NovoCrops: Accelerated domestication of resilient climate-change friendly plant Species

We propose that domestication occurred through changes in only a few domestication genes and that these events can be mimicked by mutagenesis of homologous genes in underutilized crops and even wild plants. Using targeted genome editing techniques, including non-GMO approaches, we will de novo domesticate six future crops, by increasing their yield, modifying their flowering behavior and preventing transport of toxic compounds into their edible parts. The project is organized in four method packages providing technology to be used across six work packages, each focusing on an individual future crop.

Method platform (MP) 1: Transformation and mutagenesis

MP1 will establish protocols for the transformation, regeneration, and genome editing of alfalfa and intermediate wheatgrass.

Contact: Caixiao Gao cxgao@plen.ku.dk

Method platform 2: Plant genomic resources

Different WPs will use RNA-seq to determine when and where genes of interest are expressed. To guarantee the comparability of the collected data, MP2 will develop standard methods for sequencing library preparation and subsequent data analysis.

Contact: Stephan Wenkel wenkel@plen.ku.dk

Method platform 3: Transport engineering

The presence of antinutritional defense compounds has hampered the domestication of wild species of quinoa, lupin, potato, and other plants. To domesticate these plants, the quantity and distribution of these compounds must be altered in a tissue-specific manner. For this, we have established a unique functional genomics technology platform for identifying and characterizing transporters of plant defense compounds and to perform transport engineering crop improvement.

Contact: Hussam Nour-Eldin huha@plen.ku.dk

Method platform 4: Phenotyping

Phenotyping of NovoCrops species requires rapid propagation under a controlled environment. Speed breeding, which involves the use of supplementary lighting, controlled temperatures, and extended photoperiods in greenhouses and growth chambers to substantially reduce generation times. Plants will be phenotypically characterized in DK and abroad in various stress environments, including field trials.

Contact: Henrik Brinch-Pedersen hbp@mbg.au.dk

Work Package (WP) 1: De novo domestication of wild barley

Cultivated barley (Hordeum vulgare ssp. vulgare) is the fourth most important cereal crop worldwide and is highly adapted to marginal land. Despite its global value, yields over the past 50 years have stagnated in several regions, including parts of Europe. Moreover, genome projects have revealed a serious erosion of genetic diversity among modern barley varieties. New variation is required, and sequencing of wild barley has revealed distinctly higher genetic diversity compared to cultivated barley. Furthermore, wild barley is more resistant to pathogens, more tolerant to water and salt stress, and has a higher seed protein content, better nitrogen use efficiency, and better phosphate bioavailability than cultivated barley.

Contact: Henrik Brinch-Pedersen hbp@mbg.au.dk

WP2 De novo domestication of wild potato

Several wild ancestors of potato are highly resilient to late blight disease, which is controlled in domesticated potatoes by the heavy use of pesticides during cultivation. In addition, unlike modern cultivars, many wild potatoes have a low glycemic index and are thus less likely to contribute to the development of type-2 diabetes. As a starting point for de novo domestication, we employ wild potato species/accessions with promising characteristics regarding compatibility, tuber formation, and disease resistance.

Contact: Kim Hebelstrup kim.hebelstrup@mbg.au.dk

WP3 Accelerated domestication of alfalfa

Alfalfa is an important legume fodder crop with many excellent traits, such as cold resistance, salt tolerance, adaptability, high yield, resistance to frequent cutting, and soil amelioration properties. A major obstacle in alfalfa breeding is early flowering, which reduces the production of vegetative material. The process of flowering control in alfalfa is poorly understood. Based on knowledge from Arabidopsis, we will induce CRISPR-guided mutations in the genes encoding master flowering regulators.

Contact: Stephan Wenkel wenkel@plen.ku.dk

WP4 Accelerated domestication of lupin

In WP4, we characterize newly identified alkaloid transporters with respect to expression patterns and sub-cellular localization, thus establishing a spatiotemporal working model for alkaloid transport to the seeds. Using a non-GMO mutagenesis and screening platform established in collaboration with the Carlsberg Research Laboratories, selected specific transporter genes are knocked out in a high-alkaloid variety. This work should result in a herbivore-resistant lupin variety with high levels of defensive alkaloids in the vegetative parts but alkaloid-free seeds.

Contact: Fernando Geu-Flores feg@plen.ku.dk

WP5 Accelerated domestication of quinoa

Quinoa is a stress tolerant plant that is highly nutritious with an amino acid composition of its grain proteins comparable to that of legume seeds. In collaboration with Carlsberg Laboratories, we are currently generating a non-GMO mutant library of quinoa plants. We will phenotypically screen our quinoa mutant library for plants with higher yields.

Contact: Rosa Lopez-Marques rlo@plen.ku.dk

WP6 Accelerated domestication of intermediate wheatgrass

The perennial grass intermediate wheatgrass is closely related to wheat and has superior characteristics with respect to carbon storage, soil preservation and nutrient and water use efficiencies. Wheatgrass has been semidomesticated into the variety known as Kernza but the small size of seeds and their tendency to shatter are among traits that limit the use of this crop and therefore represent primary breeding objectives.

Contact: Michael Palmgren palmgren@plen.ku.dk

Zhang Y, Pribil M, Palmgren M, Gao C (2020) A CRISPR way for accelerating improvement of food crops. Nature Food 1: 200-205.

Shin-Young Hong, Esther Botterweg-Paredes, Jasmin Doll, et al. et Stephan Wenkel (2020) Multi-level analysis of the interactions between REVOLUTA and MORE AXILLARY BRANCHES 2 in controlling plant development reveals parallel, independent and antagonistic functions. Development 2020 147: dev183681.

DeHaan L, Larson S, López-Marqués RL, Wenkel S, Gao C, Palmgren M (2020) Roadmap for accelerated domestication of an emerging perennial grain crop. Trends in Plant Science 25: 525-537.

López-Marqués RL, Nørrevang AF, Ache P, Moog M, Visintainer D, Wendt T, Østerberg JT, Dockter C, Jørgensen ME, Salvador AT, Hedrich R, Gao C, Jacobsen S-E, Shabala S, Palmgren M (2020) Prospects for accelerated improvement of the resilient crop quinoa. Journal of Experimental Botany, Vol. 71, No. 18 pp. 5333–5347.

Davis JA, Pares RB, Palmgren M, López-Marques RL, Harper JF (2020) A potential pathway for flippase-facilitated glucosylceramide catabolism in plants. Plant Signaling and Behavior, 1783486.

Kaushal Kumar Bhati, Valdeko Kruusvee, Daniel Straub, Anil Kumar Nalini Chandran, Ki-Hong Jung and Stephan Wenkel (2020 ) Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation. G3: GENES, GENOMES, GENETICS, vol. 10 no. 10 3709-3717.

Rosa L. López-Marqués, Pontus Gourdon, Thomas G. Pomorski & Michael Palmgren (2020) The transport mechanism of plant lipid flippases. Biochem J 477 (19): 3769–3790.

Department of Molecular Biology and Genetics, Aarhus University