1
|
Kaseja K, Mucha S, Yates J, Smith E, Banos G, Conington J. Genome-wide association study of health and production traits in meat sheep. Animal 2023; 17:100968. [PMID: 37738702 DOI: 10.1016/j.animal.2023.100968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/11/2023] [Accepted: 08/25/2023] [Indexed: 09/24/2023] Open
Abstract
Genotypes are currently widely used in animal breeding programmes to enhance the speed of genetic progress. With sufficient data, a Genome-Wide Association Study (GWAS) can be performed to identify informative markers. The aim of this study was to investigate the genetic background of health (footrot and mastitis) and production (birth weight, weaning weight, scan weight, and fat and muscle depth) traits using the available phenotypic and Single Nucleotide Polymorphism (SNP) data collected on the UK Texel sheep population. Initially, 10 193 genotypes were subject to quality control, leaving 9 505 genotypes for further analysis. Selected genotypes, recorded on four different Illumina chip types from low density (15 k SNPs) to high density (606 006 SNPs), were imputed to a subset of 45 686 markers from 50 k array, distributed on 27 chromosomes. Phenotypes collected on 32 farms across the UK for footrot and mastitis and extracted from the UK National database (iTexel) for the production traits were used along with pre-estimated variance components to obtain de-regressed breeding values and used to perform GWAS. Results showed three SNPs being significant on the genome-wise level ('OAR8_62240378.1' on chromosome 8 for birth weight, 's14444.1' on chromosome 19 for weaning weight and 's65197.1' on chromosome 23 for scan weight). Fourteen subsequent SNPs were found to be significant at the chromosome-wise level. These SNPs are located within or close to previously reported QTLs impacting on animal health (such as faecal egg count or somatic cell count) and production (such as body or carcass weight and fat amount). These results indicate that the studied traits are highly polygenic with complex genetic architecture.
Collapse
Affiliation(s)
- K Kaseja
- SRUC Easter Bush, Roslin Institute Building, Edinburgh EH25 9RG, UK.
| | - S Mucha
- SRUC Easter Bush, Roslin Institute Building, Edinburgh EH25 9RG, UK
| | - J Yates
- The British Texel Sheep Society, Stoneleigh Park, Warwickshire CV8 2LG, UK
| | - E Smith
- The British Texel Sheep Society, Stoneleigh Park, Warwickshire CV8 2LG, UK
| | - G Banos
- SRUC Easter Bush, Roslin Institute Building, Edinburgh EH25 9RG, UK
| | - J Conington
- SRUC Easter Bush, Roslin Institute Building, Edinburgh EH25 9RG, UK
| |
Collapse
|
2
|
Jang S, Ros-Freixedes R, Hickey JM, Chen CY, Holl J, Herring WO, Misztal I, Lourenco D. Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs. Genet Sel Evol 2023; 55:55. [PMID: 37495982 PMCID: PMC10373252 DOI: 10.1186/s12711-023-00831-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/18/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Whole-genome sequence (WGS) data harbor causative variants that may not be present in standard single nucleotide polymorphism (SNP) chip data. The objective of this study was to investigate the impact of using preselected variants from WGS for single-step genomic predictions in maternal and terminal pig lines with up to 1.8k sequenced and 104k sequence imputed animals per line. METHODS Two maternal and four terminal lines were investigated for eight and seven traits, respectively. The number of sequenced animals ranged from 1365 to 1491 for the maternal lines and 381 to 1865 for the terminal lines. Imputation to sequence occurred within each line for 66k to 76k animals for the maternal lines and 29k to 104k animals for the terminal lines. Two preselected SNP sets were generated based on a genome-wide association study (GWAS). Top40k included the SNPs with the lowest p-value in each of the 40k genomic windows, and ChipPlusSign included significant variants integrated into the porcine SNP chip used for routine genotyping. We compared the performance of single-step genomic predictions between using preselected SNP sets assuming equal or different variances and the standard porcine SNP chip. RESULTS In the maternal lines, ChipPlusSign and Top40k showed an average increase in accuracy of 0.6 and 4.9%, respectively, compared to the regular porcine SNP chip. The greatest increase was obtained with Top40k, particularly for fertility traits, for which the initial accuracy based on the standard SNP chip was low. However, in the terminal lines, Top40k resulted in an average loss of accuracy of 1%. ChipPlusSign provided a positive, although small, gain in accuracy (0.9%). Assigning different variances for the SNPs slightly improved accuracies when using variances obtained from BayesR. However, increases were inconsistent across the lines and traits. CONCLUSIONS The benefit of using sequence data depends on the line, the size of the genotyped population, and how the WGS variants are preselected. When WGS data are available on hundreds of thousands of animals, using sequence data presents an advantage but this remains limited in pigs.
