High-Throughput SNP Genotyping to Accelerate Crop Improvement

By M. Thomson. 2014

349 citations recorded by the source corpus.

Recent advances in next-generation sequencing (NGS) and single nucleotide polymorphism (SNP) genotyping promise to greatly accelerate crop improvement if properly deployed. High-throughput SNP genotyping offers a number of advantages over previous marker systems, including an abundance of markers, rapid processing of large populations, a variety of genotyping systems to meet different needs, and straightforward allele calling and database storage due to the bi-allelic nature of SNP markers. NGS technologies have enabled rapid whole genome sequencing, providing extensive SNP discovery pools to select informative markers for different sets of germplasm. Highly multiplexed fixed array platforms have enabled powerful approaches such as genome-wide association studies. On the other hand, routine deployment of trait-specific SNP markers requires flexible, low-cost systems for genotyping smaller numbers of SNPs across large breeding populations, using platforms such as Fluidigm's Dynamic Arrays™, Douglas Scientific's Array Tape™, and LGC's automated systems for running KASP™ markers. At the same time, genotyping by sequencing (GBS) is rapidly becoming popular for low-cost high-density genome-wide scans through multiplexed sequencing. This review will discuss the range of options available to modern breeders for integrating SNP markers into their programs, whether by outsourcing to service providers or setting up in-house genotyping facilities, and will provide an example of SNP deployment for rice research and breeding as demonstrated by the Genotyping Services Lab at the International Rice Research Institute.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/fbbf0cd91eee3fff00881a238f11fe473b1aca55

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In Genetics

In Molecular Biology

In Plant Science

Citations in the corpus

History and Current Status of Sugarcane Breeding, Germplasm Development and Molecular Genetics in Brazil (2021, background): “In the first case, hundreds to thousands of markers can be obtained per sample, while in the second case, the number of markers is much smaller, in the tens if multiplexing is used (Slater et al. 2013; Thomson 2014; Puckett 2017; Rasheed et al. 2017; Ahmad et al. 2018).”
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, background): “…loci, since the number of invariant sites at each locus is observed and easy to calculate, but high-throughput SNP genotyping methods that only interrogate prescreened SNPs (Thomson 2014) provide no information on invariant sites, which makes the conditional likelihood method a useful alternative.”
Rice grain quality—traditional traits for high quality rice and health-plus substances (2019, background): “Highthroughput sequencing technology and chip technology can effectively solve this problem (Varshney et al. 2009; Thomson 2014).”