101
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Boison S, Santos D, Utsunomiya A, Carvalheiro R, Neves H, O’Brien A, Garcia J, Sölkner J, da Silva M. Strategies for single nucleotide polymorphism (SNP) genotyping to enhance genotype imputation in Gyr (Bos indicus) dairy cattle: Comparison of commercially available SNP chips. J Dairy Sci 2015; 98:4969-89. [DOI: 10.3168/jds.2014-9213] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/22/2015] [Indexed: 01/15/2023]
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102
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Lucot KL, Spangler ML, Trenhaile MD, Kachman SD, Ciobanu DC. Evaluation of reduced subsets of single nucleotide polymorphisms for the prediction of age at puberty in sows. Anim Genet 2015; 46:403-9. [DOI: 10.1111/age.12310] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2015] [Indexed: 11/30/2022]
Affiliation(s)
- K. L. Lucot
- Animal Science Department; University of Nebraska; Lincoln 68583 NE USA
| | - M. L. Spangler
- Animal Science Department; University of Nebraska; Lincoln 68583 NE USA
| | - M. D. Trenhaile
- Animal Science Department; University of Nebraska; Lincoln 68583 NE USA
| | - S. D. Kachman
- Department of Statistics; University of Nebraska; Lincoln 68583 NE USA
| | - D. C. Ciobanu
- Animal Science Department; University of Nebraska; Lincoln 68583 NE USA
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103
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Mészáros G, Boison SA, Pérez O'Brien AM, Ferenčaković M, Curik I, Da Silva MVB, Utsunomiya YT, Garcia JF, Sölkner J. Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle. Front Genet 2015; 6:173. [PMID: 26074948 PMCID: PMC4443735 DOI: 10.3389/fgene.2015.00173] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 04/20/2015] [Indexed: 11/30/2022] Open
Abstract
Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (FROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13–0.91 and 0.12–0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.
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Affiliation(s)
- Gábor Mészáros
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | - Solomon A Boison
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | | | - Ino Curik
- Department of Animal Science, University of Zagreb Zagreb, Croatia
| | | | | | - Jose F Garcia
- UNESP-Universidade Estadual Paulista Jaboticabal, Brazil
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
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104
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Nicolazzi EL, Biffani S, Biscarini F, Orozco Ter Wengel P, Caprera A, Nazzicari N, Stella A. Software solutions for the livestock genomics SNP array revolution. Anim Genet 2015; 46:343-53. [PMID: 25907889 DOI: 10.1111/age.12295] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2015] [Indexed: 02/04/2023]
Abstract
Since the beginning of the genomic era, the number of available single nucleotide polymorphism (SNP) arrays has grown considerably. In the bovine species alone, 11 SNP chips not completely covered by intellectual property are currently available, and the number is growing. Genomic/genotype data are not standardized, and this hampers its exchange and integration. In addition, software used for the analyses of these data usually requires not standard (i.e. case specific) input files which, considering the large amount of data to be handled, require at least some programming skills in their production. In this work, we describe a software toolkit for SNP array data management, imputation, genome-wide association studies, population genetics and genomic selection. However, this toolkit does not solve the critical need for standardization of the genotypic data and software input files. It only highlights the chaotic situation each researcher has to face on a daily basis and gives some helpful advice on the currently available tools in order to navigate the SNP array data complexity.
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Affiliation(s)
- E L Nicolazzi
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy
| | - S Biffani
- Istituto di biologia e biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy
| | - F Biscarini
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy
| | - P Orozco Ter Wengel
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - A Caprera
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy
| | - N Nazzicari
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy
| | - A Stella
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy.,Istituto di biologia e biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy
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105
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Nishio M, Satoh M. Genomic best linear unbiased prediction method including imprinting effects for genomic evaluation. Genet Sel Evol 2015; 47:32. [PMID: 25928098 PMCID: PMC4404063 DOI: 10.1186/s12711-015-0091-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/14/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic best linear unbiased prediction (GBLUP) is a statistical method used to predict breeding values using single nucleotide polymorphisms for selection in animal and plant breeding. Genetic effects are often modeled as additively acting marker allele effects. However, the actual mode of biological action can differ from this assumption. Many livestock traits exhibit genomic imprinting, which may substantially contribute to the total genetic variation of quantitative traits. Here, we present two statistical models of GBLUP including imprinting effects (GBLUP-I) on the basis of genotypic values (GBLUP-I1) and gametic values (GBLUP-I2). The performance of these models for the estimation of variance components and prediction of genetic values across a range of genetic variations was evaluated in simulations. RESULTS Estimates of total genetic variances and residual variances with GBLUP-I1 and GBLUP-I2 were close to the true values and the regression coefficients of total genetic values on their estimates were close to 1. Accuracies of estimated total genetic values in both GBLUP-I methods increased with increasing degree of imprinting and broad-sense heritability. When the imprinting variances were equal to 1.4% to 6.0% of the phenotypic variances, the accuracies of estimated total genetic values with GBLUP-I1 exceeded those with GBLUP by 1.4% to 7.8%. In comparison with GBLUP-I1, the superiority of GBLUP-I2 over GBLUP depended strongly on degree of imprinting and difference in genetic values between paternal and maternal alleles. When paternal and maternal alleles were predicted (phasing accuracy was equal to 0.979), accuracies of the estimated total genetic values in GBLUP-I1 and GBLUP-I2 were 1.7% and 1.2% lower than when paternal and maternal alleles were known. CONCLUSIONS This simulation study shows that GBLUP-I1 and GBLUP-I2 can accurately estimate total genetic variance and perform well for the prediction of total genetic values. GBLUP-I1 is preferred for genomic evaluation, while GBLUP-I2 is preferred when the imprinting effects are large, and the genetic effects differ substantially between sexes.
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Affiliation(s)
- Motohide Nishio
- NARO Institute of Livestock and Grassland Science, 305-0901, Ikenodai 2, Tsukuba, Japan.
| | - Masahiro Satoh
- NARO Institute of Livestock and Grassland Science, 305-0901, Ikenodai 2, Tsukuba, Japan.
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106
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Brøndum RF, Su G, Janss L, Sahana G, Guldbrandtsen B, Boichard D, Lund MS. Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction. J Dairy Sci 2015; 98:4107-16. [PMID: 25892697 DOI: 10.3168/jds.2014-9005] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/12/2015] [Indexed: 12/30/2022]
Abstract
This study investigated the effect on the reliability of genomic prediction when a small number of significant variants from single marker analysis based on whole genome sequence data were added to the regular 54k single nucleotide polymorphism (SNP) array data. The extra markers were selected with the aim of augmenting the custom low-density Illumina BovineLD SNP chip (San Diego, CA) used in the Nordic countries. The single-marker analysis was done breed-wise on all 16 index traits included in the breeding goals for Nordic Holstein, Danish Jersey, and Nordic Red cattle plus the total merit index itself. Depending on the trait's economic weight, 15, 10, or 5 quantitative trait loci (QTL) were selected per trait per breed and 3 to 5 markers were selected to tag each QTL. After removing duplicate markers (same marker selected for more than one trait or breed) and filtering for high pairwise linkage disequilibrium and assaying performance on the array, a total of 1,623 QTL markers were selected for inclusion on the custom chip. Genomic prediction analyses were performed for Nordic and French Holstein and Nordic Red animals using either a genomic BLUP or a Bayesian variable selection model. When using the genomic BLUP model including the QTL markers in the analysis, reliability was increased by up to 4 percentage points for production traits in Nordic Holstein animals, up to 3 percentage points for Nordic Reds, and up to 5 percentage points for French Holstein. Smaller gains of up to 1 percentage point was observed for mastitis, but only a 0.5 percentage point increase was seen for fertility. When using a Bayesian model accuracies were generally higher with only 54k data compared with the genomic BLUP approach, but increases in reliability were relatively smaller when QTL markers were included. Results from this study indicate that the reliability of genomic prediction can be increased by including markers significant in genome-wide association studies on whole genome sequence data alongside the 54k SNP set.
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Affiliation(s)
- R F Brøndum
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Blichers Allé 20, Aarhus University, DK-8830 Tjele, Denmark.
| | - G Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Blichers Allé 20, Aarhus University, DK-8830 Tjele, Denmark
| | - L Janss
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Blichers Allé 20, Aarhus University, DK-8830 Tjele, Denmark
| | - G Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Blichers Allé 20, Aarhus University, DK-8830 Tjele, Denmark
| | - B Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Blichers Allé 20, Aarhus University, DK-8830 Tjele, Denmark
| | - D Boichard
- Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - M S Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Blichers Allé 20, Aarhus University, DK-8830 Tjele, Denmark
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107
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Pimentel ECG, Edel C, Emmerling R, Götz KU. How imputation errors bias genomic predictions. J Dairy Sci 2015; 98:4131-8. [PMID: 25841966 DOI: 10.3168/jds.2014-9170] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/20/2015] [Indexed: 12/19/2022]
Abstract
The objective of this study was to investigate in detail the biasing effects of imputation errors on genomic predictions. Direct genomic values (DGV) of 3,494 Brown Swiss selection candidates for 37 production and conformation traits were predicted using either their observed 50K genotypes or their 50K genotypes imputed from a mimicked 6K chip. Changes in DGV caused by imputation errors were shown to be systematic. The DGV of top animals were, on average, underestimated and that of bottom animals were, on average, overestimated when imputed genotypes were used instead of observed genotypes. This pattern might be explained by the fact that imputation algorithms will usually suggest the most frequent haplotype from the sample whenever a haplotype cannot be determined unambiguously. That was empirically shown to cause an advantage for the bottom animals and a disadvantage for the top animals.
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Affiliation(s)
- E C G Pimentel
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, Grub 85586, Germany.
| | - C Edel
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, Grub 85586, Germany
| | - R Emmerling
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, Grub 85586, Germany
| | - K-U Götz
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, Grub 85586, Germany
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108
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García-Ruiz A, Ruiz-Lopez FJ, Wiggans GR, Van Tassell CP, Montaldo HH. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes. J Dairy Sci 2015; 98:3478-84. [PMID: 25771055 DOI: 10.3168/jds.2014-9132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/02/2015] [Indexed: 11/19/2022]
Abstract
The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNP) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local population of 2,011 genotyped Mexican Holsteins, (2) animals in scenario 1 plus 866 Holsteins in the US genotype database (GDB) with genotyped Mexican daughters, and (3) animals in scenario 1 and all US GDB Holsteins (338,073). Genotypes from 4 chip densities (2 low density, 1 mid density, and 1 high density) were imputed using findhap (version 3) to the 45,195 markers on the mid-density chip. Imputation success was determined by comparing the numbers of SNP with 1 or 2 alleles missing and the numbers of differently predicted SNP (conflicts) among the 3 scenarios. Imputation accuracy improved as chip density and numbers of genotyped ancestors increased, and the percentage of SNP with 1 missing allele was greater than that for 2 missing alleles for all scenarios. The largest numbers of conflicts were found between scenarios 1 and 3. The inclusion of information from direct ancestors (dam or sire) with US GDB genotypes in the imputation of Mexican Holstein genotypes increased imputation accuracy by 1 percentage point for low-density genotypes and by 0.5 percentage points for high-density genotypes, which was about half the gain found with information from all US GDB Holsteins. A larger reference population and the availability of genotyped ancestors improved imputation; animals with genotyped parents in a large reference population had higher imputation accuracy than those with no or few genotyped relatives in a small reference population. For small local populations, including genotypes from other related populations can aid in improving imputation accuracy.
