ArticleMolecular breeding : new strategies in plant improvement2023
CandiHap: a haplotype analysis toolkit for natural variation study.
Article in Molecular breeding : new strategies in plant improvement, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Mining QTLs and candidate genes in bread wheat associated with kernel hardness through GWAS.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Domestication of Tartary Buckwheat Shaped a Regulatory Module for Seedling Salt Tolerance by Targeting the Magnesium Transporter Gene FtMGT2.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- HaploVar: An R package for defining local haplotype variants for trait association and trait prediction analyses.Bioinformatics (Oxford, England) · 2025Article
- SiLRL1, a bHLH transcription factor from foxtail millet, promotes carotenoid accumulation and improves drought tolerance.BMC plant biology · 2025Article
- Fine Mapping ofPlants (Basel, Switzerland) · 2025Article
- Deciphering the regulatory network of lignocellulose biosynthesis in bread wheat through genome-wide association studies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Foxtail millet research in supporting climate change resilience efforts: Bibliometric analysis and focused literature review.Heliyon · 2025Review
- Mining genomic regions associated with stomatal traits and their candidate genes in bread wheat through genome-wide association study (GWAS).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Integration of GWAS and transcriptome analysis to identify temperature-dependent genes involved in germination of rapeseed (Frontiers in plant science · 2025Article
- Genome wide association study and transcriptome analysis identify candidate genes regulating wheat coleoptile length.Molecular breeding : new strategies in plant improvement · 2024Article
- Genome-wide dissection of genes shaping inflorescence morphology in 242 Chinese south-north sorghum accessions.Scientific reports · 2024Article
- Genome-Wide Identification and Characterization ofPlants (Basel, Switzerland) · 2024Article
- New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS.International journal of molecular sciences · 2024Article
- Efficient identification of QTL for agronomic traits in foxtail millet (Setaria italica) using RTM- and MLM-GWAS.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis.Journal of animal science and biotechnology · 2023Article
- crosshap: R package for local haplotype visualization for trait association analysis.Bioinformatics (Oxford, England) · 2023Review
- geneHapR: an R package for gene haplotypic statistics and visualization.BMC bioinformatics · 2023Article
- Regain flood adaptation in rice through a 14-3-3 protein OsGF14h.Nature communications · 2022Article
- HapAsmbl: A reference-aided pipeline for assembling haplotypes in Nanopore amplicon sequence data of polymorphic populations.Applications in plant sciencesArticle
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5 authors.
Funding
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Abstract
Haplotype blocks greatly assist association-based mapping of casual candidate genes by significantly reducing genotyping effort. The gene haplotype could be used to evaluate variants of affected traits captured from the gene region. While there is a rising interest in gene haplotypes, much of the corresponding analysis was carried out manually. CandiHap allows rapid and robust haplotype analysis and candidate identification preselection of candidate causal single-nucleotide polymorphisms and InDels from Sanger or next-generation sequencing data. Investigators can use CandiHap to specify a gene or linkage sites based on genome-wide association studies and explore favorable haplotypes of candidate genes for target traits. CandiHap can be run on computers with Windows, Mac, or UNIX platforms in a graphical user interface or command line, and applied to any species, such as plant, animal, and microbial. The CandiHap software, user manual, and example datasets are freely available at BioCode (https://ngdc.cncb.ac.cn/biocode/tools/BT007080) or GitHub (https://github.com/xukaili/CandiHap). Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01366-4.
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