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Marrella MA, Biase FH. A multi-omics analysis identifies molecular features associated with fertility in heifers (Bos taurus). Sci Rep 2023; 13:12664. [PMID: 37542054 PMCID: PMC10403585 DOI: 10.1038/s41598-023-39858-0] [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: 04/25/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023] Open
Abstract
Infertility or subfertility is a critical barrier to sustainable cattle production, including in heifers. The development of heifers that do not produce a calf within an optimum window of time is a critical factor for the profitability and sustainability of the cattle industry. In parallel, heifers are an excellent biomedical model for understanding the underlying etiology of infertility because well-nourished heifers can still be infertile, mostly because of inherent physiological and genetic causes. Using a high-density single nucleotide polymorphism (SNP) chip, we collected genotypic data, which were analyzed using an association analysis in PLINK with Fisher's exact test. We also produced quantitative transcriptome data and proteome data. Transcriptome data were analyzed using the quasi-likelihood test followed by the Wald's test, and the likelihood test and proteome data were analyzed using a generalized mixed model and Student's t-test. We identified two SNPs significantly associated with heifer fertility (rs110918927, chr12: 85648422, P = 6.7 × 10-7; and rs109366560, chr11:37666527, P = 2.6 × 10-5). We identified two genes with differential transcript abundance (eFDR ≤ 0.002) between the two groups (Fertile and Sub-Fertile): Adipocyte Plasma Membrane Associated Protein (APMAP, 1.16 greater abundance in the Fertile group) and Dynein Axonemal Intermediate Chain 7 (DNAI7, 1.23 greater abundance in the Sub-Fertile group). Our analysis revealed that the protein Alpha-ketoglutarate-dependent dioxygenase FTO was more abundant in the plasma collected from Fertile heifers relative to their Sub-Fertile counterparts (FDR < 0.05). Lastly, an integrative analysis of the three datasets identified a series of molecular features (SNPs, gene transcripts, and proteins) that discriminated 21 out of 22 heifers correctly based on their fertility category. Our multi-omics analyses confirm the complex nature of female fertility. Very importantly, our results also highlight differences in the molecular profile of heifers associated with fertility that transcend the constraints of breed-specific genetic background.
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Affiliation(s)
- Mackenzie A Marrella
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Fernando H Biase
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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2
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Tahir MS, Porto-Neto LR, Reverter-Gomez T, Olasege BS, Sajid MR, Wockner KB, Tan AWL, Fortes MRS. Utility of multi-omics data to inform genomic prediction of heifer fertility traits. J Anim Sci 2022; 100:skac340. [PMID: 36239447 PMCID: PMC9733504 DOI: 10.1093/jas/skac340] [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: 06/18/2022] [Accepted: 10/12/2022] [Indexed: 12/15/2022] Open
Abstract
Biologically informed single nucleotide polymorphisms (SNPs) impact genomic prediction accuracy of the target traits. Our previous genomics, proteomics, and transcriptomics work identified candidate genes related to puberty and fertility in Brahman heifers. We aimed to test this biological information for capturing heritability and predicting heifer fertility traits in another breed i.e., Tropical Composite. The SNP from the identified genes including 10 kilobases (kb) region on either side were selected as biologically informed SNP set. The SNP from the rest of the Bos taurus genes including 10-kb region on either side were selected as biologically uninformed SNP set. Bovine high-density (HD) complete SNP set (628,323 SNP) was used as a control. Two populations-Tropical Composites (N = 1331) and Brahman (N = 2310)-had records for three traits: pregnancy after first mating season (PREG1, binary), first conception score (FCS, score 1 to 3), and rebreeding score (REB, score 1 to 3.5). Using the best linear unbiased prediction method, effectiveness of each SNP set to predict the traits was tested in two scenarios: a 5-fold cross-validation within Tropical Composites using biological information from Brahman studies, and application of prediction equations from one breed to the other. The accuracy of prediction was calculated as the correlation between genomic estimated breeding values and adjusted phenotypes. Results show that biologically informed SNP set estimated heritabilities not significantly better than the control HD complete SNP set in Tropical Composites; however, it captured all the observed genetic variance in PREG1 and FCS when modeled together with the biologically uninformed SNP set. In 5-fold cross-validation within Tropical Composites, the biologically informed SNP set performed marginally better (statistically insignificant) in terms of prediction accuracies (PREG1: 0.20, FCS: 0.13, and REB: 0.12) as compared to HD complete SNP set (PREG1: 0.17, FCS: 0.10, and REB: 0.11), and biologically uninformed SNP set (PREG1: 0.16, FCS: 0.10, and REB: 0.11). Across-breed use of prediction equations still remained a challenge: accuracies by all SNP sets dropped to around zero for all traits. The performance of biologically informed SNP was not significantly better than other sets in Tropical Composites. However, results indicate that biological information obtained from Brahman was successful to predict the fertility traits in Tropical Composite population.
