoso RC, Polizel DM, Oliveira GB, Barroso JPR, Gobato LGM, Nogueira GP, Biava JS, Ferreira EM, Pires AV. Implications of growth rates and compensatory growth on puberty attainment in Nellore heifers. Domest Anim Endocrinol 2021; 74:106526. [PMID: 32810656 DOI: 10.1016/j.domaniend.2020.106526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/02/2020] [Accepted: 07/10/2020] [Indexed: 12/01/2022]
Abstract
This study investigated the effects of growth rates and compensatory growth on puberty attainment in Nellore heifers. Nellore heifers (n = 120), weaned at 8 ± 0.75 mo of age, were blocked by sire and BW (180 ± 8.6 kg) and assigned randomly to receive 1 of 4 treatments over a 10-mo period. Treatments included ad libitum feeding (high gain, HG), feed intake to gain 0.6 kg/d (medium gain, MG), restricted feeding (0.2 kg/d) for 4 mo followed by ad libitum feeding for 6 mo (compensatory gain, CG), and alternating periods of ad libitum and restricted feeding for 2 mo each throughout the trial (alternated CG, ACG). Puberty was assessed weekly by transrectal ultrasonography. Blood samples were collected at 8, 11, and 18 mo of age and at puberty to determine circulating concentrations of leptin. At 18 mo of age, nonpubertal heifers were treated with a puberty induction protocol using an intravaginal progestin device. There was no treatment effect (P = 0.17) on the percentage of heifers pubertal by 18 mo of age (HG: 66, MG: 40, CG: 58, and ACG: 52%), BW at puberty, and age at puberty. However, HG heifers had higher ADG (P < 0.01), dry matter intake (P < 0.01), and leptin concentrations (P = 0.03) than heifers from other groups. The response to the puberty induction protocol was similar (P = 0.90) among treatments. Regarding sire effects (genetic effects), there was an effect (P = 0.03) on the percentage of heifers pubertal by 18 mo of age and a tendency (P = 0.07) of sire effect in response to the puberty induction protocol. Compensatory growth appears to be an effective managerial approach to decrease feeding costs and stimulate puberty in Nellore heifers.
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Affiliation(s)
- A A Miszura
- Department of Nutrition and Animal Production, College of Veterinary and Animal Science, University of São Paulo, Duque de Caxias North Avenue, n 225, Pirassununga, São Paulo 13635-000, Brazil
| | - M V C Ferraz
- Department of Animal Science, Federal University of Amazonas, Macurany Avenue, Jacareacanga, Parintins, Amazonas 69152-240, Brazil
| | - R C Cardoso
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843-2471, USA
| | - D M Polizel
- Department of Nutrition and Animal Production, College of Veterinary and Animal Science, University of São Paulo, Duque de Caxias North Avenue, n 225, Pirassununga, São Paulo 13635-000, Brazil; Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, n 11, PO Box 09, Piracicaba, São Paulo 13418-900, Brazil
| | - G B Oliveira
- Department of Nutrition and Animal Production, College of Veterinary and Animal Science, University of São Paulo, Duque de Caxias North Avenue, n 225, Pirassununga, São Paulo 13635-000, Brazil
| | - J P R Barroso
- Department of Nutrition and Animal Production, College of Veterinary and Animal Science, University of São Paulo, Duque de Caxias North Avenue, n 225, Pirassununga, São Paulo 13635-000, Brazil
| | - L G M Gobato
- Department of Nutrition and Animal Production, College of Veterinary and Animal Science, University of São Paulo, Duque de Caxias North Avenue, n 225, Pirassununga, São Paulo 13635-000, Brazil
| | - G P Nogueira
- College of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, São Paulo 16050-680, Brazil
| | - J S Biava
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, n 11, PO Box 09, Piracicaba, São Paulo 13418-900, Brazil
| | - E M Ferreira
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, n 11, PO Box 09, Piracicaba, São Paulo 13418-900, Brazil
| | - A V Pires
- Department of Nutrition and Animal Production, College of Veterinary and Animal Science, University of São Paulo, Duque de Caxias North Avenue, n 225, Pirassununga, São Paulo 13635-000, Brazil; Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, n 11, PO Box 09, Piracicaba, São Paulo 13418-900, Brazil.
