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Silva DO, Fernandes Júnior GA, Fonseca LFS, Mota LFM, Bresolin T, Carvalheiro R, de Albuquerque LG. Genome-wide association study for stayability at different calvings in Nellore beef cattle. BMC Genomics 2024; 25:93. [PMID: 38254039 PMCID: PMC10804543 DOI: 10.1186/s12864-024-10020-y] [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: 08/07/2023] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUNDING Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal's life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female's productive life. RESULTS The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant. CONCLUSION Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.
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Affiliation(s)
- Diogo Osmar Silva
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil.
| | - Gerardo Alves Fernandes Júnior
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Larissa Fernanda Simielli Fonseca
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Lúcio Flávio Macedo Mota
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Tiago Bresolin
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Roberto Carvalheiro
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Lucia Galvão de Albuquerque
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil.
- National Council for Scientific and Technological Development (CNPq), Brasília, Brazil.
- Present address: Departamento de Zootecnia, Via de acesso Paulo Donato Castellane s/n., São Paulo, Jaboticabal, CEP: 14884-900, Brazil.
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2
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Calderón-Chagoya R, Vega-Murillo VE, García-Ruiz A, Ríos-Utrera Á, Martínez-Velázquez G, Montaño-Bermúdez M. Discovering Genomic Regions Associated with Reproductive Traits and Frame Score in Mexican Simmental and Simbrah Cattle Using Individual SNP and Haplotype Markers. Genes (Basel) 2023; 14:2004. [PMID: 38002947 PMCID: PMC10671695 DOI: 10.3390/genes14112004] [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: 09/08/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Reproductive efficiency stands as a critical determinant of profitability within beef production systems. The incorporation of molecular markers can expedite advancements in reproductive performance. While the use of SNPs in association analysis is prevalent, approaches centered on haplotypes can offer a more comprehensive insight. The study used registered Simmental and Simbrah cattle genotyped with the GGP Bovine 150 k panel. Phenotypes included scrotal circumference (SC), heifer fertility (HF), stayability (STAY), and frame score (FS). After quality control, 105,129 autosomal SNPs from 967 animals were used. Haplotype blocks were defined based on linkage disequilibrium. Comparison between haplotypes and SNPs for reproductive traits and FS was conducted using Bayesian and frequentist models. 23, 13, 7, and 2 SNPs exhibited associations with FS, SC, HF, and STAY, respectively. In addition, seven, eight, seven, and one haplotypes displayed associations with FS, SC, HF, and STAY, respectively. Within these delineated genomic segments, potential candidate genes were associated.
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Affiliation(s)
- René Calderón-Chagoya
- Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Ciudad de México 04510, Mexico;
- National Center for Disciplinary Research in Physiology and Animal Improvement, National Institute for Forestry, Agricultural and Livestock Research, Querétaro 76280, Mexico;
| | - Vicente Eliezer Vega-Murillo
- Faculty of Veterinary Medicine and Zootechnics, Veracruzana University, Veracruz 91710, Mexico; (V.E.V.-M.); (Á.R.-U.)
| | - Adriana García-Ruiz
- National Center for Disciplinary Research in Physiology and Animal Improvement, National Institute for Forestry, Agricultural and Livestock Research, Querétaro 76280, Mexico;
| | - Ángel Ríos-Utrera
- Faculty of Veterinary Medicine and Zootechnics, Veracruzana University, Veracruz 91710, Mexico; (V.E.V.-M.); (Á.R.-U.)