Collapse
Affiliation(s)
- Sungbong Jang
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA.
| | - Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Ching-Yi Chen
- The Pig Improvement Company, Genus Plc, Hendersonville, TN, USA
| | - Justin Holl
- The Pig Improvement Company, Genus Plc, Hendersonville, TN, USA
| | | | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| |
Collapse
|
3
|
Bermann M, Cesarani A, Misztal I, Lourenco D. Past, present, and future developments in single-step genomic models. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2053366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Matias Bermann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Alberto Cesarani
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Ignacy Misztal
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| |
Collapse
|
4
|
Guillenea A, Su G, Lund MS, Karaman E. Genomic prediction in Nordic Red dairy cattle considering breed origin of alleles. J Dairy Sci 2022; 105:2426-2438. [PMID: 35033341 DOI: 10.3168/jds.2021-21173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2021] [Indexed: 01/02/2023]
Abstract
This study investigated the reliability of genomic prediction (GP) using breed origin of alleles (BOA) approach in the Nordic Red (RDC) population, which has an admixed population structure. The RDC population consists of animals with varying degrees of genetic materials from the Danish Red (RDM), Swedish Red (SRB), Finnish Ayrshire (FAY), and Holstein (HOL) because bulls have been used across the breeds. The BOA approach was tested using 39,550 RDC animals in the reference population and 11,786 in the validation population. Deregressed proofs (DRP) of milk, fat and protein were used as response variable for GP. Direct genomic breeding values (DGV) for animals in the validation population were calculated with (BOA model) or without (joint model) considering breed origin of alleles. The joint model assumed homogeneous marker effects and a single set of marker effects were estimated, whereas BOA model assumed heterogeneous marker effects, and different sets of marker effects were estimated across the breeds. For the BOA approach, we tested scenarios assuming both correlated (BOA_cor) and uncorrelated (BOA_uncor) marker effects between the breeds. Additionally, we investigated GP using a standard Illumina 50K chip and including SNP selected from imputed whole-genome sequencing (50K+WGS). We also studied the effect of estimating (co)variances for genome regions of different sizes to exploit the information of the genome regions contributing to the (co)variance between the breeds. Region sizes were set as 1 SNP, a group of 30 or 100 adjacent SNP, or the whole genome. Reliability of DGV was measured as squared correlations between DGV and DRP divided by the reliability of DRP. Across the 3 traits, in general, RS30 and RS100 SNP yielded the highest reliabilities. Including WGS SNP improved reliabilities in almost all scenarios (0.297 on average for 50K and 0.307 on average for 50K+WGS). The BOA_uncor (0.233 on average) was inferior to the joint model (0.339 on average), but the reliabilities obtained using BOA_cor (0.334 on average) in most cases were not significantly different from those obtained using the joint model. The results indicate that both including additional whole-genome sequencing SNP and dividing the genome into fixed regions improve GP in the RDC. The BOA models have the potential to increase the reliability of GP, but the benefit is limited in populations with a high exchange of genetic material for a long time, as is the case for RDC.
Collapse
Affiliation(s)
- Ana Guillenea
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark.