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Affiliation(s)
- A García-Ruiz
- Facultad de Estudios Superiores Cuautitlán, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México, DF 04510, México; Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ajuchitlán, Querétaro 76280, México
| | - F J Ruiz-Lopez
- Facultad de Estudios Superiores Cuautitlán, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México, DF 04510, México; Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ajuchitlán, Querétaro 76280, México.
| | - G R Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - C P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - H H Montaldo
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México, DF 04510, México
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109
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Loberg A, Dürr JW, Fikse WF, Jorjani H, Crooks L. Estimates of genetic variance and variance of predicted genetic merits using pedigree or genomic relationship matrices in six Brown Swiss cattle populations for different traits. J Anim Breed Genet 2015; 132:376-85. [PMID: 25727736 DOI: 10.1111/jbg.12142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/27/2015] [Indexed: 01/12/2023]
Abstract
The amount of variance captured in genetic estimations may depend on whether a pedigree-based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree-based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population-trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree-based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree-based relationship matrix. The ratio of the genomic to pedigree-based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress.
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Affiliation(s)
- A Loberg
- Department of Animal Breeding and Genetics, SLU, Uppsala, SE, Sweden
| | - J W Dürr
- Department of Animal Breeding and Genetics, SLU, Uppsala, SE, Sweden.,Interbull Centre, SE, Uppsala
| | - W F Fikse
- Department of Animal Breeding and Genetics, SLU, Uppsala, SE, Sweden
| | - H Jorjani
- Department of Animal Breeding and Genetics, SLU, Uppsala, SE, Sweden.,Interbull Centre, SE, Uppsala
| | - L Crooks
- Sheffield Diagnostic Genetics Service, UK
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110
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Gorjanc G, Cleveland MA, Houston RD, Hickey JM. Potential of genotyping-by-sequencing for genomic selection in livestock populations. Genet Sel Evol 2015; 47:12. [PMID: 25887531 PMCID: PMC4344748 DOI: 10.1186/s12711-015-0102-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 01/29/2015] [Indexed: 12/12/2022] Open
Abstract
Background Next-generation sequencing techniques, such as genotyping-by-sequencing (GBS), provide alternatives to single nucleotide polymorphism (SNP) arrays. The aim of this work was to evaluate the potential of GBS compared to SNP array genotyping for genomic selection in livestock populations. Methods The value of GBS was quantified by simulation analyses in which three parameters were varied: (i) genome-wide sequence read depth (x) per individual from 0.01x to 20x or using SNP array genotyping; (ii) number of genotyped markers from 3000 to 300 000; and (iii) size of training and prediction sets from 500 to 50 000 individuals. The latter was achieved by distributing the total available x of 1000x, 5000x, or 10 000x per genotyped locus among the varying number of individuals. With SNP arrays, genotypes were called from sequence data directly. With GBS, genotypes were called from sequence reads that varied between loci and individuals according to a Poisson distribution with mean equal to x. Simulated data were analyzed with ridge regression and the accuracy and bias of genomic predictions and response to selection were quantified under the different scenarios. Results Accuracies of genomic predictions using GBS data or SNP array data were comparable when large numbers of markers were used and x per individual was ~1x or higher. The bias of genomic predictions was very high at a very low x. When the total available x was distributed among the training individuals, the accuracy of prediction was maximized when a large number of individuals was used that had GBS data with low x for a large number of markers. Similarly, response to selection was maximized under the same conditions due to increasing both accuracy and selection intensity. Conclusions GBS offers great potential for developing genomic selection in livestock populations because it makes it possible to cover large fractions of the genome and to vary the sequence read depth per individual. Thus, the accuracy of predictions is improved by increasing the size of training populations and the intensity of selection is increased by genotyping a larger number of selection candidates. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0102-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
| | - Matthew A Cleveland
- Genus Plc, 100 Bluegrass Commons Blvd., Suite 2200, Hendersonville, TN, 37075, USA.
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
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111
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Biffani S, Dimauro C, Macciotta N, Rossoni A, Stella A, Biscarini F. Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis. Genet Sel Evol 2015; 47:4. [PMID: 25651874 PMCID: PMC4318450 DOI: 10.1186/s12711-015-0094-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/16/2015] [Indexed: 11/24/2022] Open
Abstract
Background SNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific haplotypes. It is therefore convenient to have a practical statistical method for the accurate classification of individuals into carriers and non-carriers. In this paper, we present a procedure combining variable selection (i.e. the selection of predictive SNPs) and linear discriminant analysis for the identification of carriers of a haplotype on BTA19 (Bos taurus autosome 19) known to be associated with reduced cow fertility. A population of 3645 Brown Swiss cows and bulls genotyped with the 54K SNP-chip was available for the analysis. Results The overall error rate for the prediction of haplotype carriers was on average very low (∼≤1%). The error rate was found to depend on the number of SNPs in the model and their density around the region of the haplotype on BTA19. The minimum set of SNPs to still achieve accurate predictions was 5, with a total test error rate of 1.59. Conclusions The paper describes a procedure to accurately identify haplotype carriers from SNP genotypes in cattle populations. Very few misclassifications were observed, which indicates that this is a very reliable approach for potential applications in cattle breeding.
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Affiliation(s)
| | | | | | | | | | - Filippo Biscarini
- Department of Bioinformatics, PTP, Via Einstein - Loc, Cascina Codazza, Lodi 26900, Italy.
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112
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Piccoli ML, Braccini J, Cardoso FF, Sargolzaei M, Larmer SG, Schenkel FS. Accuracy of genome-wide imputation in Braford and Hereford beef cattle. BMC Genet 2014; 15:157. [PMID: 25543517 PMCID: PMC4300607 DOI: 10.1186/s12863-014-0157-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 12/18/2014] [Indexed: 12/31/2022] Open
Abstract
Background Strategies for imputing genotypes from the Illumina-Bovine3K, Illumina-BovineLD (6K), BeefLD-GGP (8K), a non-commercial-15K and IndicusLD-GGP (20K) to either Illumina-BovineSNP50 (50K) or to Illumina-BovineHD (777K) SNP panel, as well as for imputing from 50K, GGP-IndicusHD (90iK) and GGP-BeefHD (90tK) to 777K were investigated. Imputation of low density (<50K) genotypes to 777K was carried out in either one or two steps. Imputation of ungenotyped parents (n = 37 sires) with four or more offspring to the 50K panel was also assessed. There were 2,946 Braford, 664 Hereford and 88 Nellore animals, from which 71, 59 and 88 were genotyped with the 777K panel, while all others had 50K genotypes. The reference population was comprised of 2,735 animals and 175 bulls for 50K and 777K, respectively. The low density panels were simulated by masking genotypes in the 50K or 777K panel for animals born in 2011. Analyses were performed using both Beagle and FImpute software. Genotype imputation accuracy was measured by concordance rate and allelic R2 between true and imputed genotypes. Results The average concordance rate using FImpute was 0.943 and 0.921 averaged across all simulated low density panels to 50K or to 777K, respectively, in comparison with 0.927 and 0.895 using Beagle. The allelic R2 was 0.912 and 0.866 for imputation to 50K or to 777K using FImpute, respectively, and 0.890 and 0.826 using Beagle. One and two steps imputation to 777K produced averaged concordance rates of 0.806 and 0.892 and allelic R2 of 0.674 and 0.819, respectively. Imputation of low density panels to 50K, with the exception of 3K, had overall concordance rates greater than 0.940 and allelic R2 greater than 0.919. Ungenotyped animals were imputed to 50K panel with an average concordance rate of 0.950 by FImpute. Conclusion FImpute accuracy outperformed Beagle on both imputation to 50K and to 777K. Two-step outperformed one-step imputation for imputing to 777K. Ungenotyped animals that have four or more offspring can have their 50K genotypes accurately inferred using FImpute. All low density panels, except the 3K, can be used to impute to the 50K using FImpute or Beagle with high concordance rate and allelic R2.
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Affiliation(s)
- Mario L Piccoli
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil. .,GenSys Consultores Associados S/S, Porto Alegre, Brazil. .,Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada.
| | - José Braccini
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil. .,National Council for Scientific and Technological Development, Brasília, Brazil.
| | - Fernando F Cardoso
- Embrapa Southern Region Animal Husbandry, Bagé, Brazil. .,National Council for Scientific and Technological Development, Brasília, Brazil.
| | - Medhi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada. .,The Semex Alliance, Guelph, ON, Canada.
| | - Steven G Larmer
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada.
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada.
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113
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Felipe VPS, Okut H, Gianola D, Silva MA, Rosa GJM. Effect of genotype imputation on genome-enabled prediction of complex traits: an empirical study with mice data. BMC Genet 2014; 15:149. [PMID: 25544265 PMCID: PMC4333171 DOI: 10.1186/s12863-014-0149-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/10/2014] [Indexed: 02/01/2023] Open
Abstract
Background Genotype imputation is an important tool for whole-genome prediction as it allows cost reduction of individual genotyping. However, benefits of genotype imputation have been evaluated mostly for linear additive genetic models. In this study we investigated the impact of employing imputed genotypes when using more elaborated models of phenotype prediction. Our hypothesis was that such models would be able to track genetic signals using the observed genotypes only, with no additional information to be gained from imputed genotypes. Results For the present study, an outbred mice population containing 1,904 individuals and genotypes for 1,809 pre-selected markers was used. The effect of imputation was evaluated for a linear model (the Bayesian LASSO - BL) and for semi and non-parametric models (Reproducing Kernel Hilbert spaces regressions – RKHS, and Bayesian Regularized Artificial Neural Networks – BRANN, respectively). The RKHS method had the best predictive accuracy. Genotype imputation had a similar impact on the effectiveness of BL and RKHS. BRANN predictions were, apparently, more sensitive to imputation errors. In scenarios where the masking rates were 75% and 50%, the genotype imputation was not beneficial. However, genotype imputation incorporated information about important markers and improved predictive ability, especially for body mass index (BMI), when genotype information was sparse (90% masking), and for body weight (BW) when the reference sample for imputation was weakly related to the target population. Conclusions In conclusion, genotype imputation is not always helpful for phenotype prediction, and so it should be considered in a case-by-case basis. In summary, factors that can affect the usefulness of genotype imputation for prediction of yet-to-be observed traits are: the imputation accuracy itself, the structure of the population, the genetic architecture of the target trait and also the model used for phenotype prediction.
