ArticleGenetics2013
Marker density and read depth for genotyping populations using genotyping-by-sequencing.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
85 citing papers in PubMed.
- Chromosome-level genome of wild-simulated Panax ginseng identifies SNP markers for germplasm and medicinal quality evaluation.Journal of advanced research · 2026Article
- Article
- Genome-wide association study identifies quantitative trait loci associated with resistance to Verticillium dahliae race 3 in tomato.The plant genome · 2025Article
- Detection of single nucleotide polymorphisms associated with litter size in goats using genotyping-by-sequencing and association analysis.Animal bioscience · 2025Article
- Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species.BMC genomics · 2025Article
- High-resolution genetic map and SNP chip for molecular breeding inHorticulture research · 2024Article
- Article
- Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations.Animals : an open access journal from MDPI · 2023Article
- Development and authentication ofHorticulture, environment and biotechnology · 2023Article
- Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens.BMC genomics · 2023Article
- 3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes.Plant methods · 2023Article
- Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes.Frontiers in genetics · 2023Article
- Imputation of low-density marker chip data in plant breeding: Evaluation of methods based on sugar beet.The plant genome · 2022Article
- QTL Mapping for Resistance to Bacterial Wilt Caused by Two Isolates ofPlants (Basel, Switzerland) · 2022Article
- Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security.The New phytologist · 2022Review
- Selection signatures in the CIMMYT International Elite Spring and Semi-arid Wheat Yield Trials.The plant genome · 2022Article
- Pear genetics: Recent advances, new prospects, and a roadmap for the future.Horticulture research · 2022Article
- High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing.Frontiers in plant science · 2022Article
- Genotyping by Sequencing Advancements in Barley.Frontiers in plant science · 2022Review
- Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries.Gates open research · 2022Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genotyping-by-sequencing (GBS) approaches provide low-cost, high-density genotype information. However, GBS has unique technical considerations, including a substantial amount of missing data and a nonuniform distribution of sequence reads. The goal of this study was to characterize technical variation using this method and to develop methods to optimize read depth to obtain desired marker coverage. To empirically assess the distribution of fragments produced using GBS, ∼8.69 Gb of GBS data were generated on the Zea mays reference inbred B73, utilizing ApeKI for genome reduction and single-end reads between 75 and 81 bp in length. We observed wide variation in sequence coverage across sites. Approximately 76% of potentially observable cut site-adjacent sequence fragments had no sequencing reads whereas a portion had substantially greater read depth than expected, up to 2369 times the expected mean. The methods described in this article facilitate determination of sequencing depth in the context of empirically defined read depth to achieve desired marker density for genetic mapping studies.
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Registered trials
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.