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Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs. Heredity (Edinb) 2013; 110:420-9. [PMID: 23512009 DOI: 10.1038/hdy.2012.90] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The genetic architecture underlying nematode resistance and body weight in Blackface lambs was evaluated comparing genome-wide association (GWA) and regional heritability mapping (RHM) approaches. The traits analysed were faecal egg count (FEC) and immunoglobulin A activity against third-stage larvae from Teladorsagia circumcincta, as indicators of nematode resistance, and body weight in a population of 752 Scottish Blackface lambs, genotyped with the 50k single-nucleotide polymorphism (SNP) chip. FEC for both Nematodirus and Strongyles nematodes (excluding Nematodirus), as well as body weight were collected at approximately 16, 20 and 24 weeks of age. In addition, a weighted average animal effect was estimated for both FEC and body weight traits. After quality control, 44 388 SNPs were available for the GWA analysis and 42 841 for the RHM, which utilises only mapped SNPs. The same fixed effects were used in both analyses: sex, year, management group, litter size and age of dam, with day of birth as covariate. Some genomic regions of interest for both nematode resistance and body weight traits were identified, using both GWA and RHM approaches. For both methods, strong evidence for association was found on chromosome 14 for Nematodirus average animal effect, chromosome 6 for Strongyles FEC at 16 weeks and chromosome 6 for body weight at 16 weeks. Across the entire data set, RHM identified more regions reaching the suggestive level than GWA, suggesting that RHM is capable of capturing some of the variation not detected by GWA analyses.
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52
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Daetwyler HD, Kemper KE, van der Werf JHJ, Hayes BJ. Components of the accuracy of genomic prediction in a multi-breed sheep population. J Anim Sci 2013; 90:3375-84. [PMID: 23038744 DOI: 10.2527/jas.2011-4557] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In genome-wide association studies, failure to remove variation due to population structure results in spurious associations. In contrast, for predictions of future phenotypes or estimated breeding values from dense SNP data, exploiting population structure arising from relatedness can actually increase the accuracy of prediction in some cases, for example, when the selection candidates are offspring of the reference population where the prediction equation was derived. In populations with large effective population size or with multiple breeds and strains, it has not been demonstrated whether and when accounting for or removing variation due to population structure will affect the accuracy of genomic prediction. Our aim in this study was to determine whether accounting for population structure would increase the accuracy of genomic predictions, both within and across breeds. First, we have attempted to decompose the accuracy of genomic prediction into contributions from population structure or linkage disequilibrium (LD) between markers and QTL using a diverse multi-breed sheep (Ovis aries) data set, genotyped for 48,640 SNP. We demonstrate that SNP from a single chromosome can achieve up to 86% of the accuracy for genomic predictions using all SNP. This result suggests that most of the prediction accuracy is due to population structure, because a single chromosome is expected to capture relationships but is unlikely to contain all QTL. We then explored principal component analysis (PCA) as an approach to disentangle the respective contributions of population structure and LD between SNP and QTL to the accuracy of genomic predictions. Results showed that fitting an increasing number of principle components (PC; as covariates) decreased within breed accuracy until a lower plateau was reached. We speculate that this plateau is a measure of the accuracy due to LD. In conclusion, a large proportion of the accuracy for genomic predictions in our data was due to variation associated with population structure. Surprisingly, accounting for this structure generally decreased the accuracy of across breed genomic predictions.
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Affiliation(s)
- H D Daetwyler
- Biosciences Research Division, Department of Primary Industries, Bundoora, VIC 3083, Australia.
