ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2016
Estimating genomic heritabilities at the level of family-pool samples of perennial ryegrass using genotyping-by-sequencing.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 44 citations in OpenAlex.
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- Genomic and Gut Microbiome Evaluations of Growth and Feed Efficiency Traits in Broilers.Animals : an open access journal from MDPI · 2024Article
- Molecular breeding of flower load related traits in dioecious autotetraploidMolecular breeding : new strategies in plant improvement · 2024Article
- Multienvironment genomic prediction in tetraploid potato.G3 (Bethesda, Md.) · 2024Article
- Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- To be or not to be tetraploid-the impact of marker ploidy on genomic prediction and GWAS of potato.Frontiers in plant science · 2024Article
- The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato.Frontiers in plant science · 2024Article
- Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Molecular breeding : new strategies in plant improvement · 2023Article
- AGHmatrix: genetic relationship matrices in R.Bioinformatics (Oxford, England) · 2023Article
- A genome-wide association study of freezing tolerance in red clover (Frontiers in plant science · 2023Article
- Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks.The plant genome · 2022Article
- Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection.The plant genome · 2021Article
- Understanding the Effectiveness of Genomic Prediction in Tetraploid Potato.Frontiers in plant science · 2021Article
- Prospects forFrontiers in plant science · 2021Review
- Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops.G3 (Bethesda, Md.) · 2020Article
- Article
- Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs.PloS one · 2020Article
- Article
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12 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
keymessageBy using the genotyping-by-sequencing method, it is feasible to characterize genomic relationships directly at the level of family pools and to estimate genomic heritabilities from phenotypes scored on family-pools in outbreeding species. Genotyping-by-sequencing (GBS) has recently become a promising approach for characterizing plant genetic diversity on a genome-wide scale. We use GBS to extend the concept of heritability beyond individuals by genotyping family-pool samples by GBS and computing genomic relationship matrices (GRMs) and genomic heritabilities directly at the level of family-pools from pool-frequencies obtained by sequencing. The concept is of interest for species where breeding and phenotyping is not done at the individual level but operates uniquely at the level of (multi-parent) families. As an example we demonstrate the approach using a set of 990 two-parent F2 families of perennial ryegrass (Lolium Perenne). The families were phenotyped as a family-unit in field plots for heading date and crown rust resistance. A total of 728 K single nucleotide polymorphism (SNP) variants were available and were divided in groups of different sequencing depths. GRMs based on GBS data showed diagonal values biased upwards at low sequencing depth, while off-diagonals were little affected by the sequencing depth. Using variants with high sequencing depth, genomic heritability for crown rust resistance was 0.33, and for heading date 0.22, and these genomic heritabilities were biased downwards when using variants with lower sequencing depth. Broad sense heritabilities were 0.61 and 0.66, respectively. Underestimation of genomic heritability at lower sequencing depth was confirmed with simulated data. We conclude that it is feasible to use GBS to describe relationships between family-pools and to estimate genomic heritability directly at the level of F2 family-pool samples, but estimates are biased at low sequencing depth.
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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.