Solanum pan-genetics reveals paralogues as contingencies in crop engineering.

Pan-genomics and genome-editing technologies are revolutionizing breeding of global crops. A transformative opportunity lies in exchanging genotype-to-phenotype knowledge between major crops (that is, those cultivated globally) and indigenous crops (that is, those locally cultivated within a circumscribed area) to enhance our food system. However, species-specific genetic variants and their interactions with desirable natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between related crops.

Convergent evolution of plant prickles by repeated gene co-option over deep time.

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles-sharp epidermal projections-that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus .

Rapid improvement of domestication traits in an orphan crop by genome editing.

Genome editing holds great promise for increasing crop productivity, and there is particular interest in advancing breeding in orphan crops, which are often burdened by undesirable characteristics resembling wild relatives. We developed genomic resources and efficient transformation in the orphan Solanaceae crop 'groundcherry' (Physalis pruinosa) and used clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 nuclease (Cas9) (CRISPR-Cas9) to mutate orthologues of tomato domestication and improvement genes that control plant architecture, flower production and fruit size, thereby improving these major productivity traits. Thus, translating knowledge from model crops enables rapid creation of targeted allelic diversity and novel breeding germplasm in distantly related orphan crops.

Setaria viridis.

Interest in plant model systems for genetic, biological, and functional genomics studies stems from advantages they provide in terms of fast generation time, small stature, and simple growth requirements. A model species would be especially advantageous for the studies of C4 photosynthetic grasses, which currently present practical challenges. These include long seed-to-seed generation times, and because of their large size at maturity they require large growing areas.

Setaria viridis: a model for C4 photosynthesis.

C(4) photosynthesis drives productivity in several major food crops and bioenergy grasses, including maize (Zea mays), sugarcane (Saccharum officinarum), sorghum (Sorghum bicolor), Miscanthus x giganteus, and switchgrass (Panicum virgatum). Gains in productivity associated with C(4) photosynthesis include improved water and nitrogen use efficiencies. Thus, engineering C(4) traits into C(3) crops is an attractive target for crop improvement.