Revolution in genotyping platforms for crop improvement

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Abstract

In the past decade, the application of high-throughput sequencing to crop genotyping has given rise to novel platforms capable of genotyping tens of thousands of genome-wide DNA markers. Coupled with the decreasing costs of sequencing, this rapid increase in markers allows accelerated and highly accurate genotyping of entire crop populations and diversity sets using single nucleotide polymorphisms (SNPs). These revolutionary advances accelerate crop improvement by facilitating a more precise connection of phenotype to genotype through association studies, linkage mapping and diversity analysis. The platforms driving the advances in genotyping are array technologies and genotyping by sequencing (GBS) methods, which include both low-coverage whole genome resequencing (skim sequencing) and reduced representation sequencing (RRS) approaches. Here, we outline and compare these genotyping platforms and provide a perspective on the promising future of crop genotyping. While SNP arrays provide high quality, simple handling, and unchallenging analysis, the lower cost of RRS and the greater data volume produced by skim sequencing suggest that use of GBS will become more prevalent in crop genomics as sequencing costs decrease and data analysis becomes more streamlined.

Original languageEnglish
Title of host publicationAdvances in Biochemical Engineering/Biotechnology
EditorsRajeev K. Varshney, Manish K. Pandey, Annapurna Chitikineni
Place of PublicationSwitzerland
PublisherSpringer
Pages37-52
Number of pages16
DOIs
Publication statusPublished - 2018

Publication series

NameAdvances in Biochemical Engineering/Biotechnology
Volume164
ISSN (Print)0724-6145

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Cite this

Scheben, A., Batley, J., & Edwards, D. (2018). Revolution in genotyping platforms for crop improvement. In R. K. Varshney, M. K. Pandey, & A. Chitikineni (Eds.), Advances in Biochemical Engineering/Biotechnology (pp. 37-52). (Advances in Biochemical Engineering/Biotechnology; Vol. 164). Switzerland: Springer. https://doi.org/10.1007/10_2017_47