Academic Journal
Short communication: Imputation performances of 3 low-density marker panels in beef and dairy cattle
| العنوان: | Short communication: Imputation performances of 3 low-density marker panels in beef and dairy cattle |
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| المؤلفون: | Dassonneville, Romain, Fritz, S., Ducrocq, Vincent, Boichard, Didier |
| المساهمون: | Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Agence Nationale de la Recherche (Paris, France), APISGENE (Paris, France) |
| المصدر: | ISSN: 0022-0302 ; Journal of Dairy Science ; https://hal.science/hal-01003420 ; Journal of Dairy Science, 2012, 95 (7), pp.4136 - 4140. ⟨10.3168/jds.2011-5133⟩. |
| بيانات النشر: | HAL CCSD American Dairy Science Association |
| سنة النشر: | 2012 |
| المجموعة: | Institut National de la Recherche Agronomique: ProdINRA |
| مصطلحات موضوعية: | low-density chip, imputation, genomic selection, single nucleotide polymorphism (SNP) chip, HOLSTEIN POPULATIONS, GENOTYPES, RELIABILITY, VALUES, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences |
| الوصف: | Chantier qualité GA ; Low-density chips are appealing alternative tools contributing to the reduction of genotyping costs. Imputation enables researchers to predict missing genotypes to recreate the denser coverage of the standard 50K (similar to 50,000) genotype. Two alternative in silico chips were defined in this study that included markers selected to optimize minor allele frequency and spacing. The objective of this study was to compare the imputation accuracy of these custom low-density chips with a commercially available 3K chip. Data consisted of genotypes of 4,037 Holstein bulls, 1,219 Montbeliarde bulls, and 991 Blonde d'Aquitaine bulls. Criteria to select markers to include in low-density marker panels are described. To mimic a low-density genotype, all markers except the markers present on the low-density panel were masked in the validation population. Imputation was performed using the Beagle software. Combining the directed acyclic graph obtained with Beagle with the PHASEBOOK algorithm provides fast and accurate imputation that is suitable for routine genomic evaluations based on imputed genotypes. Overall, 95 to 99% of alleles were correctly imputed depending on the breed and the low-density chip used. The alternative low-density chips gave better results than the commercially available 3K chip. A low-density chip with 6,000 markers is a valuable genotyping tool suitable for both dairy and beef breeds. Such a tool could be used for preselection of young animals or large-scale screening of the female population. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | hal-01003420; https://hal.science/hal-01003420; PRODINRA: 162759; WOS: 000305363100064 |
| DOI: | 10.3168/jds.2011-5133 |
| الاتاحة: | https://hal.science/hal-01003420 https://doi.org/10.3168/jds.2011-5133 |
| رقم الانضمام: | edsbas.C56A6F01 |
| قاعدة البيانات: | BASE |
| DOI: | 10.3168/jds.2011-5133 |
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