ArticleGenetics2019
HaploBlocker: Creation of Subgroup-Specific Haplotype Blocks and Libraries.
Article in Genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Genetic dissection of grain yield and correlated proxy traits under suboptimal conditions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
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- On ARGs, pedigrees, and genetic relatedness matrices.Genetics · 2026Article
- Haplotype applications in genomic selection.Genome biology · 2026Review
- First interspecific multi-parent advanced generation inter-cross (MAGIC) population inHorticulture research · 2025Article
- Resequencing and phenotyping of the first highly inbred eggplant multiparent population revealHorticulture research · 2025Article
- Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions.BMC plant biology · 2025Article
- Optimization of recurrent rapid cycle breeding in maize for sustained long-term genetic improvement via stochastic simulations.G3 (Bethesda, Md.) · 2025Article
- On ARGs, pedigrees, and genetic relatedness matrices.bioRxiv : the preprint server for biology · 2025Article
- Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts.Nature genetics · 2024Article
- A novel tomato interspecific (Horticulture research · 2024Article
- Genomic prediction within and across maize landrace derived populations using haplotypes.Frontiers in plant science · 2024Article
- Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau.BMC biology · 2023Article
- Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets.Frontiers in plant science · 2023Article
- Genomic prediction with haplotype blocks in wheat.Frontiers in plant science · 2023Article
- Genomic prediction using information across years with epistatic models and dimension reduction via haplotype blocks.PloS one · 2023Article
- Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity.The Plant journal : for cell and molecular biology · 2022Article
- Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant.Frontiers in plant science · 2022Article
- Increasing calling accuracy, coverage, and read-depth in sequence data by the use of haplotype blocks.PLoS genetics · 2021Article
- Accounting for epistasis improves genomic prediction of phenotypes with univariate and bivariate models across environments.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The concept of haplotype blocks has been shown to be useful in genetics. Fields of application range from the detection of regions under positive selection to statistical methods that make use of dimension reduction. We propose a novel approach ("HaploBlocker") for defining and inferring haplotype blocks that focuses on linkage instead of the commonly used population-wide measures of linkage disequilibrium. We define a haplotype block as a sequence of genetic markers that has a predefined minimum frequency in the population, and only haplotypes with a similar sequence of markers are considered to carry that block, effectively screening a dataset for group-wise identity-by-descent. From these haplotype blocks, we construct a haplotype library that represents a large proportion of genetic variability with a limited number of blocks. Our method is implemented in the associated R-package HaploBlocker, and provides flexibility not only to optimize the structure of the obtained haplotype library for subsequent analyses, but also to handle datasets of different marker density and genetic diversity. By using haplotype blocks instead of single nucleotide polymorphisms (SNPs), local epistatic interactions can be naturally modeled, and the reduced number of parameters enables a wide variety of new methods for further genomic analyses such as genomic prediction and the detection of selection signatures. We illustrate our methodology with a dataset comprising 501 doubled haploid lines in a European maize landrace genotyped at 501,124 SNPs. With the suggested approach, we identified 2991 haplotype blocks with an average length of 2685 SNPs that together represent 94% of the dataset.
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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.