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Torres-Aburto VF, Barrientos-Morales M, Hernández-Flores H, Rodríguez-Andrade A, Cervantes-Acosta P, Landi V, Beltran AH, Domínguez-Mancera B. Breeding soundness examination and herd proficiency of local genetic groups of bulls in tropical environment conditions in Veracruz, Mexico. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1803773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Víctor Fernando Torres-Aburto
- Laboratory of Cell Biology, School of Veterinary Medicine and Animal Science, University of Veracruz, Veracruz, Mexico
| | - Manuel Barrientos-Morales
- Laboratory of Reproductive Biology, School of Veterinary Medicine and Animal Science, University of Veracruz, Veracruz, Mexico
| | - Herminio Hernández-Flores
- Laboratory of Cell Biology, School of Veterinary Medicine and Animal Science, University of Veracruz, Veracruz, Mexico
- Embryo-Espermex de Veracruz, Veracruz, México
| | | | - Patricia Cervantes-Acosta
- Laboratory of Molecular Biology, School of Veterinary Medicine and Animal Science, University of Veracruz, Veracruz, Mexico
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Antonio Hernández Beltran
- Laboratory of Functional Alterations, School of Veterinary Medicine and Animal Science, University of Veracruz, Veracruz, Mexico
| | - Belisario Domínguez-Mancera
- Laboratory of Cell Biology, School of Veterinary Medicine and Animal Science, University of Veracruz, Veracruz, Mexico
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Portes JV, Menezes GR, MacNeil MD, da Silva LO, Gondo A, Braccini Neto J. Selection indices for Nellore production systems in the Brazilian Cerrado. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Palaiokostas C, Jeuthe H, De Koning DJ. Assessing the potential of improving growth and survival to the eyed stage in selectively bred Arctic charr (Salvelinus alpinus). J Anim Breed Genet 2020; 138:326-337. [PMID: 33009889 PMCID: PMC8246994 DOI: 10.1111/jbg.12509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/21/2020] [Accepted: 09/05/2020] [Indexed: 11/29/2022]
Abstract
The Arctic charr breeding programme has been a main driving force for developing the aquaculture industry in Sweden. Selection has been performed for almost 40 years using animals from a closed breeding nucleus. The aim of the current study was to evaluate the potential of further improving growth-related traits taking into account the existence of genotype-by-environment interaction. Furthermore, we investigated the magnitude of the genetic component associated with survival to the eyed stage and potential associations with inbreeding coefficients. A preliminary heritability estimate of 0.23 (SE 0.20) was obtained for survival to the eyed stage using records spanning from 2000 to 2017 (n = 230). Moreover, moderate-to-high heritability estimates (0.27-0.49) were obtained for growth-related traits (body weight and length), using animals from the latest generation of selection (year class 2017). Those animals (n = 2,776), originating from 55 full-sib families, were split into two groups and reared in separate land-based facilities of commercial fish farms in Sweden. The growth-related traits were recorded twice in both sites when animals were of >1 and >2 years of age. Existence of sexual growth dimorphism was indicated with the males having on average 6%-8% higher total length and 22%-34% higher body weight. Furthermore, high genetic correlations regarding growth traits were obtained amongst animals reared at the two different sites (0.82-0.95). In addition, we assessed the accuracy of best linear unbiased prediction (BLUP)-derived estimated breeding values (EBVs) when phenotypes from each rearing site were subsequently masked and used as a validation set. A mean prediction accuracy of 0.60 (length) and 0.64 (weight) were derived for both rearing sites. Overall, our results suggest that further growth improvements should be possible in the subsequent generations of selection. Finally, even though indications for the existence of an underlying genetic component(s) involved in survival to the eyed stage were obtained additional data will be required for elucidating its magnitude.
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Affiliation(s)
- Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Jeuthe
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Aquaculture Center North, Kälarne, Sweden
| | - Dirk-Jan De Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Genetic Parameters of Birth Weight and Weaning Weight and Their Relationship with Gestation Length and Age at First Calving in Hanwoo ( Bos taurus coreanae). Animals (Basel) 2020; 10:ani10061083. [PMID: 32585973 PMCID: PMC7341273 DOI: 10.3390/ani10061083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Hanwoo cattle is considered one of the most economically important species and sources of nutrition for Koreans. Thus, both the reproductive performance and growth traits play an important role in the continuous development and productivity of Hanwoo farming. Therefore, to improve beef production and the profitability of Hanwoo farming, estimations of genetic parameters for birth weight (BW) and weaning weight (WW) and their relationship with age at first calving (AFC) and gestation length (GL) are necessary to understand and improve their responses to selection. Thus, this study estimated the variance components, heritability estimates of birth weight (BW) and weaning weight (WW) and their genetic and phenotypic relationship to age at first calving (AFC), and gestation length (GL). Results revealed a moderate and high heritability estimate for BW and WW, which suggests a sluggish and rapid response of these traits to selection, respectively. The moderate and high genetic correlation between BW and reproductive traits (AFC and GL) revealed that the selection of a heavier BW might result in a longer AFC and GL. Although the genetic correlation for BW and AFC was moderate and positive, the phenotypic correlation of close to zero may indicate that the phenotypic expression for these traits is likely to be influenced by the genotype-environment interaction (GxE). Moreover, the genetic and phenotypic correlation between WW and reproductive traits (AFC and GL) indicates that the selection of a heavier WW may not influence the AFC and GL of Hanwoo cow. These estimated genetic parameters and correlations for the studied traits can be utilized for genetic breeding programs of Hanwoo cattle. Abstract Hanwoo is one of the most economically important animal species in Korea due to its significant contribution to nutrition. However, the current selection index only focuses to improve carcass traits of Hanwoo. Thus, this study aimed to estimate the genetic parameters of birth weight (BW) and weaning weight (WW) and their genetic and phenotypic relationship to the age at first calving (AFC) and gestation length (GL) of Hanwoo. The genetic parameters for birth weight (BW) and weaning weight (WW) were estimated using the data obtained from 52,173 and 35,800 Hanwoo calves born from February 1998 to March 2017, respectively. Further, these data were used to determine their genetic and phenotypic correlation to age at first calving (AFC) and gestation length (GL). The heritability estimates of BW and WW and correlation coefficients were obtained using the average information restricted maximum likelihood (AIREML) procedure, fit in single and two-trait linear animal models. The estimated direct heritability for BW and WW was moderate (0.22 ± 0.02) and high (0.51 ± 0.03), respectively, while the maternal heritability for both traits was 0.12 ± 0.01 and 0.17 ± 0.01, respectively. The genetic correlation of BW and reproductive traits (AFC and GL) showed a moderate and high positive correlation coefficient of 0.33 ± 0.06 and 0.53 ± 0.02, respectively, while close to zero and low positive phenotypic correlations of 0.06 ± 0.01 and 0.21 ± 0.06 were also observed between the correlated traits, respectively. For the correlation analysis between WW and AFC, both the genetic and phenotypic correlation showed close to zero values of 0.04 ± 0.06 and −0.01 ± 0.01, respectively. Meanwhile, the genetic and phenotypic correlation between WW and GL showed low and negative correlations of −0.09 ± 0.06 and −0.09 ± 0.01, respectively. These obtained estimated variances for BW and WW and their corresponding genetic and phenotypic correlation to AFC and GL can be used as information for genetic improvement and subsequent economic improvement of Hanwoo farming.
