ArticleProceedings of the National Academy of Sciences of the United States of America2010
Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 182 papers, 1 of them a synthesis that pooled it.
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Who cites it
182 citing papers in PubMed, 1 synthesis or guideline pooled it.
- QTL analysis and candidate gene prediction for seed density per silique by QTL-seq and RNA-seq in spring Brassica napus L.PloS one · 2023Pooled it
- Article
- Mul-PheG2P: decoupled learning and prediction-space fusion enables robust and interpretable multi-phenotype genomic prediction.The New phytologist · 2026Article
- Development of KASP marker to enhance breeding efficiency for phytophthora blight resistance in sesame through QTL analysis.BMC plant biology · 2026Article
- Phenotypic evaluation and mapping QTLs for drought tolerance in an interspecific RIL population from a Setaria italica × Setaria viridis cross.BMC plant biology · 2026Article
- Fine Mapping and Candidate Gene Identification of ORUFILM03g000096 Gene in Weedy Rice LM8: Insights into Grain Length Regulation.Rice (New York, N.Y.) · 2025Article
- Genetic dissection of low-sulfur tolerance via linkage and genome-wide association analyses in soybean [Glycine max (L.) Merr.] seedlings.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Genetic dissection of maize grain moisture content and dehydration rate using high-density bin mapping in a recombinant inbred line population.BMC plant biology · 2025Article
- Fine mapping and candidate gene analysis of the major QTL qSW-A03 for seed weight in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Novel candidate genes and genetic basis analysis of kernel starch content in tropical maize.BMC plant biology · 2025Article
- Genetic mapping and validation of QTL controlling fruit diameter in cucumber.BMC plant biology · 2024Article
- Streamlined whole-genome genotyping through NGS-enhanced thermal asymmetric interlaced (TAIL)-PCR.Plant communications · 2024Article
- Powerful QTL mapping and favorable allele mining in an all-in-one population: a case study of heading date.National science review · 2024Article
- Single- and multiple-trait quantitative trait locus analyses for seed oil and protein contents of soybean populations with advanced breeding line background.Molecular breeding : new strategies in plant improvement · 2024Article
- Detection of two homologous major QTLs and development of diagnostic molecular markers for sucrose content in peanut.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Construction of a high-density genetic map for yardlong bean and identification of ANT1 as a regulator of anthocyanin biosynthesis.Horticulture research · 2024Article
- The Mining of Genetic Loci and the Analysis of Candidate Genes to Identify the Physical and Chemical Markers of Anti-Senescence in Rice.Plants (Basel, Switzerland) · 2023Article
- Mapping of major QTL and candidate gene analysis for hull colour in foxtail millet (Setaria italica (L.) P. Beauv.).BMC genomics · 2023Article
- Identification of QTLs Conferring Resistance to Bacterial Diseases in Rice.Plants (Basel, Switzerland) · 2023Article
- Single-gene resolution of diversity-driven overyielding in plant genotype mixtures.Nature communications · 2023Article
122 more citing papers are in PubMed but not listed here.
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9 authors.
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Abstract
Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge to genotype individual lines in a population for linkage map construction based on low-coverage sequences without the availability of high-quality genotype data of the parental lines. In this paper, we report a method for constructing ultrahigh-density linkage maps composed of high-quality single-nucleotide polymorphisms (SNPs) based on low-coverage sequences of recombinant inbred lines. First, all potential SNPs were identified to obtain drafts of parental genotypes using a maximum parsimonious inference of recombination, making maximum use of SNP information found in the entire population. Second, high-quality SNPs were identified by filtering out low-quality ones by permutations involving resampling of windows of SNPs followed by Bayesian inference. Third, lines in the mapping population were genotyped using the high-quality SNPs assisted by a hidden Markov model. With 0.05x genome sequence per line, an ultrahigh-density linkage map composed of bins of high-quality SNPs using 238 recombinant inbred lines derived from a cross between two rice varieties was constructed. Using this map, a quantitative trait locus for grain width (GW5) was localized to its presumed genomic region in a bin of 200 kb, confirming the accuracy and quality of the map. This method is generally applicable in genetic map construction with low-coverage sequence data.
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