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53
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Slate J. FROM BEAVIS TO BEAK COLOR: A SIMULATION STUDY TO EXAMINE HOW MUCH QTL MAPPING CAN REVEAL ABOUT THE GENETIC ARCHITECTURE OF QUANTITATIVE TRAITS. Evolution 2013; 67:1251-62. [DOI: 10.1111/evo.12060] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/08/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield; S10 2TN; United Kingdom
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54
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Comparing linkage and association analyses in sheep points to a better way of doing GWAS. Genet Res (Camb) 2013; 94:191-203. [PMID: 22950900 DOI: 10.1017/s0016672312000365] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genome wide association studies (GWAS) have largely succeeded family-based linkage studies in livestock and human populations as the preferred method to map loci for complex or quantitative traits. However, the type of results produced by the two analyses contrast sharply due to differences in linkage disequilibrium (LD) imposed by the design of studies. In this paper, we demonstrate that association and linkage studies are in agreement provided that (i) the effects from both studies are estimated appropriately as random effects, (ii) all markers are fitted simultaneously and (iii) appropriate adjustments are made for the differences in LD between the study designs. We demonstrate with real data that linkage results can be predicted by the sum of association effects. Our association study captured most of the linkage information because we could predict the linkage results with moderate accuracy. We suggest that the ability of common single nucleotide polymorphism (SNP) to capture the genetic variance in a population will depend on the effective population size of the study organism. The results provide further evidence for many loci of small effect underlying complex traits. The analysis suggests a more informed method for GWAS is to fit statistical models where all SNPs are analysed simultaneously and as random effects.
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55
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Bishop SC. A consideration of resistance and tolerance for ruminant nematode infections. Front Genet 2012; 3:168. [PMID: 23248638 PMCID: PMC3522420 DOI: 10.3389/fgene.2012.00168] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/15/2012] [Indexed: 11/22/2022] Open
Abstract
Debates on the relative merits of resistance (the ability of the host to control the parasite lifecycle) and tolerance (the net impact of infection on host performance) are often lively and unhindered by data or evidence. Resistance generally shows continuous, heritable variation but data are sparser for tolerance, the utility of which will depend upon the disease prevalence. Prevalence is a function of group mean resistance and infection pressure, which itself is influenced by mean resistance. Tolerance will have most value for endemic diseases with a high prevalence but will be of little value for low prevalence diseases. The conditionality of tolerance on infection status, and hence resistance, makes it difficult to estimate independently of resistance. Tolerance is potentially tractable for nematode infections, as the prevalence of infection is ca. 100% in animals grazing infected pasture, and infection level can be quantified by faecal egg count (FEC). Whilst individual animal phenotypes for tolerance are difficult to estimate, breeding values are estimable if related animals graze pastures of different contamination levels. Selection for resistance, i.e., FEC, provides both direct and indirect benefits from ever decreased pasture contamination and hence decreased infectious challenge. Modeling and experimental studies have shown that such reductions in pasture contamination may lead to substantially increased performance. It is proposed that selection goals addressing nematode infections should include both resistance and performance under challenging conditions. However, there may be benefits from exploiting large datasets in which sires are used across cohorts differing in infection level, to further explore tolerance. This may help to customise breeding objectives, with tolerance given greater weight in heavily parasitized environments.
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Affiliation(s)
- Stephen C Bishop
- Genetics and Genomics, Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh Edinburgh, UK
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56
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Ricard A, Danvy S, Legarra A. Computation of deregressed proofs for genomic selection when own phenotypes exist with an application in French show-jumping horses. J Anim Sci 2012; 91:1076-85. [PMID: 23230121 DOI: 10.2527/jas.2012-5256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genomic evaluations often use as pseudo-phenotypes corrected means of progeny performances, like daughter yield deviations (DYD) in dairy species. In horse breeding, own performances are also available and performances from other relatives (as half sibs) may play an important part in the EBV because the number of progeny remains low, even for stallions. The first step for genomic selection in horses is therefore to generate pseudo-phenotypes for genomic analysis when parental or own information is considered. This work presents an easy method to compute deregressed EBV from regular pedigree-based genetic evaluations (EBV, reliabilities) to be used in genomic evaluations. The proposed methodology builds deregressed proofs so that they combine own performances (from genotyped individuals) and performances of relatives (outside of the genotyped sample). An application to show jumping horse data is presented. A sample of 908 stallions specialized in show jumping [71% Selle Français (SF), 17% foreign sport horses (FH), 13% Anglo Arab (AA)] were genotyped. Genotyping was performed using the Illumina Equine SNP50 BeadChip, and after quality tests, 44,444 SNP were retained. Two methods were used for genomic evaluation: GBLUP and BayesCπ, and 6 validation data sets were compared, chosen according to breeds SF + FH + AA or SF + FH, family structure (more than 3 half sibs), reliability of sires (>0.97) or sons (>0.72). In spite of a favorable genetic structure [linkage disequilibrium equal to 0.24 at 50 kb pairs], results showed low advantage of genomic evaluation. On the validation sample SF + FH + AA, the correlation between deregressed proofs and GBLUP or BayesCπ predictions was 0.39, 0.37, 0.51 according to the different validation data sets, compared with 0.36, 0.33, 0.53 obtained with BLUP predictions. Correlations were much lower on the SF + FH sample. Research is pursued to understand this low advantage of genomic selection and to improve the methodology for genomic evaluation in this context, which is less favorable than dairy cattle breeding.