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Affiliation(s)
- Vivian P S Felipe
- Department of Animal Sciences, University of Wisconsin, Madison, 53706, USA.
| | - Hayrettin Okut
- Department of Animal Sciences, Biometry and Genetics Branch, University of Yuzuncu Yil, Van, 65080, Turkey.
| | - Daniel Gianola
- Department of Animal Sciences, University of Wisconsin, Madison, 53706, USA.
| | - Martinho A Silva
- Department of Animal Sciences, Federal University of Jequitinhonha and Mucuri Valleys, Minas Gerais, Brazil.
| | - Guilherme J M Rosa
- Department of Animal Sciences, University of Wisconsin, Madison, 53706, USA.
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Milanesi M, Vicario D, Stella A, Valentini A, Ajmone-Marsan P, Biffani S, Biscarini F, Jansen G, Nicolazzi EL. Imputation accuracy is robust to cattle reference genome updates. Anim Genet 2014; 46:69-72. [PMID: 25515631 DOI: 10.1111/age.12251] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2014] [Indexed: 11/26/2022]
Abstract
Genotype imputation is routinely applied in a large number of cattle breeds. Imputation has become a need due to the large number of SNP arrays with variable density (currently, from 2900 to 777,962 SNPs). Although many authors have studied the effect of different statistical methods on imputation accuracy, the impact of a (likely) change in the reference genome assembly on imputation from lower to higher density has not been determined so far. In this work, 1021 Italian Simmental SNP genotypes were remapped on the three most recent reference genome assemblies. Four imputation methods were used to assess the impact of an update in the reference genome. As expected, the four methods behaved differently, with large differences in terms of accuracy. Updating SNP coordinates on the three tested cattle reference genome assemblies determined only a slight variation on imputation results within method.
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Affiliation(s)
- M Milanesi
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, Piacenza, 29122, Italy
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115
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He S, Wang S, Fu W, Ding X, Zhang Q. Imputation of missing genotypes from low- to high-density SNP panel in different population designs. Anim Genet 2014; 46:1-7. [PMID: 25431355 DOI: 10.1111/age.12236] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2014] [Indexed: 01/28/2023]
Abstract
Imputation of missing genotypes, in particular from low density to high density, is an important issue in genomic selection and genome-wide association studies. Given the marker densities, the most important factors affecting imputation accuracy are the size of the reference population and the relationship between individuals in the reference (genotyped with high-density panel) and study (genotyped with low-density panel) populations. In this study, we investigated the imputation accuracies when the reference population (genotyped with Illumina BovineSNP50 SNP panel) contained sires, halfsibs, or both sires and halfsibs of the individuals in the study population (genotyped with Illumina BovineLD SNP panel) using three imputation programs (fimpute v2.2, findhap v2, and beagle v3.3.2). Two criteria, correlation between true and imputed genotypes and missing rate after imputation, were used to evaluate the performance of the three programs in different scenarios. Our results showed that fimpute performed the best in all cases, with correlations from 0.921 to 0.978 when imputing from sires to their daughters or between halfsibs. In general, the accuracies of imputing between halfsibs or from sires to their daughters were higher than were those imputing between non-halfsibs or from sires to non-daughters. Including both sires and halfsibs in the reference population did not improve the imputation performance in comparison with when only including halfsibs in the reference population for all the three programs.
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Affiliation(s)
- S He
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Germany
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116
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Muir WM, Cheng HW, Croney C. Methods to address poultry robustness and welfare issues through breeding and associated ethical considerations. Front Genet 2014; 5:407. [PMID: 25505483 PMCID: PMC4244538 DOI: 10.3389/fgene.2014.00407] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/03/2014] [Indexed: 11/13/2022] Open
Abstract
As consumers and society in general become more aware of ethical and moral dilemmas associated with intensive rearing systems, pressure is put on the animal and poultry industries to adopt alternative forms of housing. This presents challenges especially regarding managing competitive social interactions between animals. However, selective breeding programs are rapidly advancing, enhanced by both genomics and new quantitative genetic theory that offer potential solutions by improving adaptation of the bird to existing and proposed production environments. The outcomes of adaptation could lead to improvement of animal welfare by increasing fitness of the animal for the given environments, which might lead to increased contentment and decreased distress of birds in those systems. Genomic selection, based on dense genetic markers, will allow for more rapid improvement of traits that are expensive or difficult to measure, or have a low heritability, such as pecking, cannibalism, robustness, mortality, leg score, bone strength, disease resistance, and thus has the potential to address many poultry welfare concerns. Recently selection programs to include social effects, known as associative or indirect genetic effects (IGEs), have received much attention. Group, kin, multi-level, and multi-trait selection including IGEs have all been shown to be highly effective in reducing mortality while increasing productivity of poultry layers and reduce or eliminate the need for beak trimming. Multi-level selection was shown to increases robustness as indicated by the greater ability of birds to cope with stressors. Kin selection has been shown to be easy to implement and improve both productivity and animal well-being. Management practices and rearing conditions employed for domestic animal production will continue to change based on ethical and scientific results. However, the animal breeding tools necessary to provide an animal that is best adapted to these changing conditions are readily available and should be used, which will ultimately lead to the best possible outcomes for all impacted.
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Affiliation(s)
- William M. Muir
- Department of Animal Sciences, Purdue UniversityWest Lafayette, IN, USA
| | - Heng-Wei Cheng
- Livestock Behavior Research Unit, United States Department of Agriculture – Agricultural Research ServiceWest Lafayette, IN, USA
| | - Candace Croney
- Department of Comparative Pathobiology and Department of Animal Sciences, Purdue UniversityWest Lafayette, IN, USA
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117
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Odegård J, Moen T, Santi N, Korsvoll SA, Kjøglum S, Meuwissen THE. Genomic prediction in an admixed population of Atlantic salmon (Salmo salar). Front Genet 2014; 5:402. [PMID: 25484890 PMCID: PMC4240172 DOI: 10.3389/fgene.2014.00402] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022] Open
Abstract
Reliability of genomic selection (GS) models was tested in an admixed population of Atlantic salmon, originating from crossing of several wild subpopulations. The models included ordinary genomic BLUP models (GBLUP), using genome-wide SNP markers of varying densities (1–220 k), a genomic identity-by-descent model (IBD-GS), using linkage analysis of sparse genome-wide markers, as well as a classical pedigree-based model. Reliabilities of the models were compared through 5-fold cross-validation. The traits studied were salmon lice (Lepeophtheirus salmonis) resistance (LR), measured as (log) density on the skin and fillet color (FC), with respective estimated heritabilities of 0.14 and 0.43. All genomic models outperformed the classical pedigree-based model, for both traits and at all marker densities. However, the relative improvement differed considerably between traits, models and marker densities. For the highly heritable FC, the IBD-GS had similar reliability as GBLUP at high marker densities (>22 k). In contrast, for the lowly heritable LR, IBD-GS was clearly inferior to GBLUP, irrespective of marker density. Hence, GBLUP was robust to marker density for the lowly heritable LR, but sensitive to marker density for the highly heritable FC. We hypothesize that this phenomenon may be explained by historical admixture of different founder populations, expected to reduce short-range lice density (LD) and induce long-range LD. The relative importance of LD/relationship information is expected to decrease/increase with increasing heritability of the trait. Still, using the ordinary GBLUP, the typical long-range LD of an admixed population may be effectively captured by sparse markers, while efficient utilization of relationship information may require denser markers (e.g., 22 k or more).
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Affiliation(s)
| | - Thomas Moen
- Breeding and Genetics, AquaGen AS Trondheim, Norway
| | - Nina Santi
- Research and Development, AquaGen AS Trondheim, Norway
| | | | | | - Theo H E Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences Aas, Norway
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118
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Baes CF, Dolezal MA, Koltes JE, Bapst B, Fritz-Waters E, Jansen S, Flury C, Signer-Hasler H, Stricker C, Fernando R, Fries R, Moll J, Garrick DJ, Reecy JM, Gredler B. Evaluation of variant identification methods for whole genome sequencing data in dairy cattle. BMC Genomics 2014; 15:948. [PMID: 25361890 PMCID: PMC4289218 DOI: 10.1186/1471-2164-15-948] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/14/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less well documented. We explored the consequences of commonly recommended preparatory steps and the effects of single and multi sample variant identification methods using four publicly available software applications (Platypus, HaplotypeCaller, Samtools and UnifiedGenotyper) on whole genome sequence data of 65 key ancestors of Swiss dairy cattle populations. Accuracy of calling next-generation sequence variants was assessed by comparison to the same loci from medium and high-density single nucleotide variant (SNV) arrays. RESULTS The total number of SNVs identified varied by software and method, with single (multi) sample results ranging from 17.7 to 22.0 (16.9 to 22.0) million variants. Computing time varied considerably between software. Preparatory realignment of insertions and deletions and subsequent base quality score recalibration had only minor effects on the number and quality of SNVs identified by different software, but increased computing time considerably. Average concordance for single (multi) sample results with high-density chip data was 58.3% (87.0%) and average genotype concordance in correctly identified SNVs was 99.2% (99.2%) across software. The average quality of SNVs identified, measured as the ratio of transitions to transversions, was higher using single sample methods than multi sample methods. A consensus approach using results of different software generally provided the highest variant quality in terms of transition/transversion ratio. CONCLUSIONS Our findings serve as a reference for variant identification pipeline development in non-human organisms and help assess the implication of preparatory steps in next-generation sequencing pipelines for organisms with incomplete reference genomes (pipeline code is included). Benchmarking this information should prove particularly useful in processing next-generation sequencing data for use in genome-wide association studies and genomic selection.
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Affiliation(s)
- Christine F Baes
- Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFL, Länggasse 85, CH-3052 Zollikofen, Switzerland.
