GTA genotyping input and output

New selection methods, using trait-specific markers (i.e., marker assisted selection (MAS)) and/or genome-wide markers (i.e., genomic selection (GS)) are becoming increasingly widespread in different breeding programs. This new era requires new innovative and cost-efficient solutions for genotyping. Reduction in sequencing cost has democratized the use of high-throughput genotyping methods based on next-generation sequencing (NGS) for both genome-wide (e.g., genotyping-by-sequencing (GBS)) and targeted (e.g., amplicon sequencing (AmpSeq)) single-nucleotide polymorphism (SNP) profiling in large breeding populations efficiently. While genome-wide and targeted genotyping are commonly used for MAS and GS, no genotyping platform can produce these two types of data together for large-scale application. Here, we present the Genome-wide & Targeted Amplicon (GTA) genotyping platform, an integrated GBS and AmpSeq approach, to provide an all-in-one cost-effective genotyping solution to breeders and research communities. Custom primers carrying a tail comprising a restriction enzyme site and an alien sequence were designed to target 23 and 36 high-value molecular markers associated with key agronomical traits by multiplex PCRs in soybean and barley, respectively. The resulting amplicons were compatible with the GBS library preparation procedure allowing to provide both GBS data and targeted genotyping of trait-specific markers in very efficiently and cost-effectively way. To improve accessibility for GTA data analysis, we've introduced Fast-GBS.v3, a user friendly bioinformatic pipeline that generates comprehensive outputs from sequencing data. We believe that this high-throughput low-cost approach will greatly facilitate the application of DNA markers as it provides required markers for both MAS and GS in a single assay.