Crop origins explain variation in global agricultural relevance

Genomic loci associated with grain protein and mineral nutrients concentrations in Eragrostis tef under contrasting water regimes

Climate change is becoming a global challenge, threating agriculture's capacity to meet the food and nutritional requirements of the growing population. Underutilized crops present an opportunity to address climate change and nutritional deficiencies. Tef is a stress-resilient cereal crop, producing gluten-free grain of high nutritional quality. However, knowledge is lacking on tef's diversity of grain nutritional properties, their interaction with environmental conditions (e.g., water availability) and the underlying genomic loci. We assessed the effect of water availability on tef grain nutrient concentrations and identify the associated genomic loci. A collection of 223 tef genotypes, a subset of tef diversity panel 300 (TDP-300), were grown in the field under well-watered and water-limited conditions in 2021, and phenotyped for 11 traits including: grain protein and mineral concentrations and seed color. A genome-wide association study was conducted using 28,837 single-nucleotide polymorphisms (SNPs) and phenotypic data to identify marker-trait associations (MTAs). Tef grain nutrient concentrations exhibited wide genetic diversity with a significant influence of environment. Protein and most micronutrients were more concentrated under water-limited conditions, whereas most macronutrients were higher in the well-watered environment. A total of 59 SNPs were associated with one or more of the studied traits, resulting in 65 MTAs detected under both water treatments, and providing insights into the genetic basis of grain nutrients. Five SNPs reflected multiple associations, with four detecting the same trait under both treatments (multiple-environment effect), and one associated with both Zn and K (pleiotropic effect). In addition, two pairs of closely linked SNPs reflected multiple-environment effects. While multiple-environment associations provide greater support for the integrity of these MTAs, the pleiotropic locus hints at a common mechanism controlling two mineral ions. The identified MTAs shed new light on the genomic architecture of tef's nutritional properties and provide the basis to enhance tef grain nutritional quality alongside drought resilience.

Diversification of quantitative morphological traits in wheat

BACKGROUND AND AIMS

The development and morphology of crop plants have been profoundly altered by evolution under cultivation, initially through unconscious selection, without deliberate foresight, and later by directed breeding. Wild wheats remain an important potential source of variation for modern breeders; however, the sequence and timing of morphological changes during domestication are not fully resolved.

METHODS

We grew and measured 142 wheat accessions representing different stages in wheat evolution, including three independent domestication events, and compared their morphological traits to define the morphospace of each group.

KEY RESULTS

The results show that wild and domesticated wheats have overlapping morphospaces, but each also occupies a distinct area of morphospace from one another. Polyploid formation in wheat increased leaf biomass and seed weight but had its largest effects on tiller loss. Domestication continued to increase the sizes of wheat leaves and seeds and made wheat grow taller, with more erect architecture. Associated changes to the biomass of domesticated wheats generated more grains and achieved higher yields. Landrace improvement subsequently decreased the numbers of tillers and spikes, to focus resource allocation to the main stem, accompanied by a thicker main stem and larger flag leaves. During the Green Revolution, wheat height was reduced to increase the harvest index and therefore yield. Modern wheats also have more erect leaves and larger flower biomass proportions than landraces.

CONCLUSIONS

Quantitative trait history in wheat differs by trait. Some trait values show progressive changes in the same direction (e.g. leaf size, grain weight), whereas others change in a punctuated way at particular stages (e.g. canopy architecture), and other trait values switch directions during wheat evolution (e.g. plant height, flower biomass proportion). Agronomically valued domestication traits arose during different stages of wheat history, such that modern wheats are the product of >10 000 years of morphological evolution.

Early human selection of crops' wild progenitors explains the acquisitive physiology of modern cultivars

Crops have resource-acquisitive leaf traits, which are usually attributed to the process of domestication. However, early choices of wild plants amenable for domestication may also have played a key role in the evolution of crops' physiological traits. Here we compiled data on 1,034 annual herbs to place the ecophysiological traits of 69 crops' wild progenitors in the context of global botanical variation, and we conducted a common-garden experiment to measure the effects of domestication on crop ecophysiology. Our study found that crops' wild progenitors already had high leaf nitrogen, photosynthesis, conductance and transpiration and soft leaves. After domestication, ecophysiological traits varied little and in idiosyncratic ways. Crops did not surpass the trait boundaries of wild species. Overall, the resource-acquisitive strategy of crops is largely due to the inheritance from their wild progenitors rather than to further breeding improvements. Our study concurs with recent literature highlighting constraints of crop breeding for faster ecophysiological traits.