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Affiliation(s)
- A Ricard
- INRA, UMR 1313, 78352 Jouy-en-Josas, France.
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57
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Sallé G, Jacquiet P, Gruner L, Cortet J, Sauvé C, Prévot F, Grisez C, Bergeaud JP, Schibler L, Tircazes A, François D, Pery C, Bouvier F, Thouly JC, Brunel JC, Legarra A, Elsen JM, Bouix J, Rupp R, Moreno CR. A genome scan for QTL affecting resistance to Haemonchus contortus in sheep1. J Anim Sci 2012; 90:4690-705. [DOI: 10.2527/jas.2012-5121] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- G. Sallé
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - P. Jacquiet
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - L. Gruner
- INRA, UR1282, Infectiologie Animale et Santé Publique, F-37880 Nouzilly, France
| | - J. Cortet
- INRA, UR1282, Infectiologie Animale et Santé Publique, F-37880 Nouzilly, France
| | - C. Sauvé
- INRA, UR1282, Infectiologie Animale et Santé Publique, F-37880 Nouzilly, France
| | - F. Prévot
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - C. Grisez
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - J. P. Bergeaud
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - L. Schibler
- INRA, UMR1313, Laboratoire de Génétique Biochimique et de Cytogénétique, F-78252 Jouy-en-Josas, France
| | - A. Tircazes
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - D. François
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - C. Pery
- INRA, UE332, Domaine de la Sapinière, F-18390, Osmoy, France
| | - F. Bouvier
- INRA, UE332, Domaine de la Sapinière, F-18390, Osmoy, France
| | - J. C. Thouly
- INRA, UE332, Domaine de la Sapinière, F-18390, Osmoy, France
| | - J. C. Brunel
- INRA, UE332, Domaine de la Sapinière, F-18390, Osmoy, France
| | - A. Legarra
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - J. M. Elsen
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - J. Bouix
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - R. Rupp
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - C. R. Moreno
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
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58
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Höglund JK, Guldbrandtsen B, Lund MS, Sahana G. Analyzes of genome-wide association follow-up study for calving traits in dairy cattle. BMC Genet 2012; 13:71. [PMID: 22888914 PMCID: PMC3465222 DOI: 10.1186/1471-2156-13-71] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 08/02/2012] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND There is often a pronounced disagreement between results obtained from different genome-wide association studies in cattle. There are multiple reasons for this disagreement. Particularly the presence of false positives leads to a need to validate detected QTL before they are optimally incorporated or weighted in selection decisions or further studied for causal gene. In dairy cattle progeny testing scheme new data is routinely accumulated which can be used to validate previously discovered associations. However, the data is not an independent sample and the sample size may not be sufficient to have enough power to validate previous discoveries. Here we compared two strategies to validate previously detected QTL when new data is added from the same study population. We compare analyzing a combined dataset (COMB) including all data presently available to only analyzing a validation dataset (VAL) i.e. a new dataset not previously analyzed as an independent replication. Secondly, we confirm SNP detected in the Reference population (REF) (i.e. previously analyzed dataset consists of older bulls) in the VAL dataset. RESULTS Clearly the results from the combined (COMB) dataset which had nearly twice the sample size of other two subsets allowed the detection of far more significant associations than the two smaller subsets. The number of significant SNPs in REF (older bulls) was about four times higher compare to VAL (younger bulls) though both had similar sample sizes, 2,219 and 2,039 respectively. A total of 424 SNP-trait combinations on 22 chromosomes showed genome-wide significant association involving 284 unique SNPs in the COMB dataset. In the REF data set 101 associations (73 unique SNPs) and in the VAL 24 associations (18 unique SNPs) were found genome-wide significant. Sixty-eight percent of the SNPs in the REF dataset could be confirmed in the VAL dataset. Out of 469 unique SNPs showing chromosome-wide significant association with calving traits in the REF dataset 321 could be confirmed in the VAL dataset at P < 0.05. CONCLUSIONS The follow-up study for GWAS in cattle will depend on the aim of the study. If the aim is to discover novel QTL, analyses of the COMB dataset is recommended, while in case of identification of the causal mutation underlying a QTL, confirmation of the discovered SNPs are necessary to avoid following a false positive.