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | - Mogens Sand Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | - Emre Karaman
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| |
Collapse
|
5
|
Shi S, Zhang Z, Li B, Zhang S, Fang L. Incorporation of Trait-Specific Genetic Information into Genomic Prediction Models. Methods Mol Biol 2022; 2467:329-340. [PMID: 35451781 DOI: 10.1007/978-1-0716-2205-6_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Due to the rapid development of high-throughput sequencing technology, we can easily obtain not only the genetic variants at the whole-genome sequence level (e.g., from 1000 Genomes project and 1000 Bull Genomes project), but also a wide range of functional annotations (e.g., enhancers and promoters from ENCODE, FAANG, and FarmGTEx projects) across a wide range of tissues, cell types, developmental stages, and environmental conditions. This huge amount of information leads to a revolution in studying genetics and genomics of complex traits in humans, livestock, and plant species. In this chapter, we focused on and reviewed the genomic prediction methods that incorporate external biological information into genomic prediction, such as sequence ontology, linkage disequilibrium (LD) of SNPs, quantitative trait loci (QTL), and multi-layer omics data (e.g., transcriptome, epigenome, and microbiome).
Collapse
Affiliation(s)
- Shaolei Shi
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhe Zhang
- Department of Animal Breeding and genetics, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Bingjie Li
- The Roslin Institute Building, Scotland's Rural College, Edinburgh, UK
| | - Shengli Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
6
|
Romé H, Chu TT, Marois D, Huang C, Madsen P, Jensen J. Accounting for genetic architecture for body weight improves accuracy of predicting breeding values in a commercial line of broilers. J Anim Breed Genet 2021; 138:528-540. [PMID: 33774870 PMCID: PMC8451786 DOI: 10.1111/jbg.12546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/29/2021] [Accepted: 02/28/2021] [Indexed: 12/21/2022]
Abstract
BLUP (best linear unbiased prediction) is the standard for predicting breeding values, where different assumptions can be made on variance-covariance structure, which may influence predictive ability. Herein, we compare accuracy of prediction of four derived-BLUP models: (a) a pedigree relationship matrix (PBLUP), (b) a genomic relationship matrix (GBLUP), (c) a weighted genomic relationship matrix (WGBLUP) and (d) a relationship matrix based on genomic features that consisted of only a subset of SNP selected on a priori information (GFBLUP). We phenotyped a commercial population of broilers for body weight (BW) in five successive weeks and genotyped them using a 50k SNP array. We compared predictive ability of univariate models using conservative cross-validation method, where each full-sib group was divided into two folds. Results from cross-validation showed, with WGBLUP model, a gain in accuracy from 2% to 7% compared with GBLUP model. Splitting the additive genetic matrix into two matrices, based on significance level of SNP (Gf : estimated with only set of SNP selected on significance level, Gr : estimated with the remaining SNP), led to a gain in accuracy from 1% to 70%, depending on the proportion of SNP used to define Gf . Thus, information from GWAS in models improves predictive ability of breeding values for BW in broilers. Increasing the power of detection of SNP effects, by acquiring more data or improving methods for GWAS, will help improve predictive ability.
Collapse
Affiliation(s)
- Hélène Romé
- Center for Quantitative Genetics and GenomicsAarhus UniversityTjeleDenmark
| | - Thinh T. Chu
- Center for Quantitative Genetics and GenomicsAarhus UniversityTjeleDenmark
- Faculty of Animal ScienceVietnam National University of AgricultureGia LamVietnam
| | | | | | - Per Madsen
- Center for Quantitative Genetics and GenomicsAarhus UniversityTjeleDenmark
| | - Just Jensen
- Center for Quantitative Genetics and GenomicsAarhus UniversityTjeleDenmark
| |
Collapse
|
7
|
