ReviewFrontiers in genetics2020
Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies.
Review in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 97 citations in OpenAlex.
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- Genome-wide association analysis and candidate gene identification for plant height in Shanxi local foxtail millet varieties.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genetic architecture of phenological, morphological, and phytochemical traits in Cannabis landraces.The plant genome · 2026Article
- CartograPlant: bridging genomic, phenotypic, and environmental data to advance plant resilience and eco-evolutionary insight.Genetics · 2026Article
- A multidimensional core set development of sesame germplasm leveraging agro-morphological traits diversity for genetic improvement and climate resilience.Scientific reports · 2026Article
- Sharing approaches in predictive genomics across animals, plants and humans.Nature genetics · 2026Review
- AI-integrated digital breeding for crop improvement.Frontiers in plant science · 2026Review
- Carotenoid biosynthesis drives root plasticity through aerenchyma and iron plaque formation in rice.Nature plants · 2026Article
- Application of Genome-Assisted Prediction (GAP) for Apple Fruit Weight.Plants (Basel, Switzerland) · 2025Article
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- Genomic prediction models for morpho-phenological traits in durum wheat based on Vrn, Ppd, and Rht alleles.The plant genome · 2025Article
- SAGA (Simplified Association Genome-wide Analyses): a user-friendly Pipeline to Democratize Genome-Wide Association Studies.bioRxiv : the preprint server for biology · 2025Article
- Drought Response and Genetic Variation in Scots Pine Seedlings' Provenances: Insights From High-Throughput Phenotyping for Climate-Resilient Forestry.Evolutionary applications · 2025Article
- Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome-environment association studies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach.Plant methods · 2025Article
- Comparative analysis of RAD-seq methods for SNP discovery and genetic diversity assessment in oil seed crop safflower.Scientific reports · 2025Article
- Article
- Non-destructive seed genotyping via microneedle-based DNA extraction.Plant biotechnology journal · 2025Article
- Polygenic risk scores for eGFR are associated with age at kidney failure.Journal of nephrology · 2025Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. Choosing a cost-effective genotyping method for crop GWAS requires careful examination of several aspects, namely, the purpose and the scale of the study, crop-specific genomic features, and technical and economic matters associated with each genotyping option. Once genotypic data have been obtained, quality control (QC) procedures must be applied to avoid bias and false signals in genotype-phenotype association tests. QC for human GWAS has been extensively reviewed; however, QC for crop GWAS may require different actions, depending on the GWAS population type. Here, we review most popular genotyping methods based on next-generation sequencing (NGS) and array hybridization, and report observations that should guide the investigator in the choice of the genotyping method for crop GWAS. We provide recommendations to perform QC in crop species, and deliver an overview of bioinformatics tools that can be used to accomplish all needed tasks. Overall, this work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS.
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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.