Scaling up neodomestication for climate-ready crops

Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements

Domestication can be considered a specialized mutualism in which a domesticator exerts control over the reproduction or propagation (fitness) of a domesticated species to gain resources or services. The evolution of crops by human-associated selection provides a powerful set of models to study recent evolutionary adaptations and their genetic bases. Moreover, the domestication and dispersal of crops such as rice, maize, and wheat during the Holocene transformed human social and political organization by serving as the key mechanism by which human societies fed themselves. Here we review major themes and identify emerging questions in three fundamental areas of crop domestication research: domestication phenotypes and syndromes, genetic architecture underlying crop evolution, and the ecology of domestication. Current insights on the domestication syndrome in crops largely come from research on cereal crops such as rice and maize, and recent work indicates distinct domestication phenotypes can arise from different domestication histories. While early studies on the genetics of domestication often identified single large-effect loci underlying major domestication traits, emerging evidence supports polygenic bases for many canonical traits such as shattering and plant architecture. Adaptation in human-constructed environments also influenced ecological traits in domesticates such as resource acquisition rates and interactions with other organisms such as root mycorrhizal fungi and pollinators. Understanding the ecological context of domestication will be key to developing resource-efficient crops and implementing more sustainable land management and cultivation practices.

Quality Characteristics of Twelve Advanced Lines of Avena magna ssp. domestica Grown in Three Contrasting Locations in Morocco

The popularity of oats (Avena sativa) continues to increase in the cereal market due to their health benefits. The recent domestication of Avena magna, a Moroccan oat, presents an opportunity to enhance these benefits due to their higher nutritional composition. As the impact of microclimates on A. magna grain composition has not been explored, this study evaluates twelve A. magna ssp. domestica lines across three Moroccan locations, providing new data into microclimate effects on key grain characteristics. Significant variability is observed among lines and sites for nutrients, with mean protein, fat, and dietary fiber contents at 23.1%, 8.38%, and 7.23%, respectively. High protein levels, reaching 27.1% in Alnif and 26.5% in El Kbab, surpass the 'Avery' control (21.7% and 24.2%) in these environments. Groats from Bouchane exhibited elevated fat and fiber contents (10.2% and 9.94%) compared to the control (8.83% and 7.36%). While β-glucan levels remain consistent at 2.53%, a negative correlation between protein content, fat, and starch was observed. A. magna lines exhibited higher levels of iron (7.50 × 10-3 g/100 g DM) and zinc (3.40 × 10-3 g/100 g DM) compared to other cereals. Environmental conditions significantly influence grain quality, with El Kbab yielding higher protein and ash contents, as well as Bouchane having increased fat, fiber, and starch. Stability analysis indicates that fat content was more influenced by the environment, while 25% of protein variability is influenced by genetics. Lines AT3, AT5, AT6, AT13, and AT15 consistently exceeds both the mean for protein and fiber across all sites, emphasizing their potential nutritional value. This study highlights the potential of A. magna ssp. domestica to address nutritional insecurity, particularly for protein, iron, and zinc in domestic settings.

Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities

The flavin monooxygenase (FMO) enzyme was discovered in mammalian liver cells that convert a carcinogenic compound, N-N'-dimethylaniline, into a non-carcinogenic compound, N-oxide. Since then, many FMOs have been reported in animal systems for their primary role in the detoxification of xenobiotic compounds. In plants, this family has diverged to perform varied functions like pathogen defense, auxin biosynthesis, and S-oxygenation of compounds. Only a few members of this family, primarily those involved in auxin biosynthesis, have been functionally characterized in plant species. Thus, the present study aims to identify all the members of the FMO family in 10 different wild and cultivated Oryza species. Genome-wide analysis of the FMO family in different Oryza species reveals that each species has multiple FMO members in its genome and that this family is conserved throughout evolution. Taking clues from its role in pathogen defense and its possible function in ROS scavenging, we have also assessed the involvement of this family in abiotic stresses. A detailed in silico expression analysis of the FMO family in Oryza sativa subsp. japonica revealed that only a subset of genes responds to different abiotic stresses. This is supported by the experimental validation of a few selected genes using qRT-PCR in stress-sensitive Oryza sativa subsp. indica and stress-sensitive wild rice Oryza nivara. The identification and comprehensive in silico analysis of FMO genes from different Oryza species carried out in this study will serve as the foundation for further structural and functional studies of FMO genes in rice as well as other crop types.

Prospects of Feral Crop De Novo Redomestication

Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.