ArticlePloS one2013
An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 227 papers.
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Who cites it
227 citing papers in PubMed, 476 citations in OpenAlex.
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- Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Pollen performance under controlled temperatures and chromosome stability of diploid and tetraploid citrus.BMC plant biology · 2025Article
- Dissecting genetic architecture of flowering and maturity traits in soybean using GWAS in Indian environment.BMC plant biology · 2025Article
- Using Structural Equation Models to Interpret Genome-Wide Association Studies for Morphological and Productive Traits in Soybean [Plants (Basel, Switzerland) · 2025Article
- Uncovering the genetic landscape of soybean accessions from Kazakhstan in comparison with global germplasm using whole genome resequencing.BMC genomics · 2025Article
- Comparative analysis of RAD-seq methods for SNP discovery and genetic diversity assessment in oil seed crop safflower.Scientific reports · 2025Article
- Assigning Phenologically Asynchronous Moths to Source Populations Using Individual Genotypes.Molecular ecology · 2025Article
- A cost-effective, high-throughput, highly accurate genotyping method for outbred populations.G3 (Bethesda, Md.) · 2025Article
- Population genomics of a natural Cannabis sativa L. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping.BMC plant biology · 2025Article
- Genome-wide association studies of milk composition traits in indicine Badri cattle using ddRAD sequencing approach.Tropical animal health and production · 2024Article
- Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused byPlants (Basel, Switzerland) · 2024Article
- Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association.BMC plant biology · 2024Article
- A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations.bioRxiv : the preprint server for biology · 2024Article
- Genetic Diversity and Population Structure of a Large USDA Sesame Collection.Plants (Basel, Switzerland) · 2024Article
- Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean.Plants (Basel, Switzerland) · 2024Article
- Article
- Genetic insights into agronomic and morphological traits of drug-type cannabis revealed by genome-wide association studies.Scientific reports · 2024Article
167 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Highly parallel SNP genotyping platforms have been developed for some important crop species, but these platforms typically carry a high cost per sample for first-time or small-scale users. In contrast, recently developed genotyping by sequencing (GBS) approaches offer a highly cost effective alternative for simultaneous SNP discovery and genotyping. In the present investigation, we have explored the use of GBS in soybean. In addition to developing a novel analysis pipeline to call SNPs and indels from the resulting sequence reads, we have devised a modified library preparation protocol to alter the degree of complexity reduction. We used a set of eight diverse soybean genotypes to conduct a pilot scale test of the protocol and pipeline. Using ApeKI for GBS library preparation and sequencing on an Illumina GAIIx machine, we obtained 5.5 M reads and these were processed using our pipeline. A total of 10,120 high quality SNPs were obtained and the distribution of these SNPs mirrored closely the distribution of gene-rich regions in the soybean genome. A total of 39.5% of the SNPs were present in genic regions and 52.5% of these were located in the coding sequence. Validation of over 400 genotypes at a set of randomly selected SNPs using Sanger sequencing showed a 98% success rate. We then explored the use of selective primers to achieve a greater complexity reduction during GBS library preparation. The number of SNP calls could be increased by almost 40% and their depth of coverage was more than doubled, thus opening the door to an increase in the throughput and a significant decrease in the per sample cost. The approach to obtain high quality SNPs developed here will be helpful for marker assisted genomics as well as assessment of available genetic resources for effective utilisation in a wide number of species.
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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.