ArticleGenetics, selection, evolution : GSE2016
Empirical determination of breed-of-origin of alleles in three-breed cross pigs.
Article in Genetics, selection, evolution : GSE, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 44 citations in OpenAlex.
- Accurate determination of breed origin of alleles in a simulated smallholder crossbred dairy cattle population.Genetics, selection, evolution : GSE · 2025Article
- Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available.Genetics, selection, evolution : GSE · 2023Article
- Classification of breed combinations for slaughter pigs based on genotypes-modeling DNA samples of crossbreeds as fuzzy sets from purebred founders.Frontiers in genetics · 2023Article
- Estimation of dam line composition of 3-way crossbred animals using genomic information.Genetics, selection, evolution : GSE · 2022Article
- Genomic Prediction Methods Accounting for Nonadditive Genetic Effects.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Review: optimizing genomic selection for crossbred performance by model improvement and data collection.Journal of animal science · 2021Review
- Editorial: Advances in Genomics of Crossbred Farm Animals.Frontiers in genetics · 2021Article
- Optimizing genomic reference populations to improve crossbred performance.Genetics, selection, evolution : GSE · 2020Article
- Improving Genomic Prediction of Crossbred and Purebred Dairy Cattle.Frontiers in genetics · 2020Article
- A Review of Genomic Models for the Analysis of Livestock Crossbred Data.Frontiers in genetics · 2020Review
- Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset.Poultry science · 2019Article
- Validation of genomic predictions for body weight in broilers using crossbred information and considering breed-of-origin of alleles.Genetics, selection, evolution : GSE · 2019Article
- Estimating the purebred-crossbred genetic correlation of body weight in broiler chickens with pedigree or genomic relationships.Genetics, selection, evolution : GSE · 2019Article
- Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs.PeerJ · 2019Article
- Genomic Evaluation for a Crossbreeding System Implementing Breed-of-Origin for Targeted Markers.Frontiers in genetics · 2019Article
- Effects of alleles in crossbred pigs estimated for genomic prediction depend on their breed-of-origin.BMC genomics · 2018Article
- Non-additive Effects in Genomic Selection.Frontiers in genetics · 2018Review
- Genomic evaluation for a three-way crossbreeding system considering breed-of-origin of alleles.Genetics, selection, evolution : GSE · 2017Article
- Genomic selection for crossbred performance accounting for breed-specific effects.Genetics, selection, evolution : GSE · 2017Article
- A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels.Genetics, selection, evolution : GSE · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlthough breeding programs for pigs and poultry aim at improving crossbred performance, they mainly use training populations that consist of purebred animals. For some traits, e.g. residual feed intake, the genetic correlation between purebred and crossbred performance is low and thus including crossbred animals in the training population is required. With crossbred animals, the effects of single nucleotide polymorphisms (SNPs) may be breed-specific because linkage disequilibrium patterns between a SNP and a quantitative trait locus (QTL), and allele frequencies and allele substitution effects of a QTL may differ between breeds. To estimate the breed-specific effects of alleles in a crossbred population, the breed-of-origin of alleles in crossbred animals must be known. This study was aimed at investigating the performance of an approach that assigns breed-of-origin of alleles in real data of three-breed cross pigs. Genotypic data were available for 14,187 purebred, 1354 F1, and 1723 three-breed cross pigs.
resultsOn average, 93.0 % of the alleles of three-breed cross pigs were assigned a breed-of-origin without using pedigree information and 94.6 % with using pedigree information. The assignment percentage could be improved by allowing a percentage (fr) of the copies of a haplotype to be observed in a purebred population different from the assigned breed-of-origin. Changing fr from 0 to 20 %, increased assignment of breed-of-origin by 0.6 and 0.7 % when pedigree information was and was not used, respectively, which indicates the benefit of setting fr to 20 %.
conclusionsBreed-of-origin of alleles of three-breed cross pigs can be derived empirically without the need for pedigree information, with 93.7 % of the alleles assigned a breed-of-origin. Pedigree information is useful to reduce computation time and can slightly increase the percentage of assignments. Knowledge on the breed-of-origin of alleles allows the use of models that implement breed-specific effects of SNP alleles in genomic prediction, with the aim of improving selection of purebred animals for crossbred offspring performance.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.