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Affiliation(s)
- Muhammad S Tahir
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Laercio R Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, St. Lucia, Brisbane 4072, QLD, Australia
| | - Toni Reverter-Gomez
- Commonwealth Scientific and Industrial Research Organization, St. Lucia, Brisbane 4072, QLD, Australia
| | - Babatunde S Olasege
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Mirza R Sajid
- Department of Statistics, University of Gujrat, 50700 Punjab, Pakistan
| | - Kimberley B Wockner
- Queensland Department of Agriculture and Fisheries, Brisbane 4072, QLD, Australia
| | - Andre W L Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
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Shao B, Sun H, Ahmad MJ, Ghanem N, Abdel-Shafy H, Du C, Deng T, Mansoor S, Zhou Y, Yang Y, Zhang S, Yang L, Hua G. Genetic Features of Reproductive Traits in Bovine and Buffalo: Lessons From Bovine to Buffalo. Front Genet 2021; 12:617128. [PMID: 33833774 PMCID: PMC8021858 DOI: 10.3389/fgene.2021.617128] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Bovine and buffalo are important livestock species that have contributed to human lives for more than 1000 years. Improving fertility is very important to reduce the cost of production. In the current review, we classified reproductive traits into three categories: ovulation, breeding, and calving related traits. We systematically summarized the heritability estimates, molecular markers, and genomic selection (GS) for reproductive traits of bovine and buffalo. This review aimed to compile the heritability and genome-wide association studies (GWASs) related to reproductive traits in both bovine and buffalos and tried to highlight the possible disciplines which should benefit buffalo breeding. The estimates of heritability of reproductive traits ranged were from 0 to 0.57 and there were wide differences between the populations. For some specific traits, such as age of puberty (AOP) and calving difficulty (CD), the majority beef population presents relatively higher heritability than dairy cattle. Compared to bovine, genetic studies for buffalo reproductive traits are limited for age at first calving and calving interval traits. Several quantitative trait loci (QTLs), candidate genes, and SNPs associated with bovine reproductive traits were screened and identified by candidate gene methods and/or GWASs. The IGF1 and LEP pathways in addition to non-coding RNAs are highlighted due to their crucial relevance with reproductive traits. The distribution of QTLs related to various traits showed a great differences. Few GWAS have been performed so far on buffalo age at first calving, calving interval, and days open traits. In addition, we summarized the GS studies on bovine and buffalo reproductive traits and compared the accuracy between different reports. Taken together, GWAS and candidate gene approaches can help to understand the molecular genetic mechanisms of complex traits. Recently, GS has been used extensively and can be performed on multiple traits to improve the accuracy of prediction even for traits with low heritability, and can be combined with multi-omics for further analysis.
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Affiliation(s)
- Baoshun Shao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hui Sun
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Jamil Ahmad
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Nasser Ghanem
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hamdy Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Chao Du
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tingxian Deng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Yang Zhou
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- International Joint Research Centre for Animal Genetics, Breeding and Reproduction, Wuhan, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Yifen Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Shujun Zhang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- International Joint Research Centre for Animal Genetics, Breeding and Reproduction, Wuhan, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- International Joint Research Centre for Animal Genetics, Breeding and Reproduction, Wuhan, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Guohua Hua
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- International Joint Research Centre for Animal Genetics, Breeding and Reproduction, Wuhan, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
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4
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Gutierrez-Reinoso MA, Aponte PM, Garcia-Herreros M. Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review. Animals (Basel) 2021; 11:599. [PMID: 33668747 PMCID: PMC7996307 DOI: 10.3390/ani11030599] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future.