Diversity of plant DNA in stool is linked to dietary quality, age, and household income

Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two interventional feeding studies and three observational cohorts. The number of plant taxa per sample (plant metabarcoding richness or pMR) correlated with recorded intakes in interventional diets and with indices calculated from a food frequency questionnaire in typical diets (ρ = 0.40 to 0.63). In adolescents unable to collect validated dietary survey data, trnL metabarcoding detected 111 plant taxa, with 86 consumed by more than one individual and four (wheat, chocolate, corn, and potato family) consumed by >70% of individuals. Adolescent pMR was associated with age and household income, replicating prior epidemiologic findings. Overall, trnL metabarcoding promises an objective and accurate measure of the number and types of plants consumed that is applicable to diverse human populations.

CRISPR-Cas9-mediated editing of BADH2 gene triggered fragrance revolution in rice

Fragrance is one of the most important quality traits for breeding in rice. The natural aroma substance 2-acetyl-1-pyrroline (2-AP) is a key fragrance compound among over 200 volatiles identified in fragrant rice. In addition to rice, there are other plant species that contain a germplasm that naturally produces a fragrant aroma. These other plant species all have lower activity levels of the enzyme BETAINE ALDEHYDE DEHYDROGENASE 2 (BADH2). Therefore, improving fragrance efficiency has been a focus of intensive research. Recent studies have engineered BADH2 gene, which is responsible for fragrance trait in non-fragrant cultivars of rice, using CRISPR-Cas9. Although engineering rice BADH2 can be useful for upregulating 2-AP, there are still a lot of restrictions on how it can be applied in practice. In this review article, we discuss the recent developments in BADH2 editing and propose potential future strategies to effectively target BADH2 for transcriptional regulation, with the goal of producing a better fragrance.

Bioclimatic projection of the ecological niche of curly mallow (Malva verticillata) based on the forecast of the dynamics of the geographical range in the context of global climate change

Curly mallow (Malva verticillata L.) is a promising species for cultivation to obtain valuable compounds for the application in medicine, and this species can be used in the bioenergy system to provide industry with alternative energy sources. For the highest economic efficiency, the practical use of this species requires the development of complex measures related to both agrotechnologies and selective breeding. Such measures require resources and there is an urgent problem of assessing the prospects of such investments taking into account the global climate change. Therefore, the problem that we aimed to solve was the assessment of how the global climate change would impact the curly mallow in general in the global context, as well as in the conditions of Ukraine in the next 50–70 years. The database of the Global Biodiversity Information Facility (GBIF) contains 2,104 records of curly-leaved mallow. This species is found on all the continents except Antarctica. Asia accounts for 39.1% of the species’ range, Europe – 53.3%, Africa – 3.6%, North America – 3.2%, South America – 0.1%, Australia – 0.8%. The modelling of M. verticillata response to the climatic factors showed that the best response models were V (in 31.6% of cases) and VII (in 36.8% of cases). Model V characterizes unimodal bell-shaped asymmetric response, and model VII – bimodal asymmetric response. The species response to the mean annual temperature is asymmetric bell-shaped with a shift to the right. The optimal average annual temperature for this species is 9.1 °C. Comparing the distribution of available resources and their use is the basis for identifying the features of the ecological niche of the species. The MaxEnt approach indicates that Southeast Asia and Europe have the most favourable conditions for the existence of this species. Changes in the climatic conditions over the next 50–70 years will make the conditions for the life of M. verticillata in the southern hemisphere unfavourable, and the favourable conditions for it in the northern hemisphere will shift significantly to the north. At the same time, conditions in the autochthonous range of the species will become unfavourable. Obviously, if not for the significant potential of the species to disperse, it would have died out as a result of the significant climate change. The area where favourable conditions for the species will remain unchanged is Central Europe. Conditions in Eastern Europe, including Ukraine, will moderately improve. The results indicate the perspective of the cultivation of curly mallow in Ukraine in the future.

Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L

As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.

Pathways to de novo domestication of crop wild relatives

Growing knowledge about crop domestication, combined with increasingly powerful gene-editing toolkits, sets the stage for the continual domestication of crop wild relatives and other lesser-known plant species.

Enhancing crop diversity for food security in the face of climate uncertainty

Global agriculture is dominated by a handful of species that currently supply a huge proportion of our food and feed. It additionally faces the massive challenge of providing food for 10 billion people by 2050, despite increasing environmental deterioration. One way to better plan production in the face of current and continuing climate change is to better understand how our domestication of these crops included their adaptation to environments that were highly distinct from those of their centre of origin. There are many prominent examples of this, including the development of temperate Zea mays (maize) and the alteration of day-length requirements in Solanum tuberosum (potato). Despite the pre-eminence of some 15 crops, more than 50 000 species are edible, with 7000 of these considered semi-cultivated. Opportunities afforded by next-generation sequencing technologies alongside other methods, including metabolomics and high-throughput phenotyping, are starting to contribute to a better characterization of a handful of these species. Moreover, the first examples of de novo domestication have appeared, whereby key target genes are modified in a wild species in order to confer predictable traits of agronomic value. Here, we review the scale of the challenge, drawing extensively on the characterization of past agriculture to suggest informed strategies upon which the breeding of future climate-resilient crops can be based.