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Affiliation(s)
- Johanna K Höglund
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, Tjele, DK-8830, Denmark
- VikingGenetics, Ebeltoftvej 16, Assentoft, Randers, SØ, DK-8960, Denmark
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7070, Uppsala, 750 07, Sweden
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, Tjele, DK-8830, Denmark
| | - Mogens S Lund
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, Tjele, DK-8830, Denmark
| | - Goutam Sahana
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, Tjele, DK-8830, Denmark
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59
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de la Chevrotière C, C. Bishop S, Arquet R, Bambou JC, Schibler L, Amigues Y, Moreno C, Mandonnet N. Detection of quantitative trait loci for resistance to gastrointestinal nematode infections in Creole goats. Anim Genet 2012; 43:768-75. [DOI: 10.1111/j.1365-2052.2012.02341.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2011] [Indexed: 11/28/2022]
Affiliation(s)
- C. de la Chevrotière
- INRA, UR143, Unité de Recherches Zootechniques; Domaine Duclos; 97170 Petit-Bourg; France
| | - S. C. Bishop
- The Roslin Institute and Royal (Dick) School of Veterinary Studies; University of Edinburgh; Midlothian EH25 9RG; UK
| | - R. Arquet
- INRA, UE1294, Plateforme Tropicale d'Expérimentation sur l'Animal; Domaine Duclos; 97170 Petit-Bourg; France
| | - J. C. Bambou
- INRA, UR143, Unité de Recherches Zootechniques; Domaine Duclos; 97170 Petit-Bourg; France
| | - L. Schibler
- INRA; UMR1313 Génétique Animale et Biologie Intégrative; 78252 Jouy-en-Josas; France
| | - Y. Amigues
- GIE LABOGENA; 78352 Jouy-en-Josas; France
| | - C. Moreno
- INRA, UR631; Station d'Amélioration Génétique des Animaux; 31326 Castanet-Tolosan; France
| | - N. Mandonnet
- INRA, UR143, Unité de Recherches Zootechniques; Domaine Duclos; 97170 Petit-Bourg; France
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60
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White JD, Allingham PG, Gorman CM, Emery DL, Hynd P, Owens J, Bell A, Siddell J, Harper G, Hayes BJ, Daetwyler HD, Usmar J, Goddard ME, Henshall JM, Dominik S, Brewer H, van der Werf JHJ, Nicholas FW, Warner R, Hofmyer C, Longhurst T, Fisher T, Swan P, Forage R, Oddy VH. Design and phenotyping procedures for recording wool, skin, parasite resistance, growth, carcass yield and quality traits of the SheepGENOMICS mapping flock. ANIMAL PRODUCTION SCIENCE 2012. [DOI: 10.1071/an11085] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A major aim of the research program known as SheepGENOMICS was to deliver DNA markers for commercial breeding programs. To that end, a resource flock was established, comprehensively phenotyped and genotyped with DNA markers. The flock of nearly 5000 sheep, born over two consecutive years, was extensively phenotyped, with more than 100 recorded observations being made on most of the animals. This generated more than 460 000 records over 17 months of gathering information on each animal. Here, we describe the experimental design and sample-collection procedures, and provide a summary of the basic measurements taken. Data from this project are being used to identify collections of genome markers for estimating genomic breeding values for new sheep industry traits.
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61
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Possibilities to breed for resistance to nematode parasite infections in small ruminants in tropical production systems. Animal 2012; 6:741-7. [DOI: 10.1017/s1751731111000681] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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