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119
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Carvalheiro R, Boison SA, Neves HHR, Sargolzaei M, Schenkel FS, Utsunomiya YT, O'Brien AMP, Sölkner J, McEwan JC, Van Tassell CP, Sonstegard TS, Garcia JF. Accuracy of genotype imputation in Nelore cattle. Genet Sel Evol 2014; 46:69. [PMID: 25927950 PMCID: PMC4192291 DOI: 10.1186/s12711-014-0069-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 09/19/2014] [Indexed: 01/09/2023] Open
Abstract
Background Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser chips tend to provide more reliable genomic predictions. Imputation methods rely partially on linkage disequilibrium between markers to infer unobserved genotypes. Bos indicus cattle (e.g. Nelore breed) are characterized, in general, by lower levels of linkage disequilibrium between genetic markers at short distances, compared to taurine breeds. Thus, it is important to evaluate the accuracy of imputation to better define which imputation method and chip are most appropriate for genomic applications in indicine breeds. Methods Accuracy of genotype imputation in Nelore cattle was evaluated using different LD chips, imputation software and sets of animals. Twelve commercial and customized LD chips with densities ranging from 7 K to 75 K were tested. Customized LD chips were virtually designed taking into account minor allele frequency, linkage disequilibrium and distance between markers. Software programs FImpute and BEAGLE were applied to impute genotypes. From 995 bulls and 1247 cows that were genotyped with the Illumina® BovineHD chip (HD), 793 sires composed the reference set, and the remaining 202 younger sires and all the cows composed two separate validation sets for which genotypes were masked except for the SNPs of the LD chip that were to be tested. Results Imputation accuracy increased with the SNP density of the LD chip. However, the gain in accuracy with LD chips with more than 15 K SNPs was relatively small because accuracy was already high at this density. Commercial and customized LD chips with equivalent densities presented similar results. FImpute outperformed BEAGLE for all LD chips and validation sets. Regardless of the imputation software used, accuracy tended to increase as the relatedness between imputed and reference animals increased, especially for the 7 K chip. Conclusions If the Illumina® BovineHD is considered as the target chip for genomic applications in the Nelore breed, cost-effectiveness can be improved by genotyping part of the animals with a chip containing around 15 K useful SNPs and imputing their high-density missing genotypes with FImpute. Electronic supplementary material The online version of this article (doi:10.1186/s12711-014-0069-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roberto Carvalheiro
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, 14884-900, Brazil.
| | - Solomon A Boison
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems BOKU, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria.
| | - Haroldo H R Neves
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, 14884-900, Brazil. .,GenSys Consultores Associados S/C Ltda, Porto Alegre, 90680-000, Brasil.
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G2W1, Canada. .,The Semex Alliance, Guelph, Ontario, Canada.
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G2W1, Canada.
| | - Yuri T Utsunomiya
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, 14884-900, Brazil.
| | - Ana Maria Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems BOKU, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria.
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems BOKU, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria.
| | - John C McEwan
- Centre for Reproduction and Genomics, AgResearch, Invermay, Mosgiel, New Zealand.
| | - Curtis P Van Tassell
- United States Department of Agriculture, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, 20705, USA.
| | - Tad S Sonstegard
- United States Department of Agriculture, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, 20705, USA.
| | - José Fernando Garcia
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, 14884-900, Brazil. .,UNESP, Universidad Estadual Paulista, Faculdade de Medicina Veterinária de Araçatuba, Araçatuba, São Paulo, 16050-680, Brazil.
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The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data. Genetics 2014; 198:1671-84. [PMID: 25233989 DOI: 10.1534/genetics.114.168344] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The use of dense SNPs to predict the genetic value of an individual for a complex trait is often referred to as "genomic selection" in livestock and crops, but is also relevant to human genetics to predict, for example, complex genetic disease risk. The accuracy of prediction depends on the strength of linkage disequilibrium (LD) between SNPs and causal mutations. If sequence data were used instead of dense SNPs, accuracy should increase because causal mutations are present, but demographic history and long-term negative selection also influence accuracy. We therefore evaluated genomic prediction, using simulated sequence in two contrasting populations: one reducing from an ancestrally large effective population size (Ne) to a small one, with high LD common in domestic livestock, while the second had a large constant-sized Ne with low LD similar to that in some human or outbred plant populations. There were two scenarios in each population; causal variants were either neutral or under long-term negative selection. For large Ne, sequence data led to a 22% increase in accuracy relative to ∼600K SNP chip data with a Bayesian analysis and a more modest advantage with a BLUP analysis. This advantage increased when causal variants were influenced by negative selection, and accuracy persisted when 10 generations separated reference and validation populations. However, in the reducing Ne population, there was little advantage for sequence even with negative selection. This study demonstrates the joint influence of demography and selection on accuracy of prediction and improves our understanding of how best to exploit sequence for genomic prediction.
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Macciotta N, Dimauro C, Null D, Gaspa G, Cellesi M, Cole J. Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis. J Anim Breed Genet 2014; 132:9-20. [DOI: 10.1111/jbg.12113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/03/2014] [Indexed: 11/28/2022]
Affiliation(s)
- N.P.P. Macciotta
- Dipartimento di Agraria; Sezione Scienze Zootecniche; Università di Sassari; Sassari Italy
| | - C. Dimauro
- Dipartimento di Agraria; Sezione Scienze Zootecniche; Università di Sassari; Sassari Italy
| | - D.J. Null
- Animal Genomics and Improvement Laboratory; Agricultural Research Service; USDA; Beltsville Maryland USA
| | - G. Gaspa
- Dipartimento di Agraria; Sezione Scienze Zootecniche; Università di Sassari; Sassari Italy
| | - M. Cellesi
- Dipartimento di Agraria; Sezione Scienze Zootecniche; Università di Sassari; Sassari Italy
| | - J.B. Cole
- Animal Genomics and Improvement Laboratory; Agricultural Research Service; USDA; Beltsville Maryland USA
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122
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Ferdosi MH, Boerner V. A fast method for evaluating opposing homozygosity in large SNP data sets. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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123
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Boison S, Neves H, Pérez O’Brien A, Utsunomiya Y, Carvalheiro R, da Silva M, Sölkner J, Garcia J. Imputation of non-genotyped individuals using genotyped progeny in Nellore, a Bos indicus cattle breed. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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125
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Su G, Guldbrandtsen B, Aamand GP, Strandén I, Lund MS. Genomic relationships based on X chromosome markers and accuracy of genomic predictions with and without X chromosome markers. Genet Sel Evol 2014; 46:47. [PMID: 25080199 PMCID: PMC4137273 DOI: 10.1186/1297-9686-46-47] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 06/18/2014] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Although the X chromosome is the second largest bovine chromosome, markers on the X chromosome are not used for genomic prediction in some countries and populations. In this study, we presented a method for computing genomic relationships using X chromosome markers, investigated the accuracy of imputation from a low density (7K) to the 54K SNP (single nucleotide polymorphism) panel, and compared the accuracy of genomic prediction with and without using X chromosome markers. METHODS The impact of considering X chromosome markers on prediction accuracy was assessed using data from Nordic Holstein bulls and different sets of SNPs: (a) the 54K SNPs for reference and test animals, (b) SNPs imputed from the 7K to the 54K SNP panel for test animals, (c) SNPs imputed from the 7K to the 54K panel for half of the reference animals, and (d) the 7K SNP panel for all animals. Beagle and Findhap were used for imputation. GBLUP (genomic best linear unbiased prediction) models with or without X chromosome markers and with or without a residual polygenic effect were used to predict genomic breeding values for 15 traits. RESULTS Averaged over the two imputation datasets, correlation coefficients between imputed and true genotypes for autosomal markers, pseudo-autosomal markers, and X-specific markers were 0.971, 0.831 and 0.935 when using Findhap, and 0.983, 0.856 and 0.937 when using Beagle. Estimated reliabilities of genomic predictions based on the imputed datasets using Findhap or Beagle were very close to those using the real 54K data. Genomic prediction using all markers gave slightly higher reliabilities than predictions without X chromosome markers. Based on our data which included only bulls, using a G matrix that accounted for sex-linked relationships did not improve prediction, compared with a G matrix that did not account for sex-linked relationships. A model that included a polygenic effect did not recover the loss of prediction accuracy from exclusion of X chromosome markers. CONCLUSIONS The results from this study suggest that markers on the X chromosome contribute to accuracy of genomic predictions and should be used for routine genomic evaluation.
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Affiliation(s)
- Guosheng Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele DK-8830, Denmark.
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Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications. Animal 2014; 8:1743-53. [PMID: 25045914 DOI: 10.1017/s1751731114001803] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In livestock, many studies have reported the results of imputation to 50k single nucleotide polymorphism (SNP) genotypes for animals that are genotyped with low-density SNP panels. The objective of this paper is to review different measures of correctness of imputation, and to evaluate their utility depending on the purpose of the imputed genotypes. Across studies, imputation accuracy, computed as the correlation between true and imputed genotypes, and imputation error rates, that counts the number of incorrectly imputed alleles, are commonly used measures of imputation correctness. Based on the nature of both measures and results reported in the literature, imputation accuracy appears to be a more useful measure of the correctness of imputation than imputation error rates, because imputation accuracy does not depend on minor allele frequency (MAF), whereas imputation error rate depends on MAF. Therefore imputation accuracy can be better compared across loci with different MAF. Imputation accuracy depends on the ability of identifying the correct haplotype of a SNP, but many other factors have been identified as well, including the number of genotyped immediate ancestors, the number of animals with genotypes at the high-density panel, the SNP density on the low- and high-density panel, the MAF of the imputed SNP and whether imputed SNP are located at the end of a chromosome or not. Some of these factors directly contribute to the linkage disequilibrium between imputed SNP and SNP on the low-density panel. When imputation accuracy is assessed as a predictor for the accuracy of subsequent genomic prediction, we recommend that: (1) individual-specific imputation accuracies should be used that are computed after centring and scaling both true and imputed genotypes; and (2) imputation of gene dosage is preferred over imputation of the most likely genotype, as this increases accuracy and reduces bias of the imputed genotypes and the subsequent genomic predictions.