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10
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Genetic correlations between scrotal circumference, heifer fertility and stayability in Charolais–Charbray cattle. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Reproductive performance of cows and genetic correlation with weight gains and principal components of traits used in selection of Nelore cattle. Livest Sci 2019. [DOI: 10.1016/j.livsci.2019.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Across-sex genomic-assisted genetic correlations for sex-influenced traits in Brahman cattle. Genet Sel Evol 2019; 51:41. [PMID: 31337334 PMCID: PMC6651968 DOI: 10.1186/s12711-019-0482-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/08/2019] [Indexed: 12/03/2022] Open
Abstract
Background This study aimed at estimating genetic parameters of sex-influenced production traits, evaluating the impact of genotype-by-sex interaction, and identifying the selection criteria that could be included in multiple-trait genetic evaluation to increase the rate of genetic improvement in both sexes. To achieve this goal, we used 10 male and 10 female phenotypes, which were measured in a population of 2111 Australian Brahman cattle genotyped at high-density. Results Heritability estimates ranged from very low (0.03 ± 0.03 for cows’ days to calving at first calving opportunity, DC1), to moderate (0.33 ± 0.08 for cows’ adult body weight, AWTc), and to high (0.95 ± 0.07 for cows’ hip height, HHc). Genetic correlation (rg) estimates between male and female homologous traits were favorable and ranged from moderate to high values, which indicate that selection for any of the traits in one sex would lead to a correlated response with the equivalent phenotype in the other sex. However, the estimated direct response was greater than the indirect response. Moreover, Pearson correlations between estimated breeding values obtained from each sex separately and from female and male homologous traits combined into a single trait in univariate analysis ranged from 0.74 to 0.99, which indicate that small ranking variation might appear if male and female traits are included as single or separate phenotypes. Genetic correlations between male growth and female reproductive traits were not significant, ranging from − 0.07 ± 0.13 to 0.45 ± 0.65. However, selection to improve HHc and AWTc in cows may reduce the percentage of normal sperm at 24 months of age (PNS24), possibly due to correlated effects in the same traits in males, which are related to late maturing animals. Conclusions Hip height in cows and PNS24, as well as blood insulin-like growth factor 1 (IGF1) concentration in bulls at 6 months of age are efficient selection criteria to improve male growth and female reproductive traits, simultaneously. In the presence of genotype-by-sex interactions, selection for traits in each sex results in high rates of genetic improvement, however, for the identification of animals with the highest breeding value, data for males and females may be considered a single trait. Electronic supplementary material The online version of this article (10.1186/s12711-019-0482-6) contains supplementary material, which is available to authorized users.
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Penitente-Filho JM, Fonseca E Silva F, Guimarães SEF, Miranda Neto T, da Costa EP, Siqueira JB, Waddington B, Guimarães JD. Use of nonlinear mixed models for describing testicular volume growth curve in Nellore bulls. Theriogenology 2019; 133:65-70. [PMID: 31063924 DOI: 10.1016/j.theriogenology.2019.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 01/09/2023]
Abstract
This study aimed to describe longitudinal testicular volume (TV) data of Nellore bulls by using nonlinear mixed models. Dataset consisted of 2,294 TV measurements from 505 bulls with ages ranging from 563 to 4,307 days. Nine nonlinear models were evaluated: Brody, Gompertz, Hill, Logistic I and II, Meloun, Michaelis-Menten, Mitscherlich and von Bertalanffy. Goodness of fit was evaluated by Akaike's information criterion (AIC), Bayesian information criterion (BIC), adjusted R2, percentage of convergence, error sum of squares (ESS), mean absolute deviation (MAD), and average prediction error (APE). These criteria were used to select the best model, then the absolute growth rate (AGR) for TV was estimated by the first derivate of the adjusted model related to time (∂Y/∂t). The values of adjusted R2, ESS, MAD and APE were similar among models. Percentage of convergence was higher for the Logistic I (76.8%), Logistic II (75.5%) and Mitscherlich (78.6%) models, but Logistic I and II showed the lowest values of AIC and BIC, indicating a better fit, so the Logistic I model was chosen for subsequent analyses. The TV growth occurred at a high rate until the inflection point, which was estimated at approximately 22 months of age; it stabilized and reached a plateau at approximately 2,500 days of age. This may suggest that TV is more related to sexual maturity than precocity. Additionally, the Logistic I model was used to estimate the growth curve and the AGR of the testicular length and width. As a result, testicular length increased at a higher rate than testicular width until approximately 1,600 days of age, indicating that the testes become longer with increasing age.