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Affiliation(s)
- Miguel A. Gutierrez-Reinoso
- Facultad de Ciencias Agropecuarias y Recursos Naturales, Carrera de Medicina Veterinaria, Universidad Técnica de Cotopaxi (UTC), Latacunga 05-0150, Ecuador
- Laboratorio de Biotecnología Animal, Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción (UdeC), Chillán 3780000, Chile
| | - Pedro M. Aponte
- Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Quito 170157, Ecuador
- Campus Cumbayá, Instituto de Investigaciones en Biomedicina “One-health”, Universidad San Francisco de Quito (USFQ), Quito 170157, Ecuador
| | - Manuel Garcia-Herreros
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV), 2005-048 Santarém, Portugal
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Moorey SE, Walker BN, Elmore MF, Elmore JB, Rodning SP, Biase FH. Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus). Sci Rep 2020; 10:16786. [PMID: 33033295 PMCID: PMC7544915 DOI: 10.1038/s41598-020-73694-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/18/2020] [Indexed: 12/23/2022] Open
Abstract
Infertility is a challenging phenomenon in cattle that reduces the sustainability of beef production worldwide. Here, we tested the hypothesis that gene expression profiles of protein-coding genes expressed in peripheral white blood cells (PWBCs), and circulating micro RNAs in plasma, are associated with female fertility, measured by pregnancy outcome. We drew blood samples from 17 heifers on the day of artificial insemination and analyzed transcript abundance for 10,496 genes in PWBCs and 290 circulating micro RNAs. The females were later classified as pregnant to artificial insemination, pregnant to natural breeding or not pregnant. We identified 1860 genes producing significant differential coexpression (eFDR < 0.002) based on pregnancy outcome. Additionally, 237 micro RNAs and 2274 genes in PWBCs presented differential coexpression based on pregnancy outcome. Furthermore, using a machine learning prediction algorithm we detected a subset of genes whose abundance could be used for blind categorization of pregnancy outcome. Our results provide strong evidence that transcript abundance in circulating white blood cells is associated with fertility in heifers.
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Affiliation(s)
- Sarah E Moorey
- Department of Animal Science, University of Tennessee, 2506 River Drive, Knoxville, TN, 37996, USA
| | - Bailey N Walker
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Drive, Blacksburg, VA, 24061, USA
| | - Michelle F Elmore
- Department of Animal Sciences, Auburn University, 107 Comer Hall, Auburn, AL, 36849, USA
- Alabama Cooperative Extension System, 107 Comer Hall, Auburn, AL, 36849, USA
| | - Joshua B Elmore
- Alabama Cooperative Extension System, 107 Comer Hall, Auburn, AL, 36849, USA
| | - Soren P Rodning
- Department of Animal Sciences, Auburn University, 107 Comer Hall, Auburn, AL, 36849, USA
| | - Fernando H Biase
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Drive, Blacksburg, VA, 24061, USA.
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6
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Moorey SE, Biase FH. Beef heifer fertility: importance of management practices and technological advancements. J Anim Sci Biotechnol 2020; 11:97. [PMID: 33014361 PMCID: PMC7528292 DOI: 10.1186/s40104-020-00503-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/11/2020] [Indexed: 11/12/2022] Open
Abstract
The development of replacement heifers is at the core of cow-calf beef production systems. In 2020, the USDA, National Agricultural Statistics Service reported 5.771 million beef heifers, 500 pounds and over, are under development for cow replacement. A compilation of data from several studies indicate that between 85% and 95% of these heifers will become pregnant in their first breeding season. Several thousands of heifers being raised for replacement may not deliver a calf on their first breeding season and result in economic losses to cow-calf producers. Many management procedures have been developed to maximize the reproductive potential of beef heifers. Such approaches include, but are not limited to the following: nutritional management for controlled weight gain, identification of reproductive maturity by physiological and morphological indicators, and the implementation of an estrous synchronization program. The implementation of management strategies has important positive impact(s) on the reproductive efficiency of heifers. There are limitations, however, because some heifers deemed ready to enter their first breeding season do not become pregnant. In parallel, genetic selection for fertility-related traits in beef heifers have not promoted major genetic gains on this particular area, most likely due to low heritability of female fertility traits in cattle. Technologies such as antral follicle counting, DNA genotyping and RNA profiling are being investigated as a means to aid in the identification of heifers of low fertility potential. To date, many polymorphisms have been associated with heifer fertility, but no DNA markers have been identified across herds. Antral follicle count is an indication of the ovarian reserve and is an indicator of the reproductive health of a heifer. We have been working on the identification of transcriptome profiles in heifers associated with pregnancy outcome. Our current investigations integrating protein-coding transcript abundance and artificial intelligence have identified the potential for bloodborne transcript abundance to be used as indicators of fertility potential in beef heifers. In summary, there is an ongoing pressure for reducing costs and increasing efficiency in cow-calf production systems, and new technologies can help reduce the long-standing limitations in beef heifer fertility.
