ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2014
Association studies using family pools of outcrossing crops based on allele-frequency estimates from DNA sequencing.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Genomic prediction of single cross families of perennial ryegrass under two nitrogen managements.The plant genome · 2026Article
- How Robust Are Genomic Offset Predictions to Methodological Choices? Insights From Perennial Ryegrass.Molecular ecology · 2026Article
- Phenotypic and genomic insights into alfalfa diversity: Identifying critical loci for enhanced resilience.The plant genome · 2025Article
- QTL detection and genomic prediction for resistance to anthracnose in alfalfa (Medicago sativa).The plant genome · 2025Article
- The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato.Frontiers in plant science · 2024Article
- Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids.The plant genome · 2023Article
- Genetic architecture of inter-specific and -generic grass hybrids by network analysis on multi-omics data.BMC genomics · 2023Article
- Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits inFrontiers in plant science · 2023Article
- Genome-wide genotyping data renew knowledge on genetic diversity of a worldwide alfalfa collection and give insights on genetic control of phenology traits.Frontiers in plant science · 2023Article
- Leveraging spatiotemporal genomic breeding value estimates of dry matter yield and herbage quality in ryegrass via random regression models.The plant genome · 2022Article
- A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome.Horticulture research · 2022Article
- NGS allele counts versus called genotypes for testing genetic association.Computational and structural biotechnology journal · 2022Article
- Genomic Prediction of Complex Traits in Forage Plants Species: Perennial Grasses Case.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genomic prediction in family bulks using different traits and cross-validations in pine.G3 (Bethesda, Md.) · 2021Article
- DNA marker for resistance toBreeding science · 2021Article
- Continuous Mapping Identifies Loci Associated With Weevil Resistance [Frontiers in plant science · 2021Article
- Article
- Quantitative trait loci-based genomics-assisted prediction for the degree of apple fruit cover color.The plant genome · 2020Article
- Effects of Different Strategies for Exploiting Genomic Selection in Perennial Ryegrass Breeding Programs.G3 (Bethesda, Md.) · 2020Article
- Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
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4 authors.
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Abstract
key messageWe propose a method in which GBS data can be conveniently analyzed without calling genotypes. F2 families are frequently used in breeding of outcrossing species, for instance to obtain trait measurements on plots. We propose to perform association studies by obtaining a matching "family genotype" from sequencing a pooled sample of the family, and to directly use allele frequencies computed from sequence read-counts for mapping. We show that, under additivity assumptions, there is a linear relationship between the family phenotype and family allele frequency, and that a regression of family phenotype on family allele frequency will estimate twice the allele substitution effect at a locus. However, medium-to-low sequencing depth causes underestimation of the true allele substitution effect. An expression for this underestimation is derived for the case that parents are diploid, such that F2 families have up to four dosages of every allele. Using simulation studies, estimation of the allele effect from F2-family pools was verified and it was shown that the underestimation of the allele effect is correctly described. The optimal design for an association study when sequencing budget would be fixed is obtained using large sample size and lower sequence depth, and using higher SNP density (resulting in higher LD with causative mutations) and lower sequencing depth. Therefore, association studies using genotyping by sequencing are optimal and use low sequencing depth per sample. The developed framework for association studies using allele frequencies from sequencing can be modified for other types of family pools and is also directly applicable for association studies in polyploids.
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