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Affiliation(s)
| | | | | | | | | | - Jeanne Broch Siqueira
- Institute of Agricultural Sciences, Universidade Federal Dos Vales Do Jequitinhonha e Mucuri, Unaí, Minas Gerais, Brazil.
| | - Bruna Waddington
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Schmidt PI, Campos GS, Roso VM, Souza FRP, Boligon AA. Genetic analysis of female reproductive efficiency, scrotal circumference and growth traits in Nelore cattle. Theriogenology 2019; 128:47-53. [PMID: 30743103 DOI: 10.1016/j.theriogenology.2019.01.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/21/2018] [Accepted: 01/31/2019] [Indexed: 11/16/2022]
Abstract
This study estimated the genetic variability and correlations between growth and reproductive traits in Nelore cattle. Annual genetic changes in female reproductive traits were also evaluated using repeated measures. Direct heritability was moderate for the growth traits and scrotal circumference (0.235 ± 0.015 to 0.443 ± 0.006), indicating genetic variability in these traits in the population studied. Maternal heritability was low for weaning height (0.042 ± 0.012) and weaning weight (0.112 ± 0.013). Regarding female reproductive traits, gestation length (GL) exhibited a slightly higher heritability (0.179 ± 0.006) than days to calving (DC) and calving interval (CI) (0.123 ± 0.006 and 0.105 ± 0.008, respectively). Repeatability was lower for GL (0.222 ± 0.006) compared to DC (0.318 ± 0.004) and CI (0.406 ± 0.006). Moderate and positive genetic correlations were obtained between the growth traits and scrotal circumference, ranging from 0.193 ± 0.019 to 0.519 ± 0.007. Weaning height showed low and positive genetic associations with GL (0.138 ± 0.007) and CI (0.189 ± 0.016), but was not correlated with DC (-0.016 ± 0.011). Similarly, weaning weight, yearling height or yearling weight was not associated with any of the female reproductive traits. The genetic correlations between scrotal circumference and female reproductive traits were negative and favorable, but low: -0.116 ± 0.020 (GL), -0.084 ± 0.028 (DC), and -0.054 ± 0.038 (CI). Favorable genetic associations were estimated between all female reproductive traits, ranging from 0.170 ± 0.040 to 0.442 ± 0.050. Genetic changes were favorable for GL and CI (-0.02 days/year and -0.11 days/year, respectively) and unfavorable for DC (0.16 days/year). In conclusion, selection for higher growth using the estimated breeding values for height and weight will not affect the reproductive performance of Nelore females. Nonetheless, simultaneous selection for growth and reproductive traits is possible.
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Affiliation(s)
- P I Schmidt
- Animal Science Department, Federal University of Pelotas, 96010-900, Pelotas, Brazil
| | - G S Campos
- Animal Science Department, Federal University of Rio Grande do Sul, 90040-060, Porto Alegre, Brazil
| | - V M Roso
- GenSys Associates and Consultants S/S LTDA, 90680-001, Porto Alegre, Brazil
| | - F R P Souza
- Ecology, Zoology and Genetics Department, Federal University of Pelotas, 96010-900, Pelotas, Brazil
| | - A A Boligon
- Animal Science Department, Federal University of Pelotas, 96010-900, Pelotas, Brazil.
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Penitente-Filho JM, Silva FFE, Facioni Guimarães S, Waddington B, da Costa EP, Gomez León V, Siqueira JB, Silva Okano D, Piccolo Maitan P, Guimarães JD. Relationship of testicular biometry with semen variables in breeding soundness evaluation of Nellore bulls. Anim Reprod Sci 2018; 196:168-175. [DOI: 10.1016/j.anireprosci.2018.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/05/2018] [Accepted: 07/27/2018] [Indexed: 10/28/2022]
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Abreu Silva B, Eler J, Santana M, Mattos E, Menezes I, Ferraz J. Genetic association between mature weight and early growth and heifer pregnancy traits in Nellore cattle. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Can scrotal circumference-based selection discard bulls with good productive and reproductive potential? PLoS One 2018; 13:e0193103. [PMID: 29494597 PMCID: PMC5832217 DOI: 10.1371/journal.pone.0193103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 02/05/2018] [Indexed: 12/29/2022] Open
Abstract
Nonlinear mixed models were used to describe longitudinal scrotal circumference (SC) measurements of Nellore bulls. Models comparisons were based on Akaike’s information criterion, Bayesian information criterion, error sum of squares, adjusted R2 and percentage of convergence. Sequentially, the best model was used to compare the SC growth curve in bulls divergently classified according to SC at 18–21 months of age. For this, bulls were classified into five groups: SC < 28cm; 28cm ≤ SC < 30cm, 30cm ≤ SC < 32cm, 32cm ≤ SC < 34cm and SC ≥ 34cm. Michaelis-Menten model showed the best fit according to the mentioned criteria. In this model, β1 is the asymptotic SC value and β2 represents the time to half-final growth and may be related to sexual precocity. Parameters of the individual estimated growth curves were used to create a new dataset to evaluate the effect of the classification, farms, and year of birth on β1 and β2 parameters. Bulls of the largest SC group presented a larger predicted SC along all analyzed periods; nevertheless, smaller SC group showed predicted SC similar to intermediate SC groups (28cm ≤ SC < 32cm), around 1200 days of age. In this context, bulls classified as improper for reproduction at 18–21 months old can reach a similar condition to those considered as good condition. In terms of classification at 18–21 months, asymptotic SC was similar among groups, farms and years; however, β2 differed among groups indicating that differences in growth curves are related to sexual precocity. In summary, it seems that selection based on SC at too early ages may lead to discard bulls with suitable reproductive potential.