Gautason E, Sahana G, Su G, Benjamínsson BH, Jóhannesson G, Guldbrandtsen B. Short communication: investigation of the feasibility of genomic selection in Icelandic Cattle. J Anim Sci 2021; 99:6263455. [PMID: 33942082 DOI: 10.1093/jas/skab139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Icelandic Cattle is a local dairy cattle breed in Iceland. With about 26,000 breeding females, it is by far the largest among the indigenous Nordic cattle breeds. The objective of this study was to investigate the feasibility of genomic selection in Icelandic Cattle. Pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) were compared. Accuracy, bias, and dispersion of estimated breeding values (EBV) for milk yield (MY), fat yield (FY), protein yield (PY), and somatic cell score (SCS) were estimated in a cross validation-based design. Accuracy (r^) was estimated by the correlation between EBV and corrected phenotype in a validation set. The accuracy (r^) of predictions using ssGBLUP increased by 13, 23, 19, and 20 percentage points for MY, FY, PY, and SCS for genotyped animals, compared with PBLUP. The accuracy of nongenotyped animals was not improved for MY and PY, but increased by 0.9 and 3.5 percentage points for FY and SCS. We used the linear regression (LR) method to quantify relative improvements in accuracy, bias (Δ^), and dispersion (b^) of EBV. Using the LR method, the relative improvements in accuracy of validation from PBLUP to ssGBLUP were 43%, 60%, 50%, and 48% for genotyped animals for MY, FY, PY, and SCS. Single-step GBLUP EBV were less underestimated (Δ^), and less overdispersed (b^) than PBLUP EBV for FY and PY. Pedigree-based BLUP EBV were close to unbiased for MY and SCS. Single-step GBLUP underestimated MY EBV but overestimated SCS EBV. Based on the average accuracy of 0.45 for ssGBLUP EBV obtained in this study, selection intensities according to the breeding scheme of Icelandic Cattle, and assuming a generation interval of 2.0 yr for sires of bulls, sires of dams and dams of bulls, genetic gain in Icelandic Cattle could be increased by about 50% relative to the current breeding scheme.
Collapse
Affiliation(s)
- Egill Gautason
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | | | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark.,Department of Animal Sciences, University of Bonn, 53115 Bonn, Germany
| |
Collapse
|
8
|
Ferrão LFV, Amadeu RR, Benevenuto J, de Bem Oliveira I, Munoz PR. Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:676326. [PMID: 34194453 PMCID: PMC8236943 DOI: 10.3389/fpls.2021.676326] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/12/2021] [Indexed: 05/17/2023]
Abstract
Blueberry (Vaccinium corymbosum and hybrids) is a specialty crop with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to expanding production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the globe. The breeding program has historically focused on recurrent phenotypic selection. As an autopolyploid, outcrossing, perennial, long juvenile phase crop, blueberry breeding cycles are costly and time consuming, which results in low genetic gains per unit of time. Motivated by applying molecular markers for a more accurate selection in the early stages of breeding, we performed pioneering genomic selection studies and optimization for its implementation in the blueberry breeding program. We have also addressed some complexities of sequence-based genotyping and model parametrization for an autopolyploid crop, providing empirical contributions that can be extended to other polyploid species. We herein revisited some of our previous genomic selection studies and showed for the first time its application in an independent validation set. In this paper, our contribution is three-fold: (i) summarize previous results on the relevance of model parametrizations, such as diploid or polyploid methods, and inclusion of dominance effects; (ii) assess the importance of sequence depth of coverage and genotype dosage calling steps; (iii) demonstrate the real impact of genomic selection on leveraging breeding decisions by using an independent validation set. Altogether, we propose a strategy for using genomic selection in blueberry, with the potential to be applied to other polyploid species of a similar background.
