ArticleHeredity2018
A novel linkage-disequilibrium corrected genomic relationship matrix for SNP-heritability estimation and genomic prediction.
Article in Heredity, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Advancing crop improvement through GWAS and beyond in mung bean.Frontiers in plant science · 2024Pooled it
- Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea.Nature communications · 2026Article
- SNPs with High Linkage Disequilibrium Increase the Explained Genetic Variance and the Reliability of Genomic Predictions.Animals : an open access journal from MDPI · 2026Article
- Leveraging genetic resources and genomic prediction to enhance flavonol content in cranberry fruit.The plant genome · 2025Article
- Interpreting SNP heritability in admixed populations.Genetics · 2025Article
- Interpreting SNP heritability in admixed populations.bioRxiv : the preprint server for biology · 2025Article
- Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species.BMC genomics · 2025Article
- Loss-of-function mutations in the fruit softening geneHorticulture research · 2025Article
- Leveraging haplotype information in heritability estimation and polygenic prediction.Nature communications · 2025Article
- Genomic prediction in a backcross population using relationship matrices.Archives animal breeding · 2025Article
- Structure-informed clustering for population stratification in association studies.BMC bioinformatics · 2023Article
- Genetic Parameter and Hyper-Parameter Estimation Underlie Nitrogen Use Efficiency in Bread Wheat.International journal of molecular sciences · 2023Article
- Local and Bayesian Survival FDR Estimations to Identify Reliable Associations in Whole Genome of Bread Wheat.International journal of molecular sciences · 2023Article
- Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry.The plant genome · 2023Article
- PHARP: a pig haplotype reference panel for genotype imputation.Scientific reports · 2022Article
- Impact of linkage disequilibrium heterogeneity along the genome on genomic prediction and heritability estimation.Genetics, selection, evolution : GSE · 2022Article
- Genomic prediction through machine learning and neural networks for traits with epistasis.Computational and structural biotechnology journal · 2022Article
- Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.International journal of molecular sciences · 2021Review
- Article
- Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in strawberry.The plant genome · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphism (SNP)-heritability estimation is an important topic in several research fields, including animal, plant and human genetics, as well as in ecology. Linear mixed model estimation of SNP-heritability uses the structures of genomic relationships between individuals, which is constructed from genome-wide sets of SNP-markers that are generally weighted equally in their contributions. Proposed methods to handle dependence between SNPs include, "thinning" the marker set by linkage disequilibrium (LD)-pruning, the use of haplotype-tagging of SNPs, and LD-weighting of the SNP-contributions. For improved estimation, we propose a new conceptual framework for genomic relationship matrix, in which Mahalanobis distance-based LD-correction is used in a linear mixed model estimation of SNP-heritability. The superiority of the presented method is illustrated and compared to mixed-model analyses using a VanRaden genomic relationship matrix, a matrix used by GCTA and a matrix employing LD-weighting (as implemented in the LDAK software) in simulated (using real human, rice and cattle genotypes) and real (maize, rice and mice) datasets. Despite of the computational difficulties, our results suggest that by using the proposed method one can improve the accuracy of SNP-heritability estimates in datasets with high LD.
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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.