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Teixeira B, MacNeil M, da Costa R, Dionello N, Yokoo M, Cardoso F. Genetic parameters and trends for traits of the Hereford and Braford breeds in Brazil. Livest Sci 2018. [DOI: 10.1016/j.livsci.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Takada L, Barbero MMD, Oliveira HN, de Camargo GMF, Fernandes Júnior GA, Aspilcueta-Borquis RR, Souza FRP, Boligon AA, Melo TP, Regatieri IC, Feitosa FLB, Fonseca LFS, Magalhães AFB, Costa RB, Albuquerque LG. Genomic association for sexual precocity in beef heifers using pre-selection of genes and haplotype reconstruction. PLoS One 2018; 13:e0190197. [PMID: 29293544 PMCID: PMC5749767 DOI: 10.1371/journal.pone.0190197] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
Reproductive traits are of the utmost importance for any livestock farming, but are difficult to measure and to interpret since they are influenced by various factors. The objective of this study was to detect associations between known polymorphisms in candidate genes related to sexual precocity in Nellore heifers, which could be used in breeding programs. Records of 1,689 precocious and non-precocious heifers from farms participating in the Conexão Delta G breeding program were analyzed. A subset of single nucleotide polymorphisms (SNP) located in the region of the candidate genes at a distance of up to 5 kb from the boundaries of each gene, were selected from the panel of 777,000 SNPs of the High-Density Bovine SNP BeadChip. Linear mixed models were used for statistical analysis of early heifer pregnancy, relating the trait with isolated SNPs or with haplotype groups. The model included the contemporary group (year and month of birth) as fixed effect and parent of the animal (sire effect) as random effect. The fastPHASE® and GenomeStudio® were used for reconstruction of the haplotypes and for analysis of linkage disequilibrium based on r2 statistics. A total of 125 candidate genes and 2,024 SNPs forming haplotypes were analyzed. Statistical analysis after Bonferroni correction showed that nine haplotypes exerted a significant effect (p<0.05) on sexual precocity. Four of these haplotypes were located in the Pregnancy-associated plasma protein-A2 gene (PAPP-A2), two in the Estrogen-related receptor gamma gene (ESRRG), and one each in the Pregnancy-associated plasma protein-A gene (PAPP-A), Kell blood group complex subunit-related family (XKR4) and mannose-binding lectin genes (MBL-1) genes. Although the present results indicate that the PAPP-A2, PAPP-A, XKR4, MBL-1 and ESRRG genes influence sexual precocity in Nellore heifers, further studies are needed to evaluate their possible use in breeding programs.
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Affiliation(s)
- Luciana Takada
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Marina M D Barbero
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Henrique N Oliveira
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | | | | | | | - Fabio R P Souza
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Arione A Boligon
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Thaise P Melo
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Inaê C Regatieri
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Fabieli L B Feitosa
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Larissa F S Fonseca
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Ana F B Magalhães
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Raphael B Costa
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Lucia G Albuquerque
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
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Boligon AA, Farias PP, Roso VM, Santana ML, Bignardi AB, Souza FRP. Genetic relations and indirect response to selection based on indices for scrotal circumference, visual scores and weight gain in beef cattle. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an16365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Genetic improvement in beef cattle involves evaluation for fertility, growth, carcass and visual scores traits. In general, genetic and economic parameters of these traits are considered for selection index construction. The present study was conducted to establish the magnitude of genetic and phenotypic correlations between visual scores of conformation, precocity and muscling at weaning and at yearling, birth to weaning weight gain, weaning to yearling weight gain and yearling scrotal circumference, and between these traits with selection indices applied in this population. In addition, the expected gains were obtained in such traits by taking under consideration the adopted selection criteria based on indices. Positive and high genetic correlations were estimated between weaning traits (visual scores and weight gain), ranging from 0.70 ± 0.02 to 0.97 ± 0.01. In genetic terms, the same visual scores, but evaluated in two ages (weaning and yearling) showed positive and high associations, with values of 0.90 ± 0.01 (conformation), 0.88 ± 0.01 (precocity) and 0.84 ± 0.02 (muscling). Genetic associations between yearling visual scores with scrotal circumference and weaning to yearling weight gain ranging from 0.36 ± 0.02 to 0.53 ± 0.01. Using the weaning index, are expected genetic gains ranging from 0.26% to 0.70%/year of the phenotypic mean of each weaning trait. Using the yearling index, annual genetic gains estimated for weaning traits (ranging from 0.25% to 0.63% of the phenotypic mean of the trait) were lower than that obtained at yearling (ranging from 0.27% to 0.98% of the phenotypic mean of the trait). Selection for one of traits obtained at weaning should result, by correlated response, in gain for the others. Also, the choice of animals with higher breeding values for weaning visual scores, beyond anticipate the selection process, should lead to favourable changes in these traits at yearling. Selection for better body composition at yearling (higher scores) should provide increase in scrotal circumference and weight gain. The use of higher values of the indices should result in positively correlated response, but in different magnitudes for each trait used in these indices. However, in both weaning and yearling, higher genetic gains to visual scores are expected in the same period, when the selection is based on the values of these indices.
