Including αs1casein gene information in genomic evaluations of French dairy goats

Autor: Céline Carillier-Jacquin, H. Larroque, Christèle Robert-Granié
Přispěvatelé: Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, the French Genovicap and Phenofinlait programs (ANR, Apis-Gene, CASDAR, FranceAgriMer, France Genetique Elevage, French Ministry of Agriculture Agrifood, and Forestry), the European 3SR project, the Midi-Pyrenees region and the French National Institute for Agricultural Research (INRA) SELGEN program (XGen), the goat SNP50 BeadChip developed by the International Goat Genome Consortium (IGGC): www.goat-genome.org., University of Georgia, USA : for the blup90iod2 program
Jazyk: angličtina
Rok vydání: 2016
Předmět:
0301 basic medicine
Male
haplotype
[SDV.BIO]Life Sciences [q-bio]/Biotechnology
Genotyping Techniques
[SDV]Life Sciences [q-bio]
breeding value estimation
alpha (s1)
casein locus
relationship matrix
major gene
selection
prediction
polymorphism
population
accuracy
Breeding
Gene Frequency
Polymorphism (computer science)
Casein
Genotype
Genetics(clinical)
Genetics
education.field_of_study
Goats
Caseins
04 agricultural and veterinary sciences
General Medicine
Genomics
Dairying
Phenotype
Female
Research Article
Population
Locus (genetics)
Biology
Best linear unbiased prediction
Polymorphism
Single Nucleotide
03 medical and health sciences
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
Genetic variation
Animals
education
Allele frequency
Ecology
Evolution
Behavior and Systematics
Models
Genetic
0402 animal and dairy science
040201 dairy & animal science
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
030104 developmental biology
Animal Science and Zoology
Zdroj: Genetics Selection Evolution
Genetics Selection Evolution, 2016, 48 (1), pp.54. ⟨10.1186/s12711-016-0233-x⟩
Genetics Selection Evolution, BioMed Central, 2016, 48 (1), ⟨10.1186/s12711-016-0233-x⟩
Genetics, Selection, Evolution : GSE
Genetics Selection Evolution 54 (48), Non Paginé. (2016)
ISSN: 1297-9686
0999-193X
DOI: 10.1186/s12711-016-0233-x⟩
Popis: Genomic best linear unbiased prediction methods assume that all markers explain the same fraction of the genetic variance and do not account effectively for genes with major effects such as the α s1 casein polymorphism in dairy goats. In this study, we investigated methods to include the available α s1 casein genotype effect in genomic evaluations of French dairy goats. First, the α s1 casein genotype was included as a fixed effect in genomic evaluation models based only on bucks that were genotyped at the α s1 casein locus. Less than 1 % of the females with phenotypes were genotyped at the α s1 casein gene. Thus, to incorporate these female phenotypes in the genomic evaluation, two methods that allowed for this large number of missing α s1 casein genotypes were investigated. Probabilities for each possible α s1 casein genotype were first estimated for each female of unknown genotype based on iterative peeling equations. The second method is based on a multiallelic gene content approach. For each model tested, we used three datasets each divided into a training and a validation set: (1) two-breed population (Alpine + Saanen), (2) Alpine population, and (3) Saanen population. The α s1 casein genotype had a significant effect on milk yield, fat content and protein content. Including an α s1 casein effect in genetic and genomic evaluations based only on male known α s1 casein genotypes improved accuracies (from 6 to 27 %). In genomic evaluations based on all female phenotypes, the gene content approach performed better than the other tested methods but the improvement in accuracy was only slightly better (from 1 to 14 %) than that of a genomic model without the α s1 casein effect. Including the α s1 casein effect in a genomic evaluation model for French dairy goats is possible and useful to improve accuracy. Difficulties in predicting the genotypes for ungenotyped animals limited the improvement in accuracy of the obtained estimated breeding values.
Databáze: OpenAIRE
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