Climate change is a major environmental stress threatening biodiversity and human civilization. The best hope to secure staple food for humans and animal feed by future crop improvement depends on wild progenitors. We examined 10 wild emmer wheat (Triticum dicoccoides Koern.) populations and 10 wild barley (Hordeum spontaneum K. Koch) populations in Israel, sampling them in 1980 and again in 2008, and performed phenotypic and genotypic analyses on the collected samples. We witnessed the profound adaptive changes of these wild cereals in Israel over the last 28 y in flowering time and simple sequence repeat allelic turnover. The revealed evolutionary changes imply unrealized risks present in genetic resources for crop improvement and human food production.climate warming | phenotypic and genotypic diversity | plant genetic resources I n recent decades there have been increasing concerns about the future of food production influenced by climate change (1-7) to feed a fast growing world population reaching 9-10 billion by 2050 (8). Aridization has alarmingly increased in summer, resulting in dry regions of wheat growing areas, particularly in the Americas, Asia, and Africa, and in the area of origin and diversity of wild emmer wheat in the Near East (9). Cultivated wheat, the number one world food staple, is genetically impoverished by long-term selective breeding (10). The wild progenitors of cultivated cereals, especially wild emmer wheat Triticum dicoccoides Koern. (TD) (9) and wild barley Hordeum spontaneum K. Koch (HS) (11), have become eroded by urbanization and agriculture (12). Both progenitors are rich in genetic resources adapted to abiotic (e.g., solar radiation, temperature, drought, and mineral poverty) and biotic (e.g., pathogens and parasites) stresses. These progenitors are the best genetic hope for improving genetically impoverished cultivars for human food production (9-17). Thus, it is crucial to evaluate the evolutionary adaptation in natural populations of the progenitors under climate change and to understand the hidden risk in human food security. Here we examined 10 TD populations and 10 HS populations in Israel from 1980 and again in 2008 and performed phenotypic and genotypic analyses on the collected samples. We witnessed the profound adaptive changes of these wild cereals in Israel over the last 28 y in flowering time (FT) and simple sequence repeat (SSR) allelic turnover. ResultsPhenotypic Analysis. In a greenhouse experiment, we compared the time from germination until flowering of ∼800 genotypes in 20 natural populations from different habitats and climates that were subjected to 28 y of climate change. The sampled populations (16, 17) were distributed across 350 km of their Israeli range (SI Appendix, Fig. S1 and Table S1). A total of 57 independent pair-wise comparisons were made under dry (300 mm) and wet (600 mm) irrigation regimes. Dramatically, in all TD and HS populations, without exception, the 2008 populations reached FT earlier than those collected in 1980 (Sign test, P < 1...

Key message Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. AbstractWe investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2762-7) contains supplementary material, which is available to authorized users.

Key messageMaximizing crop yield while at the same time minimizing crop failure for sustainable agriculture requires a better understanding of the impacts of plant breeding on crop genetic diversity. This review identifies knowledge gaps and shows the need for more research into genetic diversity changes under plant breeding.AbstractModern plant breeding has made a profound impact on food production and will continue to play a vital role in world food security. For sustainable agriculture, a compromise should be sought between maximizing crop yield under changing climate and minimizing crop failure under unfavorable conditions. Such a compromise requires better understanding of the impacts of plant breeding on crop genetic diversity. Efforts have been made over the last three decades to assess crop genetic diversity using molecular marker technologies. However, these assessments have revealed some temporal diversity patterns that are largely inconsistent with our perception that modern plant breeding reduces crop genetic diversity. An attempt was made in this review to explain such discrepancies by examining empirical assessments of crop genetic diversity and theoretical investigations of genetic diversity changes over time under artificial selection. It was found that many crop genetic diversity assessments were not designed to assess diversity impacts from specific plant breeding programs, while others were experimentally inadequate and contained technical biases from the sampling of cultivars and genomes. Little attention has been paid to theoretical investigations on crop genetic diversity changes from plant breeding. A computer simulation of five simplified breeding schemes showed the substantial effects of plant breeding on the retention of heterozygosity over generations. It is clear that more efforts are needed to investigate crop genetic diversity in space and time under plant breeding to achieve sustainable crop production.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2585-y) contains supplementary material, which is available to authorized users.

Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A. sativa and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies.

A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (sad2), obtained from 30 accessions of cultivated and pale flax (Linum spp.), to elucidate the history of flax domestication. The analysis supports a single domestication origin for extant cultivated flax. The phylogenetic evidence indicates that flax was first domesticated for oil, rather than fibre. The genetic diversity of the sad2 locus in cultivated flax is low when compared to that of the pale flax assayed. An absolute archaeological date could be applied to the synonymous substitution rate of sad2 in cultivated flax, yielding a high estimate of 1.60-1.71x10(-7) substitutions/site/year. The occurrence of nonsynonymous substitutions at conserved positions of the third exon in alleles from cultivated flax suggests that the locus may have been subjected to an artificial selection pressure. The elevated synonymous substitution rate is also compatible with a population expansion of flax since domestication, followed by a population decline in historic times. These findings provide new insight into flax domestication and are significant for the continuous exploration of the flax germplasm for utilization.