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Sargolzaei M, Chesnais JP, Schenkel FS. A new approach for efficient genotype imputation using information from relatives. BMC Genomics 2014; 15:478. [PMID: 24935670 PMCID: PMC4076979 DOI: 10.1186/1471-2164-15-478] [Citation(s) in RCA: 586] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 06/10/2014] [Indexed: 01/21/2023] Open
Abstract
Background Genotype imputation can help reduce genotyping costs particularly for implementation of genomic selection. In applications entailing large populations, recovering the genotypes of untyped loci using information from reference individuals that were genotyped with a higher density panel is computationally challenging. Popular imputation methods are based upon the Hidden Markov model and have computational constraints due to an intensive sampling process. A fast, deterministic approach, which makes use of both family and population information, is presented here. All individuals are related and, therefore, share haplotypes which may differ in length and frequency based on their relationships. The method starts with family imputation if pedigree information is available, and then exploits close relationships by searching for long haplotype matches in the reference group using overlapping sliding windows. The search continues as the window size is shrunk in each chromosome sweep in order to capture more distant relationships. Results The proposed method gave higher or similar imputation accuracy than Beagle and Impute2 in cattle data sets when all available information was used. When close relatives of target individuals were present in the reference group, the method resulted in higher accuracy compared to the other two methods even when the pedigree was not used. Rare variants were also imputed with higher accuracy. Finally, computing requirements were considerably lower than those of Beagle and Impute2. The presented method took 28 minutes to impute from 6 k to 50 k genotypes for 2,000 individuals with a reference size of 64,429 individuals. Conclusions The proposed method efficiently makes use of information from close and distant relatives for accurate genotype imputation. In addition to its high imputation accuracy, the method is fast, owing to its deterministic nature and, therefore, it can easily be used in large data sets where the use of other methods is impractical.
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Affiliation(s)
- Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Animal and Poultry Science Department, University of Guelph, 50 Stone Road East, Guelph, ON, Canada.
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128
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Cole J, Waurich B, Wensch-Dorendorf M, Bickhart D, Swalve H. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. J Dairy Sci 2014; 97:3156-72. [DOI: 10.3168/jds.2013-7409] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 01/28/2014] [Indexed: 02/04/2023]
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Accuracy of estimation of genomic breeding values in pigs using low-density genotypes and imputation. G3-GENES GENOMES GENETICS 2014; 4:623-31. [PMID: 24531728 PMCID: PMC4059235 DOI: 10.1534/g3.114.010504] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genomic selection has the potential to increase genetic progress. Genotype imputation of high-density single-nucleotide polymorphism (SNP) genotypes can improve the cost efficiency of genomic breeding value (GEBV) prediction for pig breeding. Consequently, the objectives of this work were to: (1) estimate accuracy of genomic evaluation and GEBV for three traits in a Yorkshire population and (2) quantify the loss of accuracy of genomic evaluation and GEBV when genotypes were imputed under two scenarios: a high-cost, high-accuracy scenario in which only selection candidates were imputed from a low-density platform and a low-cost, low-accuracy scenario in which all animals were imputed using a small reference panel of haplotypes. Phenotypes and genotypes obtained with the PorcineSNP60 BeadChip were available for 983 Yorkshire boars. Genotypes of selection candidates were masked and imputed using tagSNP in the GeneSeek Genomic Profiler (10K). Imputation was performed with BEAGLE using 128 or 1800 haplotypes as reference panels. GEBV were obtained through an animal-centric ridge regression model using de-regressed breeding values as response variables. Accuracy of genomic evaluation was estimated as the correlation between estimated breeding values and GEBV in a 10-fold cross validation design. Accuracy of genomic evaluation using observed genotypes was high for all traits (0.65−0.68). Using genotypes imputed from a large reference panel (accuracy: R2 = 0.95) for genomic evaluation did not significantly decrease accuracy, whereas a scenario with genotypes imputed from a small reference panel (R2 = 0.88) did show a significant decrease in accuracy. Genomic evaluation based on imputed genotypes in selection candidates can be implemented at a fraction of the cost of a genomic evaluation using observed genotypes and still yield virtually the same accuracy. On the other side, using a very small reference panel of haplotypes to impute training animals and candidates for selection results in lower accuracy of genomic evaluation.
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Hozé C, Fritz S, Phocas F, Boichard D, Ducrocq V, Croiseau P. Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population. J Dairy Sci 2014; 97:3918-29. [PMID: 24704232 DOI: 10.3168/jds.2013-7761] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/25/2014] [Indexed: 01/13/2023]
Abstract
Single-breed genomic selection (GS) based on medium single nucleotide polymorphism (SNP) density (~50,000; 50K) is now routinely implemented in several large cattle breeds. However, building large enough reference populations remains a challenge for many medium or small breeds. The high-density BovineHD BeadChip (HD chip; Illumina Inc., San Diego, CA) containing 777,609 SNP developed in 2010 is characterized by short-distance linkage disequilibrium expected to be maintained across breeds. Therefore, combining reference populations can be envisioned. A population of 1,869 influential ancestors from 3 dairy breeds (Holstein, Montbéliarde, and Normande) was genotyped with the HD chip. Using this sample, 50K genotypes were imputed within breed to high-density genotypes, leading to a large HD reference population. This population was used to develop a multi-breed genomic evaluation. The goal of this paper was to investigate the gain of multi-breed genomic evaluation for a small breed. The advantage of using a large breed (Normande in the present study) to mimic a small breed is the large potential validation population to compare alternative genomic selection approaches more reliably. In the Normande breed, 3 training sets were defined with 1,597, 404, and 198 bulls, and a unique validation set included the 394 youngest bulls. For each training set, estimated breeding values (EBV) were computed using pedigree-based BLUP, single-breed BayesC, or multi-breed BayesC for which the reference population was formed by any of the Normande training data sets and 4,989 Holstein and 1,788 Montbéliarde bulls. Phenotypes were standardized by within-breed genetic standard deviation, the proportion of polygenic variance was set to 30%, and the estimated number of SNP with a nonzero effect was about 7,000. The 2 genomic selection (GS) approaches were performed using either the 50K or HD genotypes. The correlations between EBV and observed daughter yield deviations (DYD) were computed for 6 traits and using the different prediction approaches. Compared with pedigree-based BLUP, the average gain in accuracy with GS in small populations was 0.057 for the single-breed and 0.086 for multi-breed approach. This gain was up to 0.193 and 0.209, respectively, with the large reference population. Improvement of EBV prediction due to the multi-breed evaluation was higher for animals not closely related to the reference population. In the case of a breed with a small reference population size, the increase in correlation due to multi-breed GS was 0.141 for bulls without their sire in reference population compared with 0.016 for bulls with their sire in reference population. These results demonstrate that multi-breed GS can contribute to increase genomic evaluation accuracy in small breeds.
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Affiliation(s)
- C Hozé
- Institut National de la Recherche Agronomique (INRA), UMR 1313, Génétique Animale et Biologie Intégrative (GABI), 78350 Jouy-en-Josas, France; Union Nationales des Coopératives d'Élevages et d'Insémination Animales (UNCEIA), 149 rue de Bercy, 75012 Paris, France.
| | - S Fritz
- Union Nationales des Coopératives d'Élevages et d'Insémination Animales (UNCEIA), 149 rue de Bercy, 75012 Paris, France
| | - F Phocas
- Institut National de la Recherche Agronomique (INRA), UMR 1313, Génétique Animale et Biologie Intégrative (GABI), 78350 Jouy-en-Josas, France
| | - D Boichard
- Institut National de la Recherche Agronomique (INRA), UMR 1313, Génétique Animale et Biologie Intégrative (GABI), 78350 Jouy-en-Josas, France
| | - V Ducrocq
- Institut National de la Recherche Agronomique (INRA), UMR 1313, Génétique Animale et Biologie Intégrative (GABI), 78350 Jouy-en-Josas, France
| | - P Croiseau
- Institut National de la Recherche Agronomique (INRA), UMR 1313, Génétique Animale et Biologie Intégrative (GABI), 78350 Jouy-en-Josas, France
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Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3. PLoS One 2014; 9:e92769. [PMID: 24667746 PMCID: PMC3965462 DOI: 10.1371/journal.pone.0092769] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 02/26/2014] [Indexed: 01/13/2023] Open
Abstract
The recent discovery of bovine haplotypes with negative effects on fertility in the Brown Swiss, Holstein, and Jersey breeds has allowed producers to identify carrier animals using commercial single nucleotide polymorphism (SNP) genotyping assays. This study was devised to identify the causative mutations underlying defective bovine embryo development contained within three of these haplotypes (Brown Swiss haplotype 1 and Holstein haplotypes 2 and 3) by combining exome capture with next generation sequencing. Of the 68,476,640 sequence variations (SV) identified, only 1,311 genome-wide SNP were concordant with the haplotype status of 21 sequenced carriers. Validation genotyping of 36 candidate SNP identified only 1 variant that was concordant to Holstein haplotype 3 (HH3), while no variants located within the refined intervals for HH2 or BH1 were concordant. The variant strictly associated with HH3 is a non-synonymous SNP (T/C) within exon 24 of the Structural Maintenance of Chromosomes 2 (SMC2) on Chromosome 8 at position 95,410,507 (UMD3.1). This polymorphism changes amino acid 1135 from phenylalanine to serine and causes a non-neutral, non-tolerated, and evolutionarily unlikely substitution within the NTPase domain of the encoded protein. Because only exome capture sequencing was used, we could not rule out the possibility that the true causative mutation for HH3 might lie in a non-exonic genomic location. Given the essential role of SMC2 in DNA repair, chromosome condensation and segregation during cell division, our findings strongly support the non-synonymous SNP (T/C) in SMC2 as the likely causative mutation. The absence of concordant variations for HH2 or BH1 suggests either the underlying causative mutations lie within a non-exomic region or in exome regions not covered by the capture array.
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Neves HHR, Carvalheiro R, O'Brien AMP, Utsunomiya YT, do Carmo AS, Schenkel FS, Sölkner J, McEwan JC, Van Tassell CP, Cole JB, da Silva MVGB, Queiroz SA, Sonstegard TS, Garcia JF. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genet Sel Evol 2014; 46:17. [PMID: 24575732 PMCID: PMC4014866 DOI: 10.1186/1297-9686-46-17] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 02/18/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and fertility in this breed. We present the first results of the implementation of genomic prediction in a Bos indicus (Nellore) population. METHODS Influential bulls were genotyped with the Illumina Bovine HD chip in order to assess genomic predictive ability for weight and carcass traits, gestation length, scrotal circumference and two selection indices. 685 samples and 320 238 single nucleotide polymorphisms (SNPs) were used in the analyses. A forward-prediction scheme was adopted to predict the genomic breeding values (DGV). In the training step, the estimated breeding values (EBV) of bulls were deregressed (dEBV) and used as pseudo-phenotypes to estimate marker effects using four methods: genomic BLUP with or without a residual polygenic effect (GBLUP20 and GBLUP0, respectively), a mixture model (Bayes C) and Bayesian LASSO (BLASSO). Empirical accuracies of the resulting genomic predictions were assessed based on the correlation between DGV and dEBV for the testing group. RESULTS Accuracies of genomic predictions ranged from 0.17 (navel at weaning) to 0.74 (finishing precocity). Across traits, Bayesian regression models (Bayes C and BLASSO) were more accurate than GBLUP. The average empirical accuracies were 0.39 (GBLUP0), 0.40 (GBLUP20) and 0.44 (Bayes C and BLASSO). Bayes C and BLASSO tended to produce deflated predictions (i.e. slope of the regression of dEBV on DGV greater than 1). Further analyses suggested that higher-than-expected accuracies were observed for traits for which EBV means differed significantly between two breeding subgroups that were identified in a principal component analysis based on genomic relationships. CONCLUSIONS Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. Recurrent updates of the training population would be required to enable accurate prediction of the genetic merit of young animals. The technical feasibility of applying genomic prediction in a Bos indicus (Nellore) population was demonstrated. Further research is needed to permit cost-effective selection decisions using genomic information.
