The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application
Open accessAbstract
Summary: In the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practice. New methods allowing rapid, high‐throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping‐by‐sequencing (GBS) methods include over a dozen reduced‐representation sequencing (RRS) approaches and at least four whole‐genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best‐suited method seem a daunting task. We review the most common genotyping methods used today and compare their suitability for linkage mapping, genomewide association studies (GWAS), marker‐assisted and genomic selection and genome assembly and improvement in crops with various genome sizes and complexity. Furthermore, we give an outline of bioinformatics tools for analysis of genotyping data. WGR is well suited to genotyping biparental cross populations with complex, small‐ to moderate‐sized genomes and provides the lowest cost per marker data point. RRS approaches differ in their suitability for various tasks, but demonstrate similar costs per marker data point. These approaches are generally better suited for de novo applications and more cost‐effective when genotyping populations with large genomes or high heterozygosity. We expect that although RRS approaches will remain the most cost‐effective for some time, WGR will become more widespread for crop genotyping as sequencing costs continue to decrease.
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Cited by
Hunt, S. E., McLaren, W., Gil, L., Thormann, A., Schuilenburg, H., Sheppard, D., Parton, A., Armean, I. M., Trevanion, S. J., Flicek, P., et al. (2018) · Database · doi:10.1093/database/bay119 · Cited by 452
Accelerating crop genetic gains with genomic selection
Voss-Fels, K. P., Cooper, M., & Hayes, B. J. (2019) · Theoretical and Applied Genetics · doi:10.1007/s00122-018-3270-8 · Cited by 381
Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants
Xu, Y., Liu, X., Fu, J., Wang, H., Wang, J., Huang, C., Prasanna, B. M., Olsen, M. S., Wang, G., & Zhang, A. (2020) · Plant Communications · doi:10.1016/j.xplc.2019.100005 · Cited by 281
(2022) · doi:10.1038/s41467-022-35621-7 · Cited by 34
Metadata
- Authors
- Scheben, A., Batley, J., & Edwards, D.
- Venue
- Plant Biotechnology Journal
- Publisher
- Wiley
- Published
- 2017-01-24
- Volume
- 15
- Issue
- 2
- Pages
- 149-161
- ISSN
- 1467-7644 (ISSN-L)
- 1467-7652
- OpenAlex
- W2529596433
- Cited by
- 303
- References
- 12
- FWCI
- 17.12
- Type
- journal article
- Language
- en
- Open access
- gold
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