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Jiménez JM, Morales RM, Menéndez-Buxadera A, Demyda-Peyrás S, Laseca N, Molina A. Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle. Animals (Basel) 2023; 13:ani13030501. [PMID: 36766391 PMCID: PMC9913610 DOI: 10.3390/ani13030501] [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: 12/15/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
In this study, we analyzed the variation of reproductive efficiency, estimated as the deviation between the optimal and real parity number of females at each stage of the cow's life, in 12,554 cows belonging to the Retinta Spanish cattle breed, using classical repeatability and random regression models. The results of the analyses using repeatability model and the random regression model suggest that reproductive efficiency is not homogeneous throughout the cow's life. The h2 estimate for this model was 0.30, while for the random regression model it increased across the parities, from 0.24 at the first calving to 0.51 at calving number 9. Additionally, we performed a preliminary genome-wide association study for this trait in a population of 252 Retinta cows genotyped using the Axiom Bovine Genotyping v3 Array. The results showed 5 SNPs significantly associated with reproductive efficiency, located in two genomic regions (BTA4 and BTA28). The functional analysis revealed the presence of 5 candidate genes located within these regions, which were previously involved in different aspects related to fertility in cattle and mice models. This new information could give us a better understanding of the genetic architecture of reproductive traits in this species, as well as allow us to accurately select more fertile cows.
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Affiliation(s)
| | - Rosa María Morales
- Department of Genetics, Veterinary School, Campus de Rabanales, University of Córdoba, Edificio Gregor Mendel, Ctra. Madrid-Cádiz, km 396, 14014 Córdoba, Spain
- Correspondence: ; Tel.: +34-957-21-10-70
| | - Alberto Menéndez-Buxadera
- Department of Genetics, Veterinary School, Campus de Rabanales, University of Córdoba, Edificio Gregor Mendel, Ctra. Madrid-Cádiz, km 396, 14014 Córdoba, Spain
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1900, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata 1900, Argentina
| | - Nora Laseca
- Department of Genetics, Veterinary School, Campus de Rabanales, University of Córdoba, Edificio Gregor Mendel, Ctra. Madrid-Cádiz, km 396, 14014 Córdoba, Spain
| | - Antonio Molina
- Department of Genetics, Veterinary School, Campus de Rabanales, University of Córdoba, Edificio Gregor Mendel, Ctra. Madrid-Cádiz, km 396, 14014 Córdoba, Spain
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Warburton CL, Engle BN, Ross EM, Costilla R, Moore SS, Corbet NJ, Allen JM, Laing AR, Fordyce G, Lyons RE, McGowan MR, Burns BM, Hayes BJ. Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers. Genet Sel Evol 2020; 52:28. [PMID: 32460805 PMCID: PMC7251835 DOI: 10.1186/s12711-020-00547-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
Background In tropically-adapted beef heifers, application of genomic prediction for age at puberty has been limited due to low prediction accuracies. Our aim was to investigate novel methods of pre-selecting whole-genome sequence (WGS) variants and alternative analysis methodologies; including genomic best linear unbiased prediction (GBLUP) with multiple genomic relationship matrices (MGRM) and Bayesian (BayesR) analyses, to determine if prediction accuracy for age at puberty can be improved. Methods Genotypes and phenotypes were obtained from two research herds. In total, 868 Brahman and 960 Tropical Composite heifers were recorded in the first population and 3695 Brahman, Santa Gertrudis and Droughtmaster heifers were recorded in the second population. Genotypes were imputed to 23 million whole-genome sequence variants. Eight strategies were used to pre-select variants from genome-wide association study (GWAS) results using conditional or joint (COJO) analyses. Pre-selected variants were included in three models, GBLUP with a single genomic relationship matrix (SGRM), GBLUP MGRM and BayesR. Five-way cross-validation was used to test the effect of marker panel density (6 K, 50 K and 800 K), analysis model, and inclusion of pre-selected WGS variants on prediction accuracy. Results In all tested scenarios, prediction accuracies for age at puberty were highest in BayesR analyses. The addition of pre-selected WGS variants had little effect on the accuracy of prediction when BayesR was used. The inclusion of WGS variants that were pre-selected using a meta-analysis with COJO analyses by chromosome, fitted in a MGRM model, had the highest prediction accuracies in the GBLUP analyses, regardless of marker density. When the low-density (6 K) panel was used, the prediction accuracy of GBLUP was equal (0.42) to that with the high-density panel when only six additional sequence variants (identified using meta-analysis COJO by chromosome) were included. Conclusions While BayesR consistently outperforms other methods in terms of prediction accuracies, reasonable improvements in accuracy can be achieved when using GBLUP and low-density panels with the inclusion of a relatively small number of highly relevant WGS variants.