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Affiliation(s)
- Sarah E. Moorey
- Department of Animal Science, University of Tennessee, Knoxville, TN USA
| | - Fernando H. Biase
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Drive, Blacksburg, VA 24061 USA
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Bermann M, Legarra A, Hollifield MK, Masuda Y, Lourenco D, Misztal I. Validation of single-step GBLUP genomic predictions from threshold models using the linear regression method: An application in chicken mortality. J Anim Breed Genet 2020; 138:4-13. [PMID: 32985749 PMCID: PMC7756448 DOI: 10.1111/jbg.12507] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/27/2020] [Accepted: 08/18/2020] [Indexed: 11/30/2022]
Abstract
The objective of this study was to determine whether the linear regression (LR) method could be used to validate genomic threshold models. Statistics for the LR method were computed from estimated breeding values (EBVs) using the whole and truncated data sets with variances from the reference and validation populations. The method was tested using simulated and real chicken data sets. The simulated data set included 10 generations of 4,500 birds each; genotypes were available for the last three generations. Each animal was assigned a continuous trait, which was converted to a binary score assuming an incidence of failure of 7%. The real data set included the survival status of 186,596 broilers (mortality rate equal to 7.2%) and genotypes of 18,047 birds. Both data sets were analysed using best linear unbiased predictor (BLUP) or single-step GBLUP (ssGBLUP). The whole data set included all phenotypes available, whereas in the partial data set, phenotypes of the most recent generation were removed. In the simulated data set, the accuracies based on the LR formulas were 0.45 for BLUP and 0.76 for ssGBLUP, whereas the correlations between true breeding values and EBVs (i.e. true accuracies) were 0.37 and 0.65, respectively. The gain in accuracy by adding genomic information was overestimated by 0.09 when using the LR method compared to the true increase in accuracy. However, when the estimated ratio between the additive variance computed based on pedigree only and on pedigree and genomic information was considered, the difference between true and estimated gain was <0.02. Accuracies of BLUP and ssGBLUP with the real data set were 0.41 and 0.47, respectively. This small improvement in accuracy when using ssGBLUP with the real data set was due to population structure and lower heritability. The LR method is a useful tool for estimating improvements in accuracy of EBVs due to the inclusion of genomic information when traditional validation methods as k-fold validation and predictive ability are not applicable.
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Affiliation(s)
- Matias Bermann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | | | | | - Yutaka Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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Xu L, Gao N, Wang Z, Xu L, Liu Y, Chen Y, Xu L, Gao X, Zhang L, Gao H, Zhu B, Li J. Incorporating Genome Annotation Into Genomic Prediction for Carcass Traits in Chinese Simmental Beef Cattle. Front Genet 2020; 11:481. [PMID: 32499816 PMCID: PMC7243208 DOI: 10.3389/fgene.2020.00481] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/17/2020] [Indexed: 01/08/2023] Open
Abstract
Various methods have been proposed for genomic prediction (GP) in livestock. These methods have mainly focused on statistical considerations and did not include genome annotation information. In this study, to improve the predictive performance of carcass traits in Chinese Simmental beef cattle, we incorporated the genome annotation information into GP. Single nucleotide polymorphisms (SNPs) were annotated to five genomic classes: intergenic, gene, exon, protein coding sequences, and 3'/5' untranslated region. Haploblocks were constructed for all markers and these five genomic classes by defining a biologically functional unit, and haplotype effects were modeled in both numerical dosage and categorical coding strategies. The first-order epistatic effects among SNPs and haplotypes were modeled using a categorical epistasis model. For all makers, the extension from the SNP-based model to a haplotype-based model improved the accuracy by 5.4-9.8% for carcass weight (CW), live weight (LW), and striploin (SI). For the five genomic classes using the haplotype-based prediction model, the incorporation of gene class information into the model improved the accuracies by an average of 1.4, 2.1, and 1.3% for CW, LW, and SI, respectively, compared with their corresponding results for all markers. Including the first-order epistatic effects into the prediction models improved the accuracies in some traits and genomic classes. Therefore, for traits with moderate-to-high heritability, incorporating genome annotation information of gene class into haplotype-based prediction models could be considered as a promising tool for GP in Chinese Simmental beef cattle, and modeling epistasis in prediction can further increase the accuracy to some degree.