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Affiliation(s)
- Haroldo H R Neves
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900, Brazil.
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Bickhart DM, Liu GE. The challenges and importance of structural variation detection in livestock. Front Genet 2014; 5:37. [PMID: 24600474 PMCID: PMC3927395 DOI: 10.3389/fgene.2014.00037] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/31/2014] [Indexed: 01/25/2023] Open
Abstract
Recent studies in humans and other model organisms have demonstrated that structural variants (SVs) comprise a substantial proportion of variation among individuals of each species. Many of these variants have been linked to debilitating diseases in humans, thereby cementing the importance of refining methods for their detection. Despite progress in the field, reliable detection of SVs still remains a problem even for human subjects. Many of the underlying problems that make SVs difficult to detect in humans are amplified in livestock species, whose lower quality genome assemblies and incomplete gene annotation can often give rise to false positive SV discoveries. Regardless of the challenges, SV detection is just as important for livestock researchers as it is for human researchers, given that several productive traits and diseases have been linked to copy number variations (CNVs) in cattle, sheep, and pig. Already, there is evidence that many beneficial SVs have been artificially selected in livestock such as a duplication of the agouti signaling protein gene that causes white coat color in sheep. In this review, we will list current SV and CNV discoveries in livestock and discuss the problems that hinder routine discovery and tracking of these polymorphisms. We will also discuss the impacts of selective breeding on CNV and SV frequencies and mention how SV genotyping could be used in the future to improve genetic selection.
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Affiliation(s)
- Derek M Bickhart
- Animal Improvement Programs Laboratory, United States Department of Agriculture-Agricultural Research Service Beltsville, MD, USA
| | - George E Liu
- Bovine Functional Genomics Laboratory, United States Department of Agriculture-Agricultural Research Service Beltsville, MD, USA
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Nicolazzi EL, Picciolini M, Strozzi F, Schnabel RD, Lawley C, Pirani A, Brew F, Stella A. SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock. BMC Genomics 2014; 15:123. [PMID: 24517501 PMCID: PMC3923093 DOI: 10.1186/1471-2164-15-123] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 02/06/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Currently, six commercial whole-genome SNP chips are available for cattle genotyping, produced by two different genotyping platforms. Technical issues need to be addressed to combine data that originates from the different platforms, or different versions of the same array generated by the manufacturer. For example: i) genome coordinates for SNPs may refer to different genome assemblies; ii) reference genome sequences are updated over time changing the positions, or even removing sequences which contain SNPs; iii) not all commercial SNP ID's are searchable within public databases; iv) SNPs can be coded using different formats and referencing different strands (e.g. A/B or A/C/T/G alleles, referencing forward/reverse, top/bottom or plus/minus strand); v) Due to new information being discovered, higher density chips do not necessarily include all the SNPs present in the lower density chips; and, vi) SNP IDs may not be consistent across chips and platforms. Most researchers and breed associations manage SNP data in real-time and thus require tools to standardise data in a user-friendly manner. DESCRIPTION Here we present SNPchiMp, a MySQL database linked to an open access web-based interface. Features of this interface include, but are not limited to, the following functions: 1) referencing the SNP mapping information to the latest genome assembly, 2) extraction of information contained in dbSNP for SNPs present in all commercially available bovine chips, and 3) identification of SNPs in common between two or more bovine chips (e.g. for SNP imputation from lower to higher density). In addition, SNPchiMp can retrieve this information on subsets of SNPs, accessing such data either via physical position on a supported assembly, or by a list of SNP IDs, rs or ss identifiers. CONCLUSIONS This tool combines many different sources of information, that otherwise are time consuming to obtain and difficult to integrate. The SNPchiMp not only provides the information in a user-friendly format, but also enables researchers to perform a large number of operations with a few clicks of the mouse. This significantly reduces the time needed to execute the large number of operations required to manage SNP data.
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Santana MHA, Utsunomiya YT, Neves HHR, Gomes RC, Garcia JF, Fukumasu H, Silva SL, Oliveira Junior GA, Alexandre PA, Leme PR, Brassaloti RA, Coutinho LL, Lopes TG, Meirelles FV, Eler JP, Ferraz JBS. Genome-wide association analysis of feed intake and residual feed intake in Nellore cattle. BMC Genet 2014; 15:21. [PMID: 24517472 PMCID: PMC3925773 DOI: 10.1186/1471-2156-15-21] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/04/2014] [Indexed: 11/30/2022] Open
Abstract
Background Feed intake plays an important economic role in beef cattle, and is related with feed efficiency, weight gain and carcass traits. However, the phenotypes collected for dry matter intake and feed efficiency are scarce when compared with other measures such as weight gain and carcass traits. The use of genomic information can improve the power of inference of studies on these measures, identifying genomic regions that affect these phenotypes. This work performed the genome-wide association study (GWAS) for dry matter intake (DMI) and residual feed intake (RFI) of 720 Nellore cattle (Bos taurus indicus). Results In general, no genomic region extremely associated with both phenotypic traits was observed, as expected for the variables that have their regulation controlled by many genes. Three SNPs surpassed the threshold for the Bonferroni multiple test for DMI and two SNPs for RFI. These markers are located on chromosomes 4, 8, 14 and 21 in regions near genes regulating appetite and ion transport and close to important QTL as previously reported to RFI and DMI, thus corroborating the literature that points these two processes as important in the physiological regulation of intake and feed efficiency. Conclusions This study showed the first GWAS of DMI to identify genomic regions associated with feed intake and efficiency in Nellore cattle. Some genes and QTLs previously described for DMI and RFI, in other subspecies (Bos taurus taurus), that influences these phenotypes are confirmed in this study.
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Affiliation(s)
- Miguel H A Santana
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Av, Duque de Caxias Norte, 225, 13635-900 Pirassununga, São Paulo, Brazil.
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Sun C, VanRaden PM. Increasing long-term response by selecting for favorable minor alleles. PLoS One 2014; 9:e88510. [PMID: 24505495 PMCID: PMC3914995 DOI: 10.1371/journal.pone.0088510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022] Open
Abstract
Long-term response of genomic selection can be improved by considering allele frequencies of selected markers or quantitative trait loci (QTLs). A previous formula to weight allele frequency of favorable minor alleles was tested, and 2 new formulas were developed. The previous formula used nonlinear weights based on square root of frequency of the favorable allele. The new formulas included a parameter δ to balance long- and short-term progress; one used square root and the other used simple linear weights. The formulas were tested by simulation of 20 generations (population size of 3,000 for each generation) with direct selection on 3,000 QTLs (100 per chromosome). A QTL distribution with normally distributed allele effects and a heavy-tailed distribution were tested. Optimum δ from simulation was applied to data from Holstein, Jersey and Brown Swiss dairy cattle to compare differences of adjusted and official genomic evaluations. From simulation, optimum δ was 0.4 for the heavy-tailed QTL distribution but only 0.1 or 0.2 for a normal distribution. The previous formula had slower response than unweighted selection in early generations and did not recover by generation 20. Long-term response was slightly greater with the new formulas than with unweighted selection; the linear formula may be best for routine use because of more progress in early generations compared to nonlinear formula. Official and adjusted U.S. evaluations based on actual genotypes and estimated marker effects were correlated by 0.994 for Holsteins and Jerseys and 0.989 for Brown Swiss using linear weighting of allele frequency, which was higher than nonlinear weighting. The difference between adjusted and official evaluations was highly correlated negatively with an animal's average genomic relationship to the population. Thus, strategies to reduce genomic inbreeding may achieve almost as much long-term progress as selection of favorable minor alleles.
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Affiliation(s)
- Chuanyu Sun
- National Association of Animal Breeders, Columbia, Missouri, United States of America
| | - Paul M. VanRaden
- Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
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Schrooten C, Dassonneville R, Ducrocq V, Brøndum RF, Lund MS, Chen J, Liu Z, González-Recio O, Pena J, Druet T. Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip. Genet Sel Evol 2014; 46:10. [PMID: 24495554 PMCID: PMC3929158 DOI: 10.1186/1297-9686-46-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 12/02/2013] [Indexed: 11/20/2022] Open
Abstract
Background Imputation of genotypes from low-density to higher density chips is a cost-effective method to obtain high-density genotypes for many animals, based on genotypes of only a relatively small subset of animals (reference population) on the high-density chip. Several factors influence the accuracy of imputation and our objective was to investigate the effects of the size of the reference population used for imputation and of the imputation method used and its parameters. Imputation of genotypes was carried out from 50 000 (moderate-density) to 777 000 (high-density) SNPs (single nucleotide polymorphisms). Methods The effect of reference population size was studied in two datasets: one with 548 and one with 1289 Holstein animals, genotyped with the Illumina BovineHD chip (777 k SNPs). A third dataset included the 548 animals genotyped with the 777 k SNP chip and 2200 animals genotyped with the Illumina BovineSNP50 chip. In each dataset, 60 animals were chosen as validation animals, for which all high-density genotypes were masked, except for the Illumina BovineSNP50 markers. Imputation was studied in a subset of six chromosomes, using the imputation software programs Beagle and DAGPHASE. Results Imputation with DAGPHASE and Beagle resulted in 1.91% and 0.87% allelic imputation error rates in the dataset with 548 high-density genotypes, when scale and shift parameters were 2.0 and 0.1, and 1.0 and 0.0, respectively. When Beagle was used alone, the imputation error rate was 0.67%. If the information obtained by Beagle was subsequently used in DAGPHASE, imputation error rates were slightly higher (0.71%). When 2200 moderate-density genotypes were added and Beagle was used alone, imputation error rates were slightly lower (0.64%). The least imputation errors were obtained with Beagle in the reference set with 1289 high-density genotypes (0.41%). Conclusions For imputation of genotypes from the 50 k to the 777 k SNP chip, Beagle gave the lowest allelic imputation error rates. Imputation error rates decreased with increasing size of the reference population. For applications for which computing time is limiting, DAGPHASE using information from Beagle can be considered as an alternative, since it reduces computation time and increases imputation error rates only slightly.