Collapse
Affiliation(s)
- Luís Felipe V. Ferrão
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Rodrigo R. Amadeu
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Juliana Benevenuto
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Ivone de Bem Oliveira
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- Hortifrut North America, Inc., Estero, FL, United States
| | - Patricio R. Munoz
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| |
Collapse
|
9
|
Karaman E, Su G, Croue I, Lund MS. Genomic prediction using a reference population of multiple pure breeds and admixed individuals. Genet Sel Evol 2021; 53:46. [PMID: 34058971 PMCID: PMC8168010 DOI: 10.1186/s12711-021-00637-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In dairy cattle populations in which crossbreeding has been used, animals show some level of diversity in their origins. In rotational crossbreeding, for instance, crossbred dams are mated with purebred sires from different pure breeds, and the genetic composition of crossbred animals is an admixture of the breeds included in the rotation. How to use the data of such individuals in genomic evaluations is still an open question. In this study, we aimed at providing methodologies for the use of data from crossbred individuals with an admixed genetic background together with data from multiple pure breeds, for the purpose of genomic evaluations for both purebred and crossbred animals. A three-breed rotational crossbreeding system was mimicked using simulations based on animals genotyped with the 50 K single nucleotide polymorphism (SNP) chip. RESULTS For purebred populations, within-breed genomic predictions generally led to higher accuracies than those from multi-breed predictions using combined data of pure breeds. Adding admixed population's (MIX) data to the combined pure breed data considering MIX as a different breed led to higher accuracies. When prediction models were able to account for breed origin of alleles, accuracies were generally higher than those from combining all available data, depending on the correlation of quantitative trait loci (QTL) effects between the breeds. Accuracies varied when using SNP effects from any of the pure breeds to predict the breeding values of MIX. Using those breed-specific SNP effects that were estimated separately in each pure breed, while accounting for breed origin of alleles for the selection candidates of MIX, generally improved the accuracies. Models that are able to accommodate MIX data with the breed origin of alleles approach generally led to higher accuracies than models without breed origin of alleles, depending on the correlation of QTL effects between the breeds. CONCLUSIONS Combining all available data, pure breeds' and admixed population's data, in a multi-breed reference population is beneficial for the estimation of breeding values for pure breeds with a small reference population. For MIX, such an approach can lead to higher accuracies than considering breed origin of alleles for the selection candidates, and using breed-specific SNP effects estimated separately in each pure breed. Including MIX data in the reference population of multiple breeds by considering the breed origin of alleles, accuracies can be further improved. Our findings are relevant for breeding programs in which crossbreeding is systematically applied, and also for populations that involve different subpopulations and between which exchange of genetic material is routine practice.
Collapse
Affiliation(s)
- Emre Karaman
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | | | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| |
Collapse
|
10
|
Mehrban H, Naserkheil M, Lee DH, Cho C, Choi T, Park M, Ibáñez-Escriche N. Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle. Genes (Basel) 2021; 12:genes12020266. [PMID: 33673102 PMCID: PMC7917987 DOI: 10.3390/genes12020266] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 01/20/2023] Open
Abstract
The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait best linear unbiased prediction methods in Hanwoo beef cattle: pedigree-based (PBLUP), un-weighted (ssGBLUP), and weighted (WssGBLUP) single-step genomic methods. We also assessed the impact of alternative single and window weighting methods according to their effects on the traits of interest. The data was comprised of 15,796 phenotypic records for yearling weight (YW) and 5622 records for carcass traits (backfat thickness: BFT, carcass weight: CW, eye muscle area: EMA, and marbling score: MS). Also, the genotypic data included 6616 animals for YW and 5134 for carcass traits on the 43,950 single-nucleotide polymorphisms. The ssGBLUP showed significant improvement in genomic prediction accuracy for carcass traits (71%) and yearling weight (99%) compared to the pedigree-based method. The window weighting procedures performed better than single SNP weighting for CW (11%), EMA (11%), MS (3%), and YW (6%), whereas no gain in accuracy was observed for BFT. Besides, the improvement in accuracy between window WssGBLUP and the un-weighted method was low for BFT and MS, while for CW, EMA, and YW resulted in a gain of 22%, 15%, and 20%, respectively, which indicates the presence of relevant quantitative trait loci for these traits. These findings indicate that WssGBLUP is an appropriate method for traits with a large quantitative trait loci effect.
Collapse
Affiliation(s)
- Hossein Mehrban
- Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran;
| | - Masoumeh Naserkheil
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran;
- Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si 17579, Gyeonggi-do, Korea
| | - Deuk Hwan Lee
- Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si 17579, Gyeonggi-do, Korea
- Correspondence: ; Tel.: +82-316-705-091
| | - Chungil Cho
- Hanwoo Genetic Improvement Center, NongHyup Agribusiness Group Inc., Seosan 31948, Korea;
| | - Taejeong Choi
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea; (T.C.); (M.P.)
| | - Mina Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea; (T.C.); (M.P.)
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 València, Spain;
| |
Collapse
|