| | - Guillermo Martínez-Velázquez
- Experimental Field Santiago Ixcuintla, National Institute for Forestry, Agricultural and Livestock Research, Nayarit 63570, Mexico;
| | - Moisés Montaño-Bermúdez
- National Center for Disciplinary Research in Physiology and Animal Improvement, National Institute for Forestry, Agricultural and Livestock Research, Querétaro 76280, Mexico;
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3
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Smith JL, Wilson ML, Nilson SM, Rowan TN, Schnabel RD, Decker JE, Seabury CM. Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle. BMC Genomics 2022; 23:517. [PMID: 35842584 PMCID: PMC9287884 DOI: 10.1186/s12864-022-08667-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled a dataset consisting of 15,815 Red Angus beef cattle distributed across the continental U.S. and a union set of 836,118 imputed SNPs to conduct genome-wide association analyses (GWAA) for growth traits using univariate linear mixed models (LMM); including birth weight, weaning weight, and yearling weight. Genomic relationship matrix heritability estimates were produced for all growth traits, and genotype-by-environment (GxE) interactions were investigated. Results Moderate to high heritabilities with small standard errors were estimated for birth weight (0.51 ± 0.01), weaning weight (0.25 ± 0.01), and yearling weight (0.42 ± 0.01). GWAA revealed 12 pleiotropic QTL (BTA6, BTA14, BTA20) influencing Red Angus birth weight, weaning weight, and yearling weight which met a nominal significance threshold (P ≤ 1e-05) for polygenic traits using 836K imputed SNPs. Moreover, positional candidate genes associated with Red Angus growth traits in this study (i.e., LCORL, LOC782905, NCAPG, HERC6, FAM184B, SLIT2, MMRN1, KCNIP4, CCSER1, GRID2, ARRDC3, PLAG1, IMPAD1, NSMAF, PENK, LOC112449660, MOS, SH3PXD2B, STC2, CPEB4) were also previously associated with feed efficiency, growth, and carcass traits in beef cattle. Collectively, 14 significant GxE interactions were also detected, but were less consistent among the investigated traits at a nominal significance threshold (P ≤ 1e-05); with one pleiotropic GxE interaction detected on BTA28 (24 Mb) for Red Angus weaning weight and yearling weight. Conclusions Sixteen well-supported QTL regions detected from the GWAA and GxE GWAA for growth traits (birth weight, weaning weight, yearling weight) in U.S. Red Angus cattle were found to be pleiotropic. Twelve of these pleiotropic QTL were also identified in previous studies focusing on feed efficiency and growth traits in multiple beef breeds and/or their composites. In agreement with other beef cattle GxE studies our results implicate the role of vasodilation, metabolism, and the nervous system in the genetic sensitivity to environmental stress. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08667-6.
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Affiliation(s)
- Johanna L Smith
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Miranda L Wilson
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
| | - Troy N Rowan
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA.,Informatics Institute, University of Missouri, Columbia, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA.,Informatics Institute, University of Missouri, Columbia, 65211, USA
| | - Christopher M Seabury
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA.
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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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5
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Sustainable Intensification of Beef Production in the Tropics: The Role of Genetically Improving Sexual Precocity of Heifers. Animals (Basel) 2022; 12:ani12020174. [PMID: 35049797 PMCID: PMC8772995 DOI: 10.3390/ani12020174] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Tropical pasture-based beef production systems play a vital role in global food security. The importance of promoting sustainable intensification of such systems has been debated worldwide. Demand for beef is growing together with concerns over the impact of its production on the environment. Implementing sustainable livestock intensification programs relies on animal genetic improvement. In tropical areas, the lack of sexual precocity is a bottleneck for cattle efficiency, directly impacting the sustainability of production systems. In the present review we present and discuss the state of the art of genetic evaluation for sexual precocity in Bos indicus beef cattle, covering the definition of measurable traits, genetic parameter estimates, genomic analyses, and a case study of selection for sexual precocity in Nellore breeding programs. Abstract Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.
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6
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Alves AAC, Espigolan R, Bresolin T, Costa RM, Fernandes Júnior GA, Ventura RV, Carvalheiro R, Albuquerque LG. Genome-enabled prediction of reproductive traits in Nellore cattle using parametric models and machine learning methods. Anim Genet 2020; 52:32-46. [PMID: 33191532 DOI: 10.1111/age.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 12/31/2022]
Abstract
This study aimed to assess the predictive ability of different machine learning (ML) methods for genomic prediction of reproductive traits in Nellore cattle. The studied traits were age at first calving (AFC), scrotal circumference (SC), early pregnancy (EP) and stayability (STAY). The numbers of genotyped animals and SNP markers available were 2342 and 321 419 (AFC), 4671 and 309 486 (SC), 2681 and 319 619 (STAY) and 3356 and 319 108 (EP). Predictive ability of support vector regression (SVR), Bayesian regularized artificial neural network (BRANN) and random forest (RF) were compared with results obtained using parametric models (genomic best linear unbiased predictor, GBLUP, and Bayesian least absolute shrinkage and selection operator, BLASSO). A 5-fold cross-validation strategy was performed and the average prediction accuracy (ACC) and mean squared errors (MSE) were computed. The ACC was defined as the linear correlation between predicted and observed breeding values for categorical traits (EP and STAY) and as the correlation between predicted and observed adjusted phenotypes divided by the square root of the estimated heritability for continuous traits (AFC and SC). The average ACC varied from low to moderate depending on the trait and model under consideration, ranging between 0.56 and 0.63 (AFC), 0.27 and 0.36 (SC), 0.57 and 0.67 (EP), and 0.52 and 0.62 (STAY). SVR provided slightly better accuracies than the parametric models for all traits, increasing the prediction accuracy for AFC to around 6.3 and 4.8% compared with GBLUP and BLASSO respectively. Likewise, there was an increase of 8.3% for SC, 4.5% for EP and 4.8% for STAY, comparing SVR with both GBLUP and BLASSO. In contrast, the RF and BRANN did not present competitive predictive ability compared with the parametric models. The results indicate that SVR is a suitable method for genome-enabled prediction of reproductive traits in Nellore cattle. Further, the optimal kernel bandwidth parameter in the SVR model was trait-dependent, thus, a fine-tuning for this hyper-parameter in the training phase is crucial.
