ArticleAsian-Australasian journal of animal sciences2016
Imputation Accuracy from Low to Moderate Density Single Nucleotide Polymorphism Chips in a Thai Multibreed Dairy Cattle Population.
Article in Asian-Australasian journal of animal sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Advancing genetic evaluation of milk yield and composition using a genomic-polygenic model in smallholder dairy cattle farms in Thailand.Tropical animal health and production · 2026Article
- Impact of pedigree completeness on genomic-polygenic evaluations for milk yield, fat percentage, and age at first calving in Thai multibreed dairy cattle.Archives animal breeding · 2026Article
- Evaluation of Low-Coverage Sequencing Strategies for Whole-Genome Imputation in Pacific AbaloneInternational journal of molecular sciences · 2025Article
- Inclusion of imputed genotypes from non-genotyped dairy cattle in a Thai multibreed genomic-polygenic evaluation.Animal bioscience · 2025Article
- Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits.Horticulture research · 2024Article
- Genetic factors influencing milk and fat yields in tropically adapted dairy cattle: insights from quantitative trait loci analysis and gene associations.Animal bioscience · 2024Article
- A comparison of five sets of overlapping and non-overlapping sliding windows for semen production traits in the Thai multibreed dairy population.Animal bioscience · 2024Article
- High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing.Animals : an open access journal from MDPI · 2021Article
- Genotype Imputation to Improve the Cost-Efficiency of Genomic Selection in Rabbits.Animals : an open access journal from MDPI · 2021Article
- Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study.Horticulture research · 2021Article
- The effectiveness of genomic selection for milk production traits of Holstein dairy cattle.Asian-Australasian journal of animal sciences · 2020Article
- Pathway enrichment and protein interaction network analysis for milk yield, fat yield and age at first calving in a Thai multibreed dairy population.Asian-Australasian journal of animal sciences · 2019Article
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4 authors.
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Abstract
The objective of this study was to investigate the accuracy of imputation from low density (LDC) to moderate density SNP chips (MDC) in a Thai Holstein-Other multibreed dairy cattle population. Dairy cattle with complete pedigree information (n = 1,244) from 145 dairy farms were genotyped with GeneSeek GGP20K (n = 570), GGP26K (n = 540) and GGP80K (n = 134) chips. After checking for single nucleotide polymorphism (SNP) quality, 17,779 SNP markers in common between the GGP20K, GGP26K, and GGP80K were used to represent MDC. Animals were divided into two groups, a reference group (n = 912) and a test group (n = 332). The SNP markers chosen for the test group were those located in positions corresponding to GeneSeek GGP9K (n = 7,652). The LDC to MDC genotype imputation was carried out using three different software packages, namely Beagle 3.3 (population-based algorithm), FImpute 2.2 (combined family- and population-based algorithms) and Findhap 4 (combined family- and population-based algorithms). Imputation accuracies within and across chromosomes were calculated as ratios of correctly imputed SNP markers to overall imputed SNP markers. Imputation accuracy for the three software packages ranged from 76.79% to 93.94%. FImpute had higher imputation accuracy (93.94%) than Findhap (84.64%) and Beagle (76.79%). Imputation accuracies were similar and consistent across chromosomes for FImpute, but not for Findhap and Beagle. Most chromosomes that showed either high (73%) or low (80%) imputation accuracies were the same chromosomes that had above and below average linkage disequilibrium (LD; defined here as the correlation between pairs of adjacent SNP within chromosomes less than or equal to 1 Mb apart). Results indicated that FImpute was more suitable than Findhap and Beagle for genotype imputation in this Thai multibreed population. Perhaps additional increments in imputation accuracy could be achieved by increasing the completeness of pedigree information.
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