Sainfoin (Onobrychis spp.) crop ontology: supporting germplasm characterization and international research collaborations

Sainfoin (Onobrychis spp.) is a perennial forage legume that is also attracting attention as a perennial pulse with potential for human consumption. The dual use of sainfoin underpins diverse research and breeding programs focused on improving sainfoin lines for forage and pulses, which is driving the generation of complex datasets describing high dimensional phenotypes in the post-omics era. To ensure that multiple user groups, for example, breeders selecting for forage and those selecting for edible seed, can utilize these rich datasets, it is necessary to develop common ontologies and accessible ontology platforms. One such platform, Crop Ontology, was created in 2008 by the Consortium of International Agricultural Research Centers (CGIAR) to host crop-specific trait ontologies that support standardized plant breeding databases. In the present study, we describe the sainfoin crop ontology (CO). An in-depth literature review was performed to develop a comprehensive list of traits measured and reported in sainfoin. Because the same traits can be measured in different ways, ultimately, a set of 98 variables (variable = plant trait + method of measurement + scale of measurement) used to describe variation in sainfoin were identified. Variables were formatted and standardized based on guidelines provided here for inclusion in the sainfoin CO. The 98 variables contained a total of 82 traits from four trait classes of which 24 were agronomic, 31 were morphological, 19 were seed and forage quality related, and 8 were phenological. In addition to the developed variables, we have provided a roadmap for developing and submission of new traits to the sainfoin CO.

New Food Crop Domestication in the Age of Gene Editing: Genetic, Agronomic and Cultural Change Remain Co-evolutionarily Entangled

The classic domestication scenario for grains and fruits has been portrayed as the lucky fixation of major-effect "domestication genes." Characterization of these genes plus recent improvements in generating novel alleles (e.g., by gene editing) have created great interest in de novo domestication of new crops from wild species. While new gene editing technologies may accelerate some genetic aspects of domestication, we caution that de novo domestication should be understood as an iterative process rather than a singular event. Changes in human social preferences and relationships and ongoing agronomic innovation, along with broad genetic changes, may be foundational. Allele frequency changes at many loci controlling quantitative traits not normally included in the domestication syndrome may be required to achieve sufficient yield, quality, defense, and broad adaptation. The environments, practices and tools developed and maintained by farmers and researchers over generations contribute to crop yield and success, yet those may not be appropriate for new crops without a history of agronomy. New crops must compete with crops that benefit from long-standing participation in human cultural evolution; adoption of new crops may require accelerating the evolution of new crops' culinary and cultural significance, the emergence of markets and trade, and the formation and support of agricultural and scholarly institutions. We provide a practical framework that highlights and integrates these genetic, agronomic, and cultural drivers of change to conceptualize de novo domestication for communities of new crop domesticators, growers and consumers. Major gene-focused domestication may be valuable in creating allele variants that are critical to domestication but will not alone result in widespread and ongoing cultivation of new crops. Gene editing does not bypass or diminish the need for classical breeding, ethnobotanical and horticultural knowledge, local agronomy and crop protection research and extension, farmer participation, and social and cultural research and outreach. To realize the ecological and social benefits that a new era of de novo domestication could offer, we call on funding agencies, proposal reviewers and authors, and research communities to value and support these disciplines and approaches as essential to the success of the breakthroughs that are expected from gene editing techniques.