ArticleGenetics2017
Evaluating Sequence-Based Genomic Prediction with an Efficient New Simulator.
Article in Genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A note on a generalized single step theory for any number of hierarchical genomic matrices.Genetics, selection, evolution : GSE · 2026Article
- Genomic selection strategies and their potential to maintain rare alleles and de-novo mutations: a long-term assessment.Genetics, selection, evolution : GSE · 2026Article
- Bridging tradition and innovation: a review of computer simulations in plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Prioritized SNP Selection from Whole-Genome Sequencing Improves Genomic Prediction Accuracy in Sturgeons Using Linear and Machine Learning Models.International journal of molecular sciences · 2025Article
- Genetic parameters and genomic prediction of growth and breast morphological traits in a crossbreed duck population.Evolutionary applications · 2024Article
- A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs.G3 (Bethesda, Md.) · 2023Article
- Strategies to improve genomic predictions for 35 duck carcass traits in an FJournal of animal science and biotechnology · 2023Article
- Utilizing Variants Identified with Multiple Genome-Wide Association Study Methods Optimizes Genomic Selection for Growth Traits in Pigs.Animals : an open access journal from MDPI · 2023Article
- XSim version 2: simulation of modern breeding programs.G3 (Bethesda, Md.) · 2022Article
- Opportunities and limits of combining microbiome and genome data for complex trait prediction.Genetics, selection, evolution : GSE · 2021Article
- Impact of Marker Pruning Strategies Based on Different Measurements of Marker Distance on Genomic Prediction in Dairy Cattle.Animals : an open access journal from MDPI · 2021Article
- MoBPS - Modular Breeding Program Simulator.G3 (Bethesda, Md.) · 2020Article
- Toxo: a library for calculating penetrance tables of high-order epistasis models.BMC bioinformatics · 2020Article
- SeqBreed: a python tool to evaluate genomic prediction in complex scenarios.Genetics, selection, evolution : GSE · 2020Article
- Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities.PloS one · 2020Article
- Using imputation-based whole-genome sequencing data to improve the accuracy of genomic prediction for combined populations in pigs.Genetics, selection, evolution : GSE · 2019Article
- Crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies.Scientific reports · 2019Article
- pSBVB: A Versatile Simulation Tool To Evaluate Genomic Selection in Polyploid Species.G3 (Bethesda, Md.) · 2019Article
- From QTLs to Adaptation Landscapes: Using Genotype-To-Phenotype Models to Characterize G×E Over Time.Frontiers in plant science · 2019Article
- A survey of functional genomic variation in domesticated chickens.Genetics, selection, evolution : GSE · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The vast amount of sequence data generated to analyze complex traits is posing new challenges in terms of the analysis and interpretation of the results. Although simulation is a fundamental tool to investigate the reliability of genomic analyses and to optimize experimental design, existing software cannot realistically simulate complete genomes. To remedy this, we have developed a new strategy (Sequence-Based Virtual Breeding, SBVB) that uses real sequence data and simulates new offspring genomes and phenotypes in a very efficient and flexible manner. Using this tool, we studied the efficiency of full sequence in genomic prediction compared to SNP arrays. We used real porcine sequences from three breeds as founder genomes of a 2500-animal pedigree and two genetic architectures: "neutral" and "selective." In the neutral architecture, frequencies and allele effects were sampled independently whereas, in the selective case, SNPs were sites putatively under selection after domestication and a negative correlation between effect and frequency was induced. We compared the effectiveness of different genotyping strategies for genomic selection, including the use of full sequence commercial arrays or randomly chosen SNP sets in both outbred and crossbred experimental designs. We found that accuracy increases using sequence instead of commercial chips but modestly, perhaps by ≤ 4%. This result was robust to extreme genetic architectures. We conclude that full sequence is unlikely to offset commercial arrays for predicting genetic value when the number of loci is relatively large and the prior given to each SNP is uniform. Using sequence to improve selection thus requires optimized prior information and, likely, increased population sizes. The code and manual for SBVB are available at https://github.com/mperezenciso/sbvb0.
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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.