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Affiliation(s)
- A A C Alves
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 14884-900, Brazil
| | - R Espigolan
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 14884-900, Brazil
| | - T Bresolin
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 14884-900, Brazil
| | - R M Costa
- Department of Exact Sciences, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 4884-900, Brazil
| | - G A Fernandes Júnior
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 14884-900, Brazil
| | - R V Ventura
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of Sao Paulo (USP), Pirassununga, 13635-900, Brazil
| | - R Carvalheiro
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 14884-900, Brazil.,National Council of Technological and Scientific Development (CNPq), Brasília, 71605-001, Brazil
| | - L G Albuquerque
- Department of Animal Science, School of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 14884-900, Brazil.,National Council of Technological and Scientific Development (CNPq), Brasília, 71605-001, Brazil
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7
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Shabalina T, Yin T, König S. Survival analyses in Holstein cows considering direct disease diagnoses and specific SNP marker effects. J Dairy Sci 2020; 103:8257-8273. [DOI: 10.3168/jds.2020-18174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
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8
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Ramos PVB, E Silva FF, da Silva LOC, Santiago GG, Menezes GRDO, Soriano Viana JM, Torres Júnior RAA, Gondo A, Brito LF. Genomic evaluation for novel stayability traits in Nellore cattle. Reprod Domest Anim 2020; 55:266-273. [PMID: 31880841 DOI: 10.1111/rda.13612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/19/2019] [Indexed: 02/01/2023]
Abstract
Cow stayability plays a major role on the overall profitability of the beef cattle industry, as it is directly related to reproductive efficiency and cow's longevity. Stayability (STAY63) is usually defined as the ability of the cow to calve at least three times until 76 months of age. This is a late-measured and lowly heritable trait, which consequently constrains genetic progress per time unit. Thus, the use of genomic information associated with novel stayability traits measured earlier in life will likely result in higher prediction accuracy and faster genetic progress for cow longevity. In this study, we aimed to compare pedigree-based and single-step GBLUP (ssGBLUP) methods as well as to estimate genetic correlations between the proposed stayability traits: STAY42, STAY53 and STAY64, which are measured at 52, 64 and 76 months of cow's age, considering at least 2, 3 and 4 calving, respectively. ssGBLUP yielded the highest prediction accuracy for all traits. The heritability estimates for STAY42, STAY53, STAY63 and STAY64 were 0.090, 0.151, 0.152 and 0.143, respectively. The genetic correlations between traits ranged from 0.899 (STAY42 and STAY53) to 0.985 (STAY53 and STAY63). The high genetic correlation between STAY42 and STAY53 suggests that besides being related to cow longevity, STAY53 is also associated with the early-stage reproductive efficiency. Thus, STAY53 is recommended as a suitable selection criterion for reproductive efficiency due to its higher heritability, favourable genetic correlation with other traits, and measured earlier in life, compared with the conventional stayability trait, that is STAY63.
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Affiliation(s)
| | | | | | - Gustavo Garcia Santiago
- Faculty of Veterinary Medicine and Animal Science, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | | | | | | | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
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9
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Guarini AR, Lourenco DAL, Brito LF, Sargolzaei M, Baes CF, Miglior F, Misztal I, Schenkel FS. Genetics and genomics of reproductive disorders in Canadian Holstein cattle. J Dairy Sci 2018; 102:1341-1353. [PMID: 30471913 DOI: 10.3168/jds.2018-15038] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/29/2018] [Indexed: 01/25/2023]
Abstract
In Canada, reproductive disorders known to affect the profitability of dairy cattle herds have been recorded by producers on a voluntary basis since 2007. Previous studies have shown the feasibility of using producer-recorded health data for genetic evaluations. Despite low heritability estimates and limited availability of phenotypic information, sufficient genetic variation has been observed for those traits to indicate that genetic progress, although slow, can be achieved. Pedigree- and genomic-based analyses were performed on producer-recorded health data of reproductive disorders, including retained placenta (RETP), metritis (METR), and cystic ovaries (CYST) using traditional BLUP and single-step genomic BLUP. Genome-wide association studies and functional analyses were carried out to unravel significant genomic regions and biological pathways, and to better understand the genetic mechanisms underlying RETP, METR, and CYST. Heritability estimates (posterior standard deviation in parentheses) were 0.02 (0.003), 0.01 (0.004), and 0.02 (0.003) for CYST, METR, and RETP, respectively. A moderate to strong genetic correlation of 0.69 (0.102) was found between METR and RETP. Averaged over all traits, sire proof reliabilities increased by approximately 11 percentage points with the incorporation of genomic data using a multiple-trait linear model. Biological pathways and associated genes underlying the studied traits were identified and will contribute to a better understanding of the biology of these 3 health disorders in dairy cattle.
