As genotyping technologies continue to evolve, so have their throughput and multiplexing capabilities. In this study, we demonstrate a new PCR-based genotyping technology that multiplexes thousands of single nucleotide polymorphism (SNP) markers with high-throughput capabilities in a simple protocol using a two-step PCR approach. The bioinformatic pipeline is user friendly and yields results that are intuitive to interpret. This method was tested on two recombinant inbred line (RIL) populations that had previous genotyping data from the Illumina Infinium assay for Triticum aestivum L. and the two data sets were found to be 100% in agreement. The genotyping by multiplexed sequencing (GMS) protocol multiplexes 1,656 wheat SNP markers, 207 syntenic barley SNP markers, and 49 known informative markers, which generate a possible 2,433 data points (including homoeoalleles and paralogs). This genotyping approach has the flexibility of being sequenced on either the Ion Torrent or Illumina next generation sequencing (NGS) platforms. Products are the result of direct sequencing and are therefore more reliable than scatter plot analysis which is the output of other genotyping methods such as the Illumina Infinium assay, komeptitive allele specific PCR and other like technologies.

Loss of crop genetic diversity due to modern plant breeding is an enduring global concern. The U.S. Pacific Northwest (PNW) is an important wheat (Triticum aestivum L.)‐producing region. We examined population structure and changes in genomic‐level and agroecosystem‐level genetic diversity of PNW wheat over the past 120 yr. Wheat varieties were slightly structured by spring and winter growth habit, but not by geographic origin or period of variety release. At the genomic level, we did not find long‐term shifts in gene diversity in either spring or winter wheat, but fluctuations were significant within market classes and within the most widely grown spring and winter varieties. Diversity in hard red spring (HRS) wheat peaked in 1970–1999 and since dropped below the level of varieties before 1930. Hard red winter (HRW) in 2000–2019 is more diverse than before 1930, whereas soft white spring (SWS) and soft white winter (SWW) are at the same level of diversity in 2000–2019 as they were before 1930. The most widely grown spring varieties had the lowest diversity in 1930–1969, whereas the most widely grown winter varieties had the lowest diversity in 2000–2019. At the agroecosystem level, Simpson's index of diversity (1 − D) has been on a rising trend since the 1990s as the dominance of acreages by a few varieties has become less common. Cultivation of multiple market classes and periodic incorporation of new germplasm by breeding programs have been able to maintain the quantitative level of genetic diversity in PNW wheat over time.

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