ArticleJournal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie2019
Parentage assignment with genotyping-by-sequencing data.
Article in Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed.
- Harnessing exotic germplasm for red clover improvement: Tracking genomic introgression and deploying genomic selection.The plant genome · 2026Article
- MixedUpParents: A New and Improved Method for Genetic Parentage Assignment in Admixed Populations.Molecular ecology resources · 2026Article
- Highly and Lowly Domesticated Endangered Fish From a Conservation Hatchery Diverge in Their Thermal Physiology, Transcriptome, and Methylome.Evolutionary applications · 2026Article
- Parentage assignment in black soldier fly (Frontiers in genetics · 2025Article
- Fieldwork on animals living in extreme conditions as a source of biomedical innovation.Science in One Health · 2025Review
- Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case ofAnimals : an open access journal from MDPI · 2023Article
- Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm.G3 (Bethesda, Md.) · 2022Article
- Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices.Genetics · 2021Article
- A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses.Frontiers in plant science · 2021Article
- Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Genotyping-free parentage assignment using RAD-seq reads.Ecology and evolution · 2020Article
- A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide.Evolutionary applications · 2020Article
- Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations.Genetics, selection, evolution : GSE · 2020Article
- High-Throughput Sequencing With the Preselection of Markers Is a Good Alternative to SNP Chips for Genomic Prediction in Broilers.Frontiers in genetics · 2020Article
- Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data.G3 (Bethesda, Md.) · 2019Article
- Parentage assignment with genotyping-by-sequencing data.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
In this paper, we evaluate using genotype-by-sequencing (GBS) data to perform parentage assignment in lieu of traditional array data. The use of GBS data raises two issues: First, for low-coverage (e.g., <2×) GBS data, it may not be possible to call the genotype at many loci, a critical first step for detecting opposing homozygous markers. Second, the amount of sequencing coverage may vary across individuals, making it challenging to directly compare the likelihood scores between putative parents. To address these issues, we extend the probabilistic framework of Huisman (Molecular Ecology Resources, 2017, 17, 1009) and evaluate putative parents by comparing their (potentially noisy) genotypes to a series of proposal distributions. These distributions describe the expected genotype probabilities for the relatives of an individual. We assign putative parents as a parent if they are classified as a parent (as opposed to e.g., an unrelated individual), and if the assignment score passes a threshold. We evaluated this method on simulated data and found that (a) high-coverage (>2×) GBS data performs similarly to array data and requires only a small number of markers to correctly assign parents and (b) low-coverage GBS data (as low as 0.1×) can also be used, provided that it is obtained across a large number of markers. When analysing the low-coverage GBS data, we also found a high number of false positives if the true parent is not contained within the list of candidate parents, but that this false positive rate can be greatly reduced by hand tuning the assignment threshold. We provide this parentage assignment method as a standalone program called AlphaAssign.
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