High-Throughput SNP Genotyping to Accelerate Crop Improvement

TLDR

Next‑generation sequencing and high‑throughput SNP genotyping, including multiplexed arrays and genotyping‑by‑sequencing, provide abundant, rapid, and cost‑effective markers that accelerate crop improvement and enable genome‑wide association studies. The review examines breeder options for integrating SNP markers—outsourcing or in‑house genotyping—and illustrates this with a rice breeding example from the IRRI Genotyping Services Lab. The authors review available SNP genotyping platforms and workflows, and demonstrate their application through a case study of rice breeding at the IRRI Genotyping Services Lab.

Abstract

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.