ArticleGenetics, selection, evolution : GSE2009
Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values.
Article in Genetics, selection, evolution : GSE, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Exploring the genetic basis of essential hypertension: association with AGT gene variants in an Iranian population.BMC genomics · 2025Article
- Genomic-based genetic parameters and genome-wide association studies for productive and reproductive traits in Beef-on-Dairy crossbreds.Frontiers in genetics · 2025Article
- Resistance haplotypes to green rice leafhopper (Breeding science · 2024Article
- Genetic variation in bovine LAP3 and SIRT1 genes associated with fertility traits in dairy cattle.BMC genomic data · 2024Article
- Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations.Heredity · 2023Article
- Genomic prediction of carcass traits using different haplotype block partitioning methods in beef cattle.Evolutionary applications · 2022Article
- Article
- Features and applications of haplotypes in crop breeding.Communications biology · 2021Review
- Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.International journal of molecular sciences · 2021Review
- Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle.Frontiers in genetics · 2021Article
- Article
- Genomic Prediction Accuracy Using Haplotypes Defined by Size and Hierarchical Clustering Based on Linkage Disequilibrium.Frontiers in genetics · 2020Article
- SNP and Haplotype-Based Genomic Selection of Quantitative Traits inPlants (Basel, Switzerland) · 2019Article
- High-frequency marker haplotypes in the genomic selection of dairy cattle.Journal of applied genetics · 2019Article
- Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle.BMC genetics · 2019Article
- Haplotype-Based Genome-Wide Prediction Models Exploit Local Epistatic Interactions Among Markers.G3 (Bethesda, Md.) · 2018Article
- Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population.Genetics, selection, evolution : GSE · 2017Article
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- Article
- A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine.Horticulture research · 2016Article
Corrections and comments
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7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.
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