ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2013
Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 129 papers.
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129 citing papers in PubMed, 274 citations in OpenAlex.
- Genome-wide association analysis of resistance to scald in an adapted multiparent winter malting barley population.The plant genome · 2026Article
- Development of an open-pollinated genetic mapping framework to facilitate the identification of QTL in apples.The plant genome · 2026Article
- Genetic mapping of quantitative trait loci associated with nematode resistance in melon using genotyping-by-sequencing.Frontiers in plant science · 2026Article
- QTL mapping and candidate gene identification of the full flowering date trait in olive trees (Olea Europaea L.).BMC plant biology · 2025Article
- Genetic diversity and population structure analyses of tropical maize inbred lines using Single Nucleotide Polymorphism markers.PloS one · 2025Article
- Genotype selection identified elite lines through quantitative trait loci mapping of agronomically important traits in wheat.Molecular breeding : new strategies in plant improvement · 2024Article
- Genetic analysis of yield components in buckwheat using high-throughput sequencing analysis and wild resource populations.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives.Scientific reports · 2024Article
- Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat.The plant genome · 2024Article
- The genetics of Ug99 stem rust resistance in spring wheat variety 'Linkert'.Frontiers in plant science · 2024Article
- A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea.Plant physiology · 2023Article
- Mining legume germplasm for genetic gains: An Indian perspective.Frontiers in genetics · 2023Review
- Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review.Life (Basel, Switzerland) · 2022Review
- High-Density Linkage Mapping of Agronomic Trait QTLs in Wheat under Water Deficit Condition using Genotyping by Sequencing (GBS).Plants (Basel, Switzerland) · 2022Article
- Identification of QTL under Brassinosteroid-Combined Cold Treatment at Seedling Stage in Rice Using Genotyping-by-Sequencing (GBS).Plants (Basel, Switzerland) · 2022Article
- Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools.Plants (Basel, Switzerland) · 2022Article
- Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq.BMC genomics · 2022Article
- Construction of High-Density Genetic Map and Identification of a Bruchid Resistance Locus in Mung Bean (Frontiers in genetics · 2022Article
- Genetic basis of maize kernel protein content revealed by high-density bin mapping using recombinant inbred lines.Frontiers in plant science · 2022Article
- Quantitative Trait Loci Mapping Analysis for Cold Tolerance Under Cold Stress and Brassinosteroid-Combined Cold Treatment at Germination and Bud Burst Stages in Rice.Frontiers in plant science · 2022Article
69 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
9 authors at 3 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genotyping by sequencing (GBS) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. Unlike other high-density genotyping technologies which have mainly been applied to general interest "reference" genomes, the low cost of GBS makes it an attractive means of saturating mapping and breeding populations with a high density of SNP markers. One barrier to the widespread use of GBS has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous SNP calls which are not easily diagnosed or corrected. In this study, we use a 384-plex GBS protocol to add 30,984 markers to an indica (IR64) × japonica (Azucena) mapping population consisting of 176 recombinant inbred lines of rice (Oryza sativa) and we release our imputation and error correction pipeline to address initial GBS data sparsity and error, and streamline the process of adding SNPs to RIL populations. Using the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. We mapped QTL for leaf width and aluminum tolerance, and were able to identify additional QTL for both phenotypes when using the full set of 30,984 SNPs that were not identified using a subset of only 1,464 SNPs, including a previously unreported QTL for aluminum tolerance located directly within a recombination hotspot on chromosome 1. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.
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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.