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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We examined the phylogeography of Synthyris sect. Dissecta (Plantaginaceae), which is restricted to the Olympic (S. lanuginosa) and Northern Rocky Mountains (S. dissecta and S. canbyi), to infer effects of sky islands and modes of speciation. Sequences of cpDNA trnT-trnL and psbA-trnH intergenic spacers resolved 22 haplotypes among 185 individuals sampled from 16 populations of the three species. Gene flow in the ancestral lineage and random capture of haplotypes in species lineages of sect. Dissecta have resulted in haplotype clades that are not exclusive to species. Nested clade analysis (NCA) indicates that allopatric fragmentation separated Olympic and Northern Rocky Mountain populations, giving rise to the Olympic endemic S. lanuginosa, which is characterized by unique haplotypes consistent with long temporal isolation. Low haplotype and nucleotide diversity in S. canbyi are consistent with newly founded populations experiencing a bottleneck. Furthermore, we infer S. canbyi evolved as a peripheral isolate of S. dissecta. NCA indicated limited migration in S. dissecta with possible isolation by distance. Both isolation on interglacial sky islands and valley glaciers during at least the last glaciation limited gene flow among populations of S. dissecta in different ranges of the Northern Rocky Mountains.

Genotyping by sequencing (GBS) and single nucleotide polymorphism (SNP) chip technologies are the primary SNP genotyping technologies used today. However, these genotyping technologies have some drawbacks that limit their usefulness in analysis. We have developed a robust protocol called genotyping by multiplexed sequencing (GMS) using SNP markers, providing informative genotypic data with greater flexibility. The genotypes derived from direct sequence reads reduce ambiguity in genetic analysis. The advantages of this protocol include: (1) This PCR-based direct sequencing protocol generates information from markers of interest and provides a more streamlined and accurate analysis process, by multiplexing hundreds of informative markers into a single sequencing run. (2) The marker sets are easily customized to the species of interest and can readily be changed. In this study we have taken the GMS protocol developed in wheat and adapted it to barley. We have identified 577 SNP markers that work well using this protocol providing adequate genome coverage for genomic selection and tag 267 QTL’s for genes of interest. Good markers have an adequate read depth of at least 5 amplicons and are reliably present across the population.

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