Abstract
Key message
Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genoty** methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration.
Abstract
Next-generation sequencing technologies provide powerful and flexible genoty** methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility. Furthermore, they provide a straightforward workflow to identify, validate, and screen genetic variants in a short time with a low cost. NGS-based genoty** methods include whole-genome re-sequencing, SNP arrays, and reduced representation sequencing, which are widely applied in crops. The main challenges facing breeders and geneticists today is how to choose an appropriate genoty** method and how to integrate genoty** data sets obtained from various sources. Here, we review and discuss the advantages and challenges of several NGS methods for genome-wide genetic marker development and genoty** in crop plants. We also discuss how imputation methods can be used to both fill in missing data in genotypic data sets and to integrate data sets obtained using different genoty** tools. It is our hope that this synthetic view of genoty** methods will help geneticists and breeders to integrate these NGS-based methods in crop plant breeding and research.
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Acknowledgements
The authors wish to acknowledge the financial support received from Génome Québec, Genome Canada, the Government of Canada, the Ministère de l’Économie, Science et Innovation du Québec, Semences Prograin Inc., Syngenta Canada Inc., Sevita Genetics, Coop Fédérée, Grain Farmers of Ontario, Saskatchewan Pulse Growers, Manitoba Pulse and Soybean Growers, the Canadian Field Crop Research Alliance and Producteurs de grains du Québec.
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Communicated by Rajeev K. Varshney.
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Torkamaneh, D., Boyle, B. & Belzile, F. Efficient genome-wide genoty** strategies and data integration in crop plants. Theor Appl Genet 131, 499–511 (2018). https://doi.org/10.1007/s00122-018-3056-z
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DOI: https://doi.org/10.1007/s00122-018-3056-z