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Affiliation(s)
- A R Guarini
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; The Semex Alliance, Guelph, ON, Canada N1H 6J2
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; Canadian Dairy Network, Guelph, ON, Canada N1K 1E5
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1.
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10
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Fennewald DJ, Weaber RL, Lamberson WR. Genotype by environment interaction for stayability of Red Angus in the United States. J Anim Sci 2018; 96:422-429. [PMID: 29385483 DOI: 10.1093/jas/skx080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bulls are used across a wide variety of environments through the use of artificial insemination. However, not all bulls rank the same for genetic merit in all environments. Sire selection could be more accurate via improved methods of characterization. The objective of this study was to evaluate the presence of genotype by environment (GxE) interaction for stayability in Red Angus in the United States. Environments were defined as nine regions within the continental United States with similar temperature-humidity indices. Stayability was defined as having a calf at age 4 given that the cow had a calf at age 2. A probit sire model was used to determine the heritability on the underlying scale. The percentage of females that calved at age 2 that also calved at age 4 ranged from 32.9 to 58.5% across regions and was 55.0% for the national data set. The heritability of stayability ranged from 0.10 to 0.57 across regions and was 0.12 for the national data set. Genetic correlations were estimated for stayability between all pairs of regions. An estimate of less than 0.80 indicates GxE at a level for concern. Genetic correlations between regions ranged from 0.32 to 0.87 and were <0.80 for 29 of 36 region pairs.
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Affiliation(s)
| | - Robert L Weaber
- Department of Animal Sciences and Industry, Kansas State University, Kansas
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11
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Oliveira DP, Lourenco DAL, Tsuruta S, Misztal I, Santos DJA, de Araújo Neto FR, Aspilcueta-Borquis RR, Baldi F, Carvalheiro R, de Camargo GMF, Albuquerque LG, Tonhati H. Reaction norm for yearling weight in beef cattle using single-step genomic evaluation. J Anim Sci 2018; 96:27-34. [PMID: 29365164 DOI: 10.1093/jas/skx006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/28/2017] [Indexed: 12/22/2022] Open
Abstract
When the environment on which the animals are raised is very diverse, selecting the best sires for different environments may require the use of models that account for genotype by environment interaction (G × E). The main objective of this study was to evaluate the existence of G × E for yearling weight (YW) in Nellore cattle using reaction norm models with only pedigree and pedigree combined with genomic relationships. Additionally, genomic regions associated with each environment gradient were identified. A total of 67,996 YW records were used in reaction norm models to calculate EBV and genomic EBV. The method of choice for genomic evaluations was single-step genomic BLUP (ssGBLUP). Traditional and genomic models were tested on the ability to predict future animal performance. Genetic parameters for YW were obtained with the average information restricted maximum likelihood method, with and without adding genomic information for 5,091 animals. Additive genetic variances explained by windows of 200 adjacent SNP were used to identify genomic regions associated with the environmental gradient. Estimated variance components for the intercept and the slope in traditional and genomic models were similar. In both models, the observed changes in heritabilities and genetic correlations for YW across environments indicate the occurrence of genotype by environment interactions. Both traditional and genomic models were capable of identifying the genotype by environment interaction; however, the inclusion of genomic information in reaction norm models improved the ability to predict animals' future performance by 7.9% on average. The proportion of genetic variance explained by the top SNP window was 0.77% for the regression intercept (BTA5) and 0.82% for the slope (BTA14). Single-step GBLUP seems to be a suitable model to predict genetic values for YW in different production environments.
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Affiliation(s)
- D P Oliveira
- Departamento of Animal Science, Sao Paulo State University, FCAV, Jaboticabal, Brazil
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - S Tsuruta
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - D J A Santos
- Departamento of Animal Science, Sao Paulo State University, FCAV, Jaboticabal, Brazil
| | - F R de Araújo Neto
- Federal Institute of Science and Technology Goiano - Campus Rio Verde, Rio Verde-GO Brazil
| | - R R Aspilcueta-Borquis
- College of Agricultural Sciences, Federal University of Grande Dourados (UFGD), Dourados-MS, Brazil
| | - F Baldi
- Departamento of Animal Science, Sao Paulo State University, FCAV, Jaboticabal, Brazil
| | - R Carvalheiro
- Departamento of Animal Science, Sao Paulo State University, FCAV, Jaboticabal, Brazil
| | - G M F de Camargo
- Departamento of Animal Science, Sao Paulo State University, FCAV, Jaboticabal, Brazil
| | - L G Albuquerque
- Departamento of Animal Science, Sao Paulo State University, FCAV, Jaboticabal, Brazil
| | - H Tonhati
- Departamento of Animal Science, Sao Paulo State University, FCAV, Jaboticabal, Brazil
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