ArticleGenetics, selection, evolution : GSE2019
Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach.
Article in Genetics, selection, evolution : GSE, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 67 citations in OpenAlex.
- Bridging the gap between legacy polymerase chain reaction-based microsatellite data with high-throughput sequencing data for conservation genomics.The Journal of heredity · 2026Article
- Genome-wide association studies on body-weight and body-size traits among Zhedong white geese based on a modified genotyping-by-sequencing method.BMC genomics · 2025Article
- Low-Coverage Whole-Genome Sequencing (lcWGS) in Cattle: Analysis of Potential and Prospects for Application.Animals : an open access journal from MDPI · 2025Review
- Mapping the regulatory genetic landscape of complex traits using a chicken advanced intercross line.Nature communications · 2025Article
- Evaluation of Low-Coverage Sequencing Strategies for Whole-Genome Imputation in Pacific AbaloneInternational journal of molecular sciences · 2025Article
- Article
- Genotype imputation in F2 crosses of inbred lines.Bioinformatics advances · 2024Article
- Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China.Animals : an open access journal from MDPI · 2023Article
- CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes.Genome research · 2023Article
- A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.Molecular ecology · 2021Article
- Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy.GigaScience · 2021Article
- Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs.BMC genomics · 2021Article
- Article
- Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundExperimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30×) and very low-coverage sequence data on intercross individuals (< 0.5×). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F
resultsWe describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb.
conclusionsA method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes .
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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.