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Ferdosi MH, Kinghorn BP, van der Werf JHJ, Gondro C. Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes. Genet Sel Evol 2014; 46:11. [PMID: 24495596 PMCID: PMC3996164 DOI: 10.1186/1297-9686-46-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 01/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying recombination events and the chromosomal segments that constitute a gamete is useful for a number of applications in genomic analyses. In livestock, genotypic data are commonly available for half-sib families. We propose a straightforward but computationally efficient method to use single nucleotide polymorphism marker genotypes on half-sibs to reconstruct the recombination and segregation events that occurred during meiosis in a sire to form the haplotypes observed in its offspring. These meiosis events determine a block structure in paternal haplotypes of the progeny and this can be used to phase the genotypes of individuals in single half-sib families, to impute haplotypes of the sire if they are not genotyped or to impute the paternal strand of the offspring's sequence based on sequence data of the sire. METHODS The hsphase algorithm exploits information from opposing homozygotes among half-sibs to identify recombination events, and the chromosomal regions from the paternal and maternal strands of the sire (blocks) that were inherited by its progeny. This information is then used to impute the sire's genotype, which, in turn, is used to phase the half-sib family. Accuracy (defined as R2) and performance of this approach were evaluated by using simulated and real datasets. Phasing results for the half-sibs were benchmarked to other commonly used phasing programs - AlphaPhase, BEAGLE and PedPhase 3. RESULTS Using a simulated dataset with 20 markers per cM, and for a half-sib family size of 4 and 40, the accuracy of block detection, was 0.58 and 0.96, respectively. The accuracy of inferring sire genotypes was 0.75 and 1.00 and the accuracy of phasing was around 0.97, respectively. hsphase was more robust to genotyping errors than PedPhase 3, AlphaPhase and BEAGLE. Computationally, hsphase was much faster than AlphaPhase and BEAGLE. CONCLUSIONS In half-sib families of size 8 and above, hsphase can accurately detect block structure of paternal haplotypes, impute genotypes of ungenotyped sires and reconstruct haplotypes in progeny. The method is much faster and more accurate than other widely used population-based phasing programs. A program implementing the method is freely available as an R package (hsphase).
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Affiliation(s)
- Mohammad H Ferdosi
- School of Environmental and Rural Science, University of New England, Armidale, Australia.
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Bouwman AC, Hickey JM, Calus MPL, Veerkamp RF. Imputation of non-genotyped individuals based on genotyped relatives: assessing the imputation accuracy of a real case scenario in dairy cattle. Genet Sel Evol 2014; 46:6. [PMID: 24490796 PMCID: PMC3929150 DOI: 10.1186/1297-9686-46-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 01/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Imputation of genotypes for ungenotyped individuals could enable the use of valuable phenotypes created before the genomic era in analyses that require genotypes. The objective of this study was to investigate the accuracy of imputation of non-genotyped individuals using genotype information from relatives. METHODS Genotypes were simulated for all individuals in the pedigree of a real (historical) dataset of phenotyped dairy cows and with part of the pedigree genotyped. The software AlphaImpute was used for imputation in its standard settings but also without phasing, i.e. using basic inheritance rules and segregation analysis only. Different scenarios were evaluated i.e.: (1) the real data scenario, (2) addition of genotypes of sires and maternal grandsires of the ungenotyped individuals, and (3) addition of one, two, or four genotyped offspring of the ungenotyped individuals to the reference population. RESULTS The imputation accuracy using AlphaImpute in its standard settings was lower than without phasing. Including genotypes of sires and maternal grandsires in the reference population improved imputation accuracy, i.e. the correlation of the true genotypes with the imputed genotype dosages, corrected for mean gene content, across all animals increased from 0.47 (real situation) to 0.60. Including one, two and four genotyped offspring increased the accuracy of imputation across all animals from 0.57 (no offspring) to 0.73, 0.82, and 0.92, respectively. CONCLUSIONS At present, the use of basic inheritance rules and segregation analysis appears to be the best imputation method for ungenotyped individuals. Comparison of our empirical animal-specific imputation accuracies to predictions based on selection index theory suggested that not correcting for mean gene content considerably overestimates the true accuracy. Imputation of ungenotyped individuals can help to include valuable phenotypes for genome-wide association studies or for genomic prediction, especially when the ungenotyped individuals have genotyped offspring.
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Affiliation(s)
- Aniek C Bouwman
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P,O, Box 135, Wageningen 6700, AC, Netherlands.
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Pryce JE, Johnston J, Hayes BJ, Sahana G, Weigel KA, McParland S, Spurlock D, Krattenmacher N, Spelman RJ, Wall E, Calus MPL. Imputation of genotypes from low density (50,000 markers) to high density (700,000 markers) of cows from research herds in Europe, North America, and Australasia using 2 reference populations. J Dairy Sci 2014; 97:1799-811. [PMID: 24472132 DOI: 10.3168/jds.2013-7368] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 12/03/2013] [Indexed: 12/30/2022]
Abstract
Combining data from research herds may be advantageous, especially for difficult or expensive-to-measure traits (such as dry matter intake). Cows in research herds are often genotyped using low-density single nucleotide polymorphism (SNP) panels. However, the precision of quantitative trait loci detection in genome-wide association studies and the accuracy of genomic selection may increase when the low-density genotypes are imputed to higher density. Genotype data were available from 10 research herds: 5 from Europe [Denmark, Germany, Ireland, the Netherlands, and the United Kingdom (UK)], 2 from Australasia (Australia and New Zealand), and 3 from North America (Canada and the United States). Heifers from the Australian and New Zealand research herds were already genotyped at high density (approximately 700,000 SNP). The remaining genotypes were imputed from around 50,000 SNP to 700,000 using 2 reference populations. Although it was not possible to use a combined reference population, which would probably result in the highest accuracies of imputation, differences arising from using 2 high-density reference populations on imputing 50,000-marker genotypes of 583 animals (from the UK) were quantified. The European genotypes (n=4,097) were imputed as 1 data set, using a reference population of 3,150 that included genotypes from 835 Australian and 1,053 New Zealand females, with the remainder being males. Imputation was undertaken using population-wide linkage disequilibrium with no family information exploited. The UK animals were also included in the North American data set (n=1,579) that was imputed to high density using a reference population of 2,018 bulls. After editing, 591,213 genotypes on 5,999 animals from 10 research herds remained. The correlation between imputed allele frequencies of the 2 imputed data sets was high (>0.98) and even stronger (>0.99) for the UK animals that were part of each imputation data set. For the UK genotypes, 2.2% were imputed differently in the 2 high-density reference data sets used. Only 0.025% of these were homozygous switches. The number of discordant SNP was lower for animals that had sires that were genotyped. Discordant imputed SNP genotypes were most common when a large difference existed in allele frequency between the 2 imputed genotype data sets. For SNP that had ≥ 20% discordant genotypes, the difference between imputed data sets of allele frequencies of the UK (imputed) genotypes was 0.07, whereas the difference in allele frequencies of the (reference) high-density genotypes was 0.30. In fact, regions existed across the genome where the frequency of discordant SNP was higher. For example, on chromosome 10 (centered on 520,948 bp), 52 SNP (out of a total of 103 SNP) had ≥ 20% discordant SNP. Four hundred and eight SNP had more than 20% discordant genotypes and were removed from the final set of imputed genotypes. We concluded that both discordance of imputed SNP genotypes and differences in allele frequencies, after imputation using different reference data sets, may be used to identify and remove poorly imputed SNP.
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Affiliation(s)
- J E Pryce
- Department of Environment and Primary Industries, Agribio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia; Dairy Futures Cooperative Research Centre, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia; La Trobe University, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia.
| | - J Johnston
- Canadian Dairy Network, Guelph, Ontario, N1K 1E5, Canada
| | - B J Hayes
- Department of Environment and Primary Industries, Agribio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia; Dairy Futures Cooperative Research Centre, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia; La Trobe University, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - G Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - K A Weigel
- Department of Dairy Science, University of Wisconsin, Madison 53706
| | - S McParland
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Co. Cork, Ireland
| | - D Spurlock
- Department of Animal Science, Iowa State University, Ames 50011
| | - N Krattenmacher
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118 Kiel, Germany
| | - R J Spelman
- LIC, Private Bag 3016, Hamilton 3240, New Zealand
| | - E Wall
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, United Kingdom
| | - M P L Calus
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 8200 AB Lelystad, the Netherlands
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Elzo M, Thomas M, Martinez C, Lamb G, Johnson D, Rae D, Wasdin J, Driver J. Genomic–polygenic evaluation of multibreed Angus–Brahman cattle for postweaning feed efficiency and growth using actual and imputed Illumina50k SNP genotypes. Livest Sci 2014. [DOI: 10.1016/j.livsci.2013.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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142
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Sun C, VanRaden P, O’Connell J, Weigel K, Gianola D. Mating programs including genomic relationships and dominance effects. J Dairy Sci 2013; 96:8014-23. [DOI: 10.3168/jds.2013-6969] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/16/2013] [Indexed: 11/19/2022]
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143
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Hozé C, Fouilloux MN, Venot E, Guillaume F, Dassonneville R, Fritz S, Ducrocq V, Phocas F, Boichard D, Croiseau P. High-density marker imputation accuracy in sixteen French cattle breeds. Genet Sel Evol 2013; 45:33. [PMID: 24004563 PMCID: PMC3846489 DOI: 10.1186/1297-9686-45-33] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 07/19/2013] [Indexed: 12/20/2022] Open
Abstract
Background Genotyping with the medium-density Bovine SNP50 BeadChip® (50K) is now standard in cattle. The high-density BovineHD BeadChip®, which contains 777 609 single nucleotide polymorphisms (SNPs), was developed in 2010. Increasing marker density increases the level of linkage disequilibrium between quantitative trait loci (QTL) and SNPs and the accuracy of QTL localization and genomic selection. However, re-genotyping all animals with the high-density chip is not economically feasible. An alternative strategy is to genotype part of the animals with the high-density chip and to impute high-density genotypes for animals already genotyped with the 50K chip. Thus, it is necessary to investigate the error rate when imputing from the 50K to the high-density chip. Methods Five thousand one hundred and fifty three animals from 16 breeds (89 to 788 per breed) were genotyped with the high-density chip. Imputation error rates from the 50K to the high-density chip were computed for each breed with a validation set that included the 20% youngest animals. Marker genotypes were masked for animals in the validation population in order to mimic 50K genotypes. Imputation was carried out using the Beagle 3.3.0 software. Results Mean allele imputation error rates ranged from 0.31% to 2.41% depending on the breed. In total, 1980 SNPs had high imputation error rates in several breeds, which is probably due to genome assembly errors, and we recommend to discard these in future studies. Differences in imputation accuracy between breeds were related to the high-density-genotyped sample size and to the genetic relationship between reference and validation populations, whereas differences in effective population size and level of linkage disequilibrium showed limited effects. Accordingly, imputation accuracy was higher in breeds with large populations and in dairy breeds than in beef breeds. More than 99% of the alleles were correctly imputed if more than 300 animals were genotyped at high-density. No improvement was observed when multi-breed imputation was performed. Conclusion In all breeds, imputation accuracy was higher than 97%, which indicates that imputation to the high-density chip was accurate. Imputation accuracy depends mainly on the size of the reference population and the relationship between reference and target populations.