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Abstract
Longer-lived cows tend to be more profitable and the stayability trait is a selection criterion correlated to longevity. An alternative to the traditional approach to evaluate stayability is its definition based on consecutive calvings, whose main advantage is the more accurate evaluation of young bulls. However, no study using this alternative approach has been conducted for Zebu breeds. Therefore, the objective of this study was to compare linear random regression models to fit stayability to consecutive calvings of Guzerá, Nelore and Tabapuã cows and to estimate genetic parameters for this trait in the respective breeds. Data up to the eighth calving were used. The models included the fixed effects of age at first calving and year-season of birth of the cow and the random effects of contemporary group, additive genetic, permanent environmental and residual. Random regressions were modeled by orthogonal Legendre polynomials of order 1 to 4 (2 to 5 coefficients) for contemporary group, additive genetic and permanent environmental effects. Using Deviance Information Criterion as the selection criterion, the model with 4 regression coefficients for each effect was the most adequate for the Nelore and Tabapuã breeds and the model with 5 coefficients is recommended for the Guzerá breed. For Guzerá, heritabilities ranged from 0.05 to 0.08, showing a quadratic trend with a peak between the fourth and sixth calving. For the Nelore and Tabapuã breeds, the estimates ranged from 0.03 to 0.07 and from 0.03 to 0.08, respectively, and increased with increasing calving number. The additive genetic correlations exhibited a similar trend among breeds and were higher for stayability between closer calvings. Even between more distant calvings (second v. eighth), stayability showed a moderate to high genetic correlation, which was 0.77, 0.57 and 0.79 for the Guzerá, Nelore and Tabapuã breeds, respectively. For Guzerá, when the models with 4 or 5 regression coefficients were compared, the rank correlations between predicted breeding values for the intercept were always higher than 0.99, indicating the possibility of practical application of the least parameterized model. In conclusion, the model with 4 random regression coefficients is recommended for the genetic evaluation of stayability to consecutive calvings in Zebu cattle.
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Boligon AA, Vicente IS, Vaz RZ, Campos GS, Souza FRP, Carvalheiro R, Albuquerque LG. Principal component analysis of breeding values for growth and reproductive traits and genetic association with adult size in beef cattle1. J Anim Sci 2016; 94:5014-5022. [DOI: 10.2527/jas.2016-0737] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Akanno EC, Plastow G, Fitzsimmons C, Miller SP, Baron V, Ominski K, Basarab JA. Genome-wide association for heifer reproduction and calf performance traits in beef cattle. Genome 2015; 58:549-57. [PMID: 26484575 DOI: 10.1139/gen-2015-0031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5-7, 9, 13-16, 19-21, 24, 25, and 27-29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.
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Affiliation(s)
- Everestus C Akanno
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Graham Plastow
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Carolyn Fitzsimmons
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,b Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, Canada
| | - Stephen P Miller
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,e AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Vern Baron
- b Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, Canada
| | - Kimberly Ominski
- d Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - John A Basarab
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,c Lacombe Research Centre, Alberta Agriculture and Rural Development, 6000 C & E Trail, Lacombe, AB, Canada
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de Camargo GMF, Porto-Neto LR, Kelly MJ, Bunch RJ, McWilliam SM, Tonhati H, Lehnert SA, Fortes MRS, Moore SS. Non-synonymous mutations mapped to chromosome X associated with andrological and growth traits in beef cattle. BMC Genomics 2015; 16:384. [PMID: 25975716 PMCID: PMC4432507 DOI: 10.1186/s12864-015-1595-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/28/2015] [Indexed: 12/31/2022] Open
Abstract
Background Previous genome-wide association analyses identified QTL regions in the X chromosome for percentage of normal sperm and scrotal circumference in Brahman and Tropical Composite cattle. These traits are important to be studied because they are indicators of male fertility and are correlated with female sexual precocity and reproductive longevity. The aim was to investigate candidate genes in these regions and to identify putative causative mutations that influence these traits. In addition, we tested the identified mutations for female fertility and growth traits. Results Using a combination of bioinformatics and molecular assay technology, twelve non-synonymous SNPs in eleven genes were genotyped in a cattle population. Three and nine SNPs explained more than 1% of the additive genetic variance for percentage of normal sperm and scrotal circumference, respectively. The SNPs that had a major influence in percentage of normal sperm were mapped to LOC100138021 and TAF7L genes; and in TEX11 and AR genes for scrotal circumference. One SNP in TEX11 was explained ~13% of the additive genetic variance for scrotal circumference at 12 months. The tested SNP were also associated with weight measurements, but not with female fertility traits. Conclusions The strong association of SNPs located in X chromosome genes with male fertility traits validates the QTL. The implicated genes became good candidates to be used for genetic evaluation, without detrimentally influencing female fertility traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1595-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregório Miguel Ferreira de Camargo
- Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Jaboticabal, SP, 14884-900, Brazil. .,Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia. .,School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia Brisbane, QLD, 4072, Australia.
| | - Laercio R Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia.
| | - Matthew J Kelly
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia Brisbane, QLD, 4072, Australia.
| | - Rowan J Bunch
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia.
| | - Sean M McWilliam
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia.
| | - Humberto Tonhati
- Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Jaboticabal, SP, 14884-900, Brazil.
| | - Sigrid A Lehnert
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, QLD, 4067, Australia.
| | - Marina R S Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia Brisbane, QLD, 4072, Australia.
| | - Stephen S Moore
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4067, Australia.
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Santana ML, Eler JP, Bignardi AB, Ferraz JBS. Two-trait random regression model to estimate the genetic association of scrotal circumference with female reproductive performance in Nelore cattle. Theriogenology 2015; 83:1534-40. [PMID: 25747195 DOI: 10.1016/j.theriogenology.2015.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/31/2015] [Accepted: 02/01/2015] [Indexed: 10/24/2022]
Abstract
In an attempt to determine when scrotal circumference (SC) could be a reasonable indicator of female reproductive performance, a series of two-trait random regression model (regression for SC on age at measurement) using Gibbs sampling was applied to field data of Nelore cattle raised in a tropical environment. The female traits evaluated were age at first calving (AFC), first calving interval (FCI), heifer pregnancy (HP), and stayability (STAY). The posterior means of heritability of female traits ranged from 0.15 for AFC to 0.46 for HP and were about 0.50 for SC. The posterior means of genetic correlations between SC and AFC, FCI, HP, STAY were up to -0.70, -0.25, 0.48, and 0.29, respectively. Genetically, SC could be a reasonable indicator of female puberty (e.g., HP) as long as it is measured at a young age (400-440 days). However, for female reproductive traits measured at an older age (e.g., STAY), SC is merely a modest or even poor indicator. The use of sire expected progeny differences for female reproductive traits will be more effective than the use of expected progeny differences for SC to improve the reproductive performance of female cattle.