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Affiliation(s)
- Ling Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ning Gao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zezhao Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Liu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Centre of Beef Cattle Genetic Evaluation, Beijing, China
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Centre of Beef Cattle Genetic Evaluation, Beijing, China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Centre of Beef Cattle Genetic Evaluation, Beijing, China
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Foxworthy HM, Enns RM, Thomas MG, Speidel SE. The estimation of heritability and repeatability of first service conception and first cycle calving in Angus cattle. Transl Anim Sci 2019; 3:1646-1649. [PMID: 32704929 PMCID: PMC6999142 DOI: 10.1093/tas/txz047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/15/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - R Mark Enns
- Department of Animal Sciences, Colorado State University, Fort Collins, CO
| | - Milton G Thomas
- Department of Animal Sciences, Colorado State University, Fort Collins, CO
| | - Scott E Speidel
- Department of Animal Sciences, Colorado State University, Fort Collins, CO
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10
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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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11
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Silva RMO, Evenhuis JP, Vallejo RL, Gao G, Martin KE, Leeds TD, Palti Y, Lourenco DAL. Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations. Genet Sel Evol 2019; 51:42. [PMID: 31387519 PMCID: PMC6683352 DOI: 10.1186/s12711-019-0484-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/30/2019] [Indexed: 01/09/2023] Open
Abstract
Background Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic information is used to evaluate the genetic potential of survival to columnaris infection in each population. Methods Two aquaculture populations were investigated: the National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. Fish that survived to 21 days post-immersion challenge were recorded as resistant. Single nucleotide polymorphism (SNP) genotypes were available for 1185 and 1137 fish from NCCCWA and TLUM, respectively. SNP effects and variances were estimated using the weighted single-step genomic best linear unbiased prediction (BLUP) for genome-wide association. Genomic regions that explained more than 1% of the additive genetic variance were considered to be associated with resistance to CD. Predictive ability was calculated in a fivefold cross-validation scheme and using a linear regression method. Results Validation on adjusted phenotypes provided a prediction accuracy close to zero, due to the binary nature of the trait. Using breeding values computed from the complete data as benchmark improved prediction accuracy of genomic models by about 40% compared to the pedigree-based BLUP. Fourteen windows located on six chromosomes were associated with resistance to CD in the NCCCWA population, of which two windows on chromosome Omy 17 jointly explained more than 10% of the additive genetic variance. Twenty-six windows located on 13 chromosomes were associated with resistance to CD in the TLUM population. Only four associated genomic regions overlapped with quantitative trait loci (QTL) between both populations. Conclusions Our results suggest that genome-wide selection for resistance to CD in rainbow trout has greater potential than selection for a few target genomic regions that were found to be associated to resistance to CD due to the polygenic architecture of this trait, and because the QTL associated with resistance to CD are not sufficiently informative for selection decisions across populations. Electronic supplementary material The online version of this article (10.1186/s12711-019-0484-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rafael M O Silva
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, 11861 Leetown Road, Leetown, WV, 25430, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, 425 River Road, Athens, GA, 30602, USA.,Zoetis, Sao Paulo, Sao Paulo, 04711-130, Brazil
| | - Jason P Evenhuis
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, 11861 Leetown Road, Leetown, WV, 25430, USA
| | - Roger L Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, 11861 Leetown Road, Leetown, WV, 25430, USA
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, 11861 Leetown Road, Leetown, WV, 25430, USA
| | - Kyle E Martin
- Troutloged, Inc., P.O. Box 1290, Sumner, WA, 98390, USA
| | - Tim D Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, 11861 Leetown Road, Leetown, WV, 25430, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, 11861 Leetown Road, Leetown, WV, 25430, USA.
| | - Daniela A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, 425 River Road, Athens, GA, 30602, USA
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