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Affiliation(s)
- Chris Hozé
- INRA, UMR 1313 Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France.
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Use of partial least squares regression to impute SNP genotypes in Italian cattle breeds. Genet Sel Evol 2013; 45:15. [PMID: 23738947 PMCID: PMC3716726 DOI: 10.1186/1297-9686-45-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 05/31/2013] [Indexed: 01/28/2023] Open
Abstract
Background The objective of the present study was to test the ability of the partial least squares regression technique to impute genotypes from low density single nucleotide polymorphisms (SNP) panels i.e. 3K or 7K to a high density panel with 50K SNP. No pedigree information was used. Methods Data consisted of 2093 Holstein, 749 Brown Swiss and 479 Simmental bulls genotyped with the Illumina 50K Beadchip. First, a single-breed approach was applied by using only data from Holstein animals. Then, to enlarge the training population, data from the three breeds were combined and a multi-breed analysis was performed. Accuracies of genotypes imputed using the partial least squares regression method were compared with those obtained by using the Beagle software. The impact of genotype imputation on breeding value prediction was evaluated for milk yield, fat content and protein content. Results In the single-breed approach, the accuracy of imputation using partial least squares regression was around 90 and 94% for the 3K and 7K platforms, respectively; corresponding accuracies obtained with Beagle were around 85% and 90%. Moreover, computing time required by the partial least squares regression method was on average around 10 times lower than computing time required by Beagle. Using the partial least squares regression method in the multi-breed resulted in lower imputation accuracies than using single-breed data. The impact of the SNP-genotype imputation on the accuracy of direct genomic breeding values was small. The correlation between estimates of genetic merit obtained by using imputed versus actual genotypes was around 0.96 for the 7K chip. Conclusions Results of the present work suggested that the partial least squares regression imputation method could be useful to impute SNP genotypes when pedigree information is not available.
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Ma P, Brøndum RF, Zhang Q, Lund MS, Su G. Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle. J Dairy Sci 2013; 96:4666-77. [PMID: 23684022 DOI: 10.3168/jds.2012-6316] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 03/28/2013] [Indexed: 12/25/2022]
Abstract
This study investigated the imputation accuracy of different methods, considering both the minor allele frequency and relatedness between individuals in the reference and test data sets. Two data sets from the combined population of Swedish and Finnish Red Cattle were used to test the influence of these factors on the accuracy of imputation. Data set 1 consisted of 2,931 reference bulls and 971 test bulls, and was used for validation of imputation from 3,000 markers (3K) to 54,000 markers (54K). Data set 2 contained 341 bulls in the reference set and 117 in the test set, and was used for validation of imputation from 54K to high density [777,000 markers (777K)]. Both test sets were divided into 4 groups according to their relationship to the reference population. Five imputation methods (Beagle, IMPUTE2, findhap, AlphaImpute, and FImpute) were used in this study. Imputation accuracy was measured as the allele correct rate and correlation between imputed and true genotypes. Results demonstrated that the accuracy was lower when imputing from 3K to 54K than from 54K to 777K. Using various imputation methods, the allele correct rates varied from 93.5 to 97.1% when imputing from 3K to 54K, and from 97.1 to 99.3% when imputing from 54K to 777K; IMPUTE2 and Beagle resulted in higher accuracies and were more robust under various conditions than the other 3 methods when imputing from 3K to 54K. The accuracy of imputation using FImpute was similar to those results from Beagle and IMPUTE2 when imputing from 54K to high density, and higher than the remaining 2 methods. The results also showed that a closer relationship between test set and reference set led to a higher accuracy for all the methods. In addition, the correct rate was higher when the minor allele frequency was lower, whereas the correlation coefficient was lower when the minor allele frequency was lower. The results indicate that Beagle and IMPUTE2 provide the most robust and accurate imputation accuracies, but considering computing time and memory usage, FImpute is another alternative method.
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Affiliation(s)
- P Ma
- Centre for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK 8830 Tjele, Denmark.
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146
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Elzo M, Martinez C, Lamb G, Johnson D, Thomas M, Misztal I, Rae D, Wasdin J, Driver J. Genomic-polygenic evaluation for ultrasound and weight traits in Angus–Brahman multibreed cattle with the Illumina3k chip. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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147
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Enlarging a training set for genomic selection by imputation of un-genotyped animals in populations of varying genetic architecture. Genet Sel Evol 2013; 45:12. [PMID: 23621897 PMCID: PMC3652763 DOI: 10.1186/1297-9686-45-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 03/24/2013] [Indexed: 02/02/2023] Open
Abstract
Background The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. Methods Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. Results Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. Conclusions Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.
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148
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Cole J, Null D. Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for 15 traits in US Brown Swiss, Holstein, and Jersey cattle. J Dairy Sci 2013; 96:2713-2726. [DOI: 10.3168/jds.2012-6008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 12/19/2012] [Indexed: 11/19/2022]
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149
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McClure M, Kim E, Bickhart D, Null D, Cooper T, Cole J, Wiggans G, Ajmone-Marsan P, Colli L, Santus E, Liu GE, Schroeder S, Matukumalli L, Van Tassell C, Sonstegard T. Fine mapping for Weaver syndrome in Brown Swiss cattle and the identification of 41 concordant mutations across NRCAM, PNPLA8 and CTTNBP2. PLoS One 2013; 8:e59251. [PMID: 23527149 PMCID: PMC3603989 DOI: 10.1371/journal.pone.0059251] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 02/13/2013] [Indexed: 12/12/2022] Open
Abstract
Bovine Progressive Degenerative Myeloencephalopathy (Weaver Syndrome) is a recessive neurological disease that has been observed in the Brown Swiss cattle breed since the 1970's in North America and Europe. Bilateral hind leg weakness and ataxia appear in afflicted animals at 6 to 18 months of age, and slowly progresses to total loss of hind limb control by 3 to 4 years of age. While Weaver has previously been mapped to Bos taurus autosome (BTA) 4∶46-56 Mb and a diagnostic test based on the 6 microsatellite (MS) markers is commercially available, neither the causative gene nor mutation has been identified; therefore misdiagnosis can occur due to recombination between the diagnostic MS markers and the causative mutation. Analysis of 34,980 BTA 4 SNPs genotypes derived from the Illumina BovineHD assay for 20 Brown Swiss Weaver carriers and 49 homozygous normal bulls refined the Weaver locus to 48-53 Mb. Genotyping of 153 SNPs, identified from whole genome sequencing of 10 normal and 10 carrier animals, across a validation set of 841 animals resulted in the identification of 41 diagnostic SNPs that were concordant with the disease. Except for one intergenic SNP all are associated with genes expressed in nervous tissues: 37 distal to NRCAM, one non-synonymous (serine to asparagine) in PNPLA8, one synonymous and one non-synonymous (lysine to glutamic acid) in CTTNBP2. Haplotype and imputation analyses of 7,458 Brown Swiss animals with Illumina BovineSNP50 data and the 41 diagnostic SNPs resulted in the identification of only one haplotype concordant with the Weaver phenotype. Use of this haplotype and the diagnostic SNPs more accurately identifies Weaver carriers in both Brown Swiss purebred and influenced herds.
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Affiliation(s)
- Matthew McClure
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Euisoo Kim
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Derek Bickhart
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Daniel Null
- USDA, ARS, ANRI, Animal Improvement Programs Laboratory, Beltsville, Maryland, United States of America
| | - Tabatha Cooper
- USDA, ARS, ANRI, Animal Improvement Programs Laboratory, Beltsville, Maryland, United States of America
| | - John Cole
- USDA, ARS, ANRI, Animal Improvement Programs Laboratory, Beltsville, Maryland, United States of America
| | - George Wiggans
- USDA, ARS, ANRI, Animal Improvement Programs Laboratory, Beltsville, Maryland, United States of America
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico, Università Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Licia Colli
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico, Università Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Enrico Santus
- Associazione Nazionale Allevatori bovini della Razza Bruna, Italian Brown Swiss Association, Bussolengo, Italy
| | - George E. Liu
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Steve Schroeder
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Lakshmi Matukumalli
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Curt Van Tassell
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Tad Sonstegard
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
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Tsuruta S, Misztal I, Lawlor TJ. Short communication: genomic evaluations of final score for US Holsteins benefit from the inclusion of genotypes on cows. J Dairy Sci 2013; 96:3332-5. [PMID: 23477821 DOI: 10.3168/jds.2012-6272] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/15/2013] [Indexed: 11/19/2022]
Abstract
Currently, the US Department of Agriculture Animal Improvement Programs Laboratory utilizes a multi-step procedure in genomic evaluations for US Holstein bulls and cows, with adjustments for cows. We used a single-step procedure to investigate whether adding cows' genotypes could increase reliability in genomic breeding values for bulls while minimizing bias. The first data set to 2007 was used to calculate genomic estimated breeding values (GEBV) for animals, including young genotyped bulls with no daughters and young cows (heifers) with no records in 2007. The second data set to 2011 was used to calculate GEBV for the same animals, including those young bulls with daughters and young cows with records in 2011. Genotypes (42,503 single nucleotide polymorphism markers) for 34,506 bulls and 5,235 cows from 356,413 bulls and 9,245,619 cows in pedigree were used to calculate single-step GEBV (ssGEBV) and multi-step GEBV (msGEBV). Regression coefficients of 2007 GEBV on 2011 progeny deviations and coefficients of determination were used as indicators of bias and reliability in 2007 GEBV for bulls with no daughters and for cows with no records in 2007, using bull genotypes only and using bull and cow genotypes. Parent averages were also calculated from estimated breeding values of parents to compare with GEBV. For genotyped bulls, inflation was larger for ssGEBV than for msGEBV, whereas reliability was higher for ssGEBV. Using all genotyped bulls and cows, reliabilities were increased by 2 to 3%. Use of genotypes of high-profile cows improves reliability in ssGEBV and msGEBV for bulls.
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Affiliation(s)
- S Tsuruta
- Animal and Dairy Science Department, University of Georgia, Athens 30602, USA.
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