ArticlePloS one2014
Construction and analysis of high-density linkage map using high-throughput sequencing data.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers, 1 of them a synthesis that pooled it.
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Who cites it
191 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Genetic dissection of flowering time and fine mapping of qFT.A02-1 in rapeseed (Brassica napus L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
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- A rare dominant alleleScience advances · 2025Article
- Natural variation in MdNAC5 contributes to fruit firmness and ripening divergence in apple.Horticulture research · 2025Article
- Integrating linkage mapping and GWAS reveals novel genetic architecture of seed weight in soybean (Frontiers in plant science · 2025Article
- The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth.Journal of advanced research · 2024Article
- Identification of Candidate Genes Associated with Flesh Firmness by Combining QTL Mapping and Transcriptome Profiling inInternational journal of molecular sciences · 2024Article
- Genetic dissection of Meloidogyne incognita resistance genes based on VIGS functional analysis in Cucumis metuliferus.BMC plant biology · 2024Article
- A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta).Heredity · 2024Article
- High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits inInternational journal of molecular sciences · 2024Article
- Quantitative Trait Locus Mapping for Plant Height and Branch Number in CCRI70 Recombinant Inbred Line Population of Upland Cotton (Gossypium hirsutum).Plants (Basel, Switzerland) · 2024Article
- Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei).BMC genomics · 2024Article
- Construction of a high-density genetic map based on large-scale marker development in Coix lacryma-jobi L. using specific-locus amplified fragment sequencing (slaf-seq).Scientific reports · 2024Article
131 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. Simulation study shows HighMap can create a linkage map with three times as many markers as ordering-only methods while offering more accurate marker orders and stable genetic distances. Using HighMap, we constructed a common carp linkage map with 10,004 markers. The singleton rate was less than one-ninth of that generated by JoinMap4.1. Its total map distance was 5,908 cM, consistent with reports on low-density maps. HighMap is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL studies. HighMap is available at http://highmap.biomarker.com.cn/.
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