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Affiliation(s)
- Christie L Warburton
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia.
| | - Bailey N Engle
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Elizabeth M Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Roy Costilla
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Nicholas J Corbet
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD, Australia
| | - Jack M Allen
- Agricultural Business Research Institute, University of New England, Armidale, NSW, Australia
| | - Alan R Laing
- Formerly Department of Agriculture and Fisheries, Ayr, QLD, Australia
| | - Geoffry Fordyce
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Russell E Lyons
- School of Veterinary Science, The University of Queensland, St Lucia, QLD, Australia.,Neogen, University of Queensland, Gatton, QLD, Australia
| | - Michael R McGowan
- School of Veterinary Science, The University of Queensland, St Lucia, QLD, Australia
| | - Brian M Burns
- Formerly Department of Agriculture and Fisheries, Rockhampton, QLD, Australia
| | - Ben J Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
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Johnston DJ, Barwick SA, Fordyce G, Holroyd RG, Williams PJ, Corbet NJ, Grant T. Genetics of early and lifetime annual reproductive performance in cows of two tropical beef genotypes in northern Australia. ANIMAL PRODUCTION SCIENCE 2014. [DOI: 10.1071/an13043] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Reproduction records from 2137 cows first mated at 2 years of age and recorded through to 8.5 years of age were used to study the genetics of early and lifetime reproductive performance from two genotypes (1020 Brahman and 1117 Tropical Composite) in tropical Australian production systems. Regular ultrasound scanning of the reproductive tract, coupled with full recording of mating, calving and weaning histories, allowed a comprehensive evaluation of a range of reproductive traits. Results showed components traits of early reproductive performance had moderate to high heritabilities, especially in Brahmans. The heritability of lactation anoestrous interval in 3-year-old cows was 0.51 ± 0.18 and 0.26 ± 0.11 for Brahman and Tropical Composite, respectively. Heritabilities of binary reproductive output traits (conception rate, pregnancy rate, calving rate and weaning rate) from first and second matings were generally moderate to high on the underlying scale. Estimates ranged from 0.15 to 0.69 in Brahman and 0.15 to 0.34 in Tropical Composite, but were considerably lower when expressed on the observed scale, particularly for those traits with high mean levels. Heritabilities of lifetime reproduction traits were low, with estimates of 0.11 ± 0.06 and 0.07 ± 0.06 for lifetime annual weaning rate in Brahman and Tropical Composite, respectively. Significant differences in mean reproductive performance were observed between the two genotypes, especially for traits associated with anoestrus in first-lactation cows. Genetic correlations between early-in-life reproductive measures and lifetime reproduction traits were moderate to high. Genetic correlations between lactation anoestrous interval and lifetime annual weaning rate were –0.62 ± 0.24 in Brahman and –0.87 ± 0.32 in Tropical Composite. The results emphasise the substantial opportunity that exists to genetically improve weaning rates in tropical beef cattle breeds by focusing recording and selection on early-in-life female reproduction traits, particularly in Brahman for traits associated with lactation anoestrus.
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Morales R, Menéndez-Buxadera A, Avilés C, Molina A. Direct and maternal genetic effects for preweaning growth in Retinta cattle estimated by a longitudinal approach throughout the calving trajectory of the cow. J Anim Breed Genet 2013; 130:425-34. [DOI: 10.1111/jbg.12038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 02/22/2013] [Indexed: 11/28/2022]
Affiliation(s)
- R. Morales
- Department of Genetics; Veterinary Faculty; University of Córdoba; Córdoba Spain
| | - A. Menéndez-Buxadera
- Department of Genetics; Veterinary Faculty; University of Córdoba; Córdoba Spain
| | - C. Avilés
- Department of Animal Production; Veterinary Faculty; University of Córdoba; Córdoba Spain
| | - A. Molina
- Department of Genetics; Veterinary Faculty; University of Córdoba; Córdoba Spain
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