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Affiliation(s)
- M L Santana
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Campus Universitário de Rondonópolis, Universidade Federal de Mato Grosso, Rondonópolis, Mato Grosso, Brazil.
| | - J P Eler
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - A B Bignardi
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Campus Universitário de Rondonópolis, Universidade Federal de Mato Grosso, Rondonópolis, Mato Grosso, Brazil
| | - J B S Ferraz
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
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Abstract
In order to achieve improvements in production efficiency in livestock, herds of high sexual precocity and good fertility are needed. These traits increase the availability of animals in herd, either for sale or selection, allowing both greater selective intensity and greater genetic progress. This study aimed at estimating genetic parameters for reproductive traits measured directly in females in order to verify whether they could be used as selection criteria for genetic improvement in Nellore cows, as well as estimating the genetic relationship among these traits and scrotal circumference (SC), the traditional selection criterion for sexual precocity in cattle. In addition to SC, stayability (STAY), number of calvings at 53 months (NC53) and heifers rebreeding (HR) were studied. The (co)variances and genetic parameters were estimated using Bayesian inference. STAY, NC53 and HR were analyzed assuming a threshold model, whereas SC was analyzed with a linear model. Heritability estimated for NC53 was 0.22, and this trait was strongly and positively correlated with STAY, meaning selection for NC53 would improve productive longevity of Nellore cows. Correlations estimated between HR and STAY (≈0.97) and between HR and NC53 (≈0.99) allow an improvement on HR rates if selection was applied to traits related to longevity. Genetic correlations among SC and female reproductive traits were positive but weak, suggesting the need to use reproductive traits directly measured in females in order to obtain greater improvements in sexual precocity and longevity.
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Eler JP, Bignardi AB, Ferraz JBS, Santana ML. Genetic relationships among traits related to reproduction and growth of Nelore females. Theriogenology 2014; 82:708-14. [PMID: 25023297 DOI: 10.1016/j.theriogenology.2014.06.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 05/29/2014] [Accepted: 06/01/2014] [Indexed: 11/29/2022]
Abstract
The objective of the study presented here was to analyze the genetic relationships among heifer pregnancy (HP), age at first calving (AFC), stayability (STAY), average annual productivity of the cow, in kilograms of weaned calf per cow per year (PRODAM), postweaning weight gain (PWG), and hip height (HH) of Nelore females from 12 Brazilian herds. (Co)variance components were obtained by six-trait animal model using Gibbs sampling. The posterior mean of the heritability estimates were 0.37, 0.18, 0.19, 0.16, 0.21, and 0.37 for HP, AFC, STAY, PRODAM, PWG, and HH, respectively. In general, the genetic correlations were strong between traits related to reproduction, for example, -0.85 between HP and AFC, and 0.94 between STAY and PRODAM. Weak genetic correlations were obtained between reproductive and growth traits (absolute values ranging from 0.02 to 0.30). Although weak, the genetic correlations between PWG and reproductive traits were favorable, whereas the genetic correlations between HH and reproductive traits were close to zero and slightly unfavorable for HP, AFC, and STAY. An increase of HH is therefore expected to have little or no negative effect on the reproductive performance of females. The posterior mean of genetic correlation between PWG and HH was moderate (0.50). On the basis of the heritability, genetic correlation estimates, and time to obtain data, HP and PRODAM seems to show the best potential as selection criteria to improve the productive and reproductive performance of Nelore females. In principle, it is possible to select for increased PWG without compromising the reproduction of Nelore females. However, selection for PWG may result in an increase of female HH as a correlated response, a fact that could increase management costs in advanced generations of selection. In the light of the results, all traits studied here can be used as selection criteria and there is no strong evidence of genetic antagonism among traits related to reproduction and growth of Nelore females.
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Affiliation(s)
- J P Eler
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - A B Bignardi
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Campus Universitário de Rondonópolis, Universidade Federal de Mato Grosso, Rondonópolis, MT, Brazil
| | - J B S Ferraz
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - M L Santana
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Campus Universitário de Rondonópolis, Universidade Federal de Mato Grosso, Rondonópolis, MT, Brazil.
