Pavan Stefano, Delvento Chiara, Ricciardi Luigi, Lotti Concetta, Ciani Elena, D'Agostino Nunzio
Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy.
Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy.
Front Genet. 2020 Jun 5;11:447. doi: 10.3389/fgene.2020.00447. eCollection 2020.
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.
高通量基因分型技术推动了作物全基因组关联研究（GWAS）的发展，使得与经济重要性状相关的单核苷酸多态性（SNP）得以鉴定。为作物GWAS选择一种经济高效的基因分型方法需要仔细考量多个方面，即研究目的与规模、作物特有的基因组特征以及与每种基因分型方法相关的技术和经济因素。一旦获得了基因型数据，就必须应用质量控制（QC）程序，以避免基因型-表型关联测试中出现偏差和错误信号。人类GWAS的QC已经得到了广泛的综述；然而，作物GWAS的QC可能需要根据GWAS群体类型采取不同的措施。在这里，我们综述了基于下一代测序（NGS）和阵列杂交的最常用基因分型方法，并报告了一些观察结果，这些结果可为研究人员选择作物GWAS的基因分型方法提供指导。我们提供了在作物物种中进行QC的建议，并概述了可用于完成所有所需任务的生物信息学工具。总体而言，这项工作旨在提供指导方针，以协调那些生成可供作物GWAS使用的SNP数据集的程序。