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Oliveira Júnior GA, Eler JP, Ramírez-Díaz J, Ferraz JBS, Santana ML. Inclusion of weaning management group as a random effect in the genetic evaluation of postweaning traits in Nellore cattle. Trop Anim Health Prod 2014; 46:1031-6. [DOI: 10.1007/s11250-014-0607-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2014] [Indexed: 10/25/2022]
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Santana M, Eler J, Ferraz J. Alternative contemporary group structure to maximize the use of field records: Application to growth traits of composite beef cattle. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Santana ML, Eler JP, Bignardi AB, Ferraz JBS. Genetic associations among average annual productivity, growth traits, and stayability: A parallel between Nelore and composite beef cattle1. J Anim Sci 2013; 91:2566-74. [DOI: 10.2527/jas.2012-5856] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- M. L. Santana
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, C. Postal 23, CEP 13635-970, Pirassununga, SP, Brazil
| | - J. P. Eler
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, C. Postal 23, CEP 13635-970, Pirassununga, SP, Brazil
| | - A. B. Bignardi
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, CEP 14884-900, Jaboticabal, SP, Brazil
| | - J. B. S. Ferraz
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, CEP 14884-900, Jaboticabal, SP, Brazil
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Santana M, Eler J, Cucco D, Bignardi A, Ferraz J. Genetic associations between hip height, body conformation scores, and pregnancy probability at 14 months in Nelore cattle. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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de Camargo GMF, Baldi F, Regitano LCA, Tonhati H. Characterization of the exonic regions of the JY-1 gene in zebu cattle and buffaloes. Reprod Domest Anim 2013; 48:918-22. [PMID: 23714232 DOI: 10.1111/rda.12186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/02/2013] [Indexed: 11/30/2022]
Abstract
Protein JY-1 is an oocyte-specific protein that plays an important regulatory role in the granulosa cell layer and during the early embryo development stages. It is the first specific protein of maternal origin discovered in a single-ovulating species. In this study, the exon regions of the JY-1 gene were characterized by sequencing in 20 unrelated cattle (Bos taurus indicus) and 20 unrelated buffaloes (Bubalus bubalis). Eighteen polymorphisms were detected in cattle and 10 polymorphisms in buffaloes. Some of the polymorphisms were identified in codifying regions and caused amino acid changes. The insertion of a thymine was detected in the codifying region of exon 3 of the buffalo sequence when compared to the cattle one. This insertion causes a change in the codons frameshift from this point onwards, modifying the 19 terminal amino acids of the buffalo protein and creating a premature stop codon. This finding may explain reproductive differences between cattle and buffaloes in terms of follicle recruitment, embryo development and incidence of twin pregnancies.
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Affiliation(s)
- G M F de Camargo
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, Brazil
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Peters SO, Kizilkaya K, Garrick DJ, Fernando RL, Reecy JM, Weaber RL, Silver GA, Thomas MG. Heritability and Bayesian genome-wide association study of first service conception and pregnancy in Brangus heifers. J Anim Sci 2012; 91:605-12. [PMID: 23148252 DOI: 10.2527/jas.2012-5580] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Brangus [3/8 Brahman (Bos indicus) × 5/8 Angus (Bos taurus); n ≈ 800] heifers from 67 sires were used to estimate heritability and conduct a genome-wide association study (GWAS) for 2 binary fertility traits: first service conception (FSC) and heifer pregnancy (HPG). Genotypes were from 53,692 loci on the BovineSNP50 (Infinium Bead Chips, Illumina, San Diego, CA). Yearling heifers were estrous synchronized, bred by AI, and then exposed to natural service breeding. Reproductive ultrasound and DNA-based parentage testing were used to determine if the heifer conceived by AI or natural service, and code for FSC and HPG traits. Success rates for FSC and HPG were 53.3% and 78.0% ± 0.01%, and corresponding heritability estimates were 0.18 ± 0.07 and 0.10 ± 0.06, respectively. The models used in obtaining these heritability estimates and GWAS included fixed effects of year (i.e., 2005 to 2007), birth location, calving season, age of dam, and contemporary group. In GWAS, simultaneous associations of 1 Mb SNP windows with phenotype were undertaken with Bayes C analyses using GenSel software. The 1 Mb windows contained 21.3 ± 1.1 SNP. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.9995 having no effect on phenotype. The windows that accounted for 1.0% of genetic variance were considered as QTL associated with FSC or HPG. Eighteen QTL existed on 15 chromosomes for the 2 traits. On average, each QTL accounted for 2.43% ± 0.2% of the genetic variance. Chromosome 8 harbored 2 QTL for FSC and 1 for HPG; however, these regions did not overlap. Chromosomes 3, 15, 16, 19, 24, 26, 27, 29, and X included QTL only for FSC, whereas chromosomes 2, 4, 10, 13, and 20 contained QTL only for HPG. The multitude of QTL detected for FSC and HPG in this GWAS involving Brangus heifers exemplifies the complex regulation of variation in heifer fertility traits of low heritability.
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Affiliation(s)
- S O Peters
- Department of Animal and Range Sciences, New Mexico State University, Las Cruces 88003
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Phenotypic plasticity of composite beef cattle performance using reaction norms model with unknown covariate. Animal 2012; 7:202-10. [PMID: 23032089 DOI: 10.1017/s1751731112001711] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The objective of the present study was to determine the presence of genotype by environment interaction (G × E) and to characterize the phenotypic plasticity of birth weight (BW), weaning weight (WW), postweaning weight gain (PWG) and yearling scrotal circumference (SC) in composite beef cattle using the reaction norms model with unknown covariate. The animals were born between 1995 and 2008 on 33 farms located throughout all Brazilian biomes between latitude -7° and -31°, longitude -40° and -63°. The contemporary group was chosen as the environmental descriptor, that is, the environmental covariate of the reaction norms. In general, higher estimates of direct heritability were observed in extreme favorable environments. The mean of direct heritability across the environmental gradient ranged from 0.05 to 0.51, 0.09 to 0.43, 0.01 to 0.43 and from 0.12 to 0.26 for BW, WW, PWG and SC, respectively. The variation in direct heritability observed indicates a different response to selection according to the environment in which the animals of the population are evaluated. The correlation between the level and slope of the reaction norm for BW and PWG was high, indicating that animals with higher average breeding values responded better to improvement in environmental conditions, a fact characterizing a scale of G × E. Low correlation between the intercept and slope was obtained for WW and SC, implying re-ranking of animals in different environments. Genetic variation exists in the sensitivity of animals to the environment, a fact that permits the selection of more plastic or robust genotypes in the population studied. Thus, the G × E is an important factor that should be considered in the genetic evaluation of the present population of composite beef cattle.
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