Engineering perennial barley

Project Information

PERLIFE

Grant agreement ID: 101002085

DOI

10.3030/101002085

EC signature date 15 April 2021

Start date 1 October 2021

End date 30 September 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 981 251,00

EU contribution

€ 1 981 251,00

Coordinated by

HEINRICH-HEINE-UNIVERSITAET DUESSELDORF
Germany

Periodic Reporting for period 2 - PERLIFE (Engineering perennial barley)

Reporting period: 2023-04-01 to 2024-09-30

Summary of the context and overall objectives of the project

• What is the problem/issue being addressed?
Today, annual crops account for more than 85% of the worldwide calorie consumption. Annual crops are sown and harvested within one growing season and, therefore, require annual tillage and application of herbicides and fertilizers that cause land and water degradation. In contrast, perennial crops grow over many seasons, require low agricultural input and thereby hold great potential for sustainable production systems and climate change adaptation. However, current efforts to breed perennial cereals are hindered by hybridization barriers between annual crops and wild perennial relatives and the trade-off between longevity and grain yield. The efficient breeding of high-yielding perennial crops thus requires information on the genetic underpinnings of annual versus perennial growth. This knowledge will be crucial for the cost and time-efficient breeding of new perennial crop species and varieties.

Why is it important for society?
PERLIFE will provide the fundamental knowledge and toolbox for the efficient and targeted generation of perennial cereals. Perennial crops are an important strategy to diversify agricultural production systems and contribute to sustainable food production in the face of climate change and a growing human population. Perennial crops are robust; they protect soil from erosion and improve soil structure. They increase ecosystem nutrient retention, carbon sequestration, and water infiltration, and can contribute to climate change adaptation and mitigation. As such, perennial crops help ensure food and water security over the long term.

• What are the overall objectives?
The objectives of PERLIFE are to unravel the genetic underpinnings of perennial versus annual growth and investigate the molecular and metabolic control of plant longevity and its relationship to reproductive output. PERLIFE will identify structural and genetic variations underpinning plant longevity using comparative genomics in annual and perennial wild relatives of the cereal crop barley. In interspecific crosses, we dissect the interrelationship of longevity and grain yield and identify linked coding and regulatory variation. Based on this information, we will design and implement strategies for the targeted modification of longevity in barley using transgenic approaches and genome editing. The engineered genotypes will be trialled in environmental simulation chambers for longevity, stable seed yield and stress resistance to select the most successful engineering strategy.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have generated de novo reference assemblies based on long-read and short-read DNA and RNA sequencing for six Hordeum species (annual, perennial sister species) and, together with the PanHordeum Consortium, have generated annotated de novo assemblies for 22 Hordeum species (publication expected to end 2024).
Furthermore, we have used reduced representation sequencing of 80 accessions from 21 species, to reconstruct the Hordeum phylogeny. The phylogeny demonstrates that there were three independent transitions between annual and perennial life history in the Hordeum clade. Further, we used the phylogeny and genetic data to identify structural and genetic variations that consistently differentiate between annual and perennial species. This allowed the identification of candidate genes with roles in development and carbon allocation which we are currently testing.

We have trialed 52 annual and perennial accessions in outdoor experiments at the Botanic Garden of the University of Düsseldorf and scored 25 vegetative and reproductive traits over three consecutive seasons. This allowed us to identify traits and trait complexes that differentiate annual and perennial species. In particular, harvest index, allocation of N and C resources, and growth parameters differentiated between life history strategies. The dissection of life history transitions and meristem development in perennial species showed, that in contrast to many perennial species, perennial Hordeum species are not characterised by a juvenile phase or intrinsic seasonality. Seasonal flowering was only controlled by external cues, primarily day length and ambient temperature. In contrast to perennial rice and wheatgrass, perennial Hordeum species do not regrow from rhizomes, but from meristems at the crown of the plants.
Furthermore, we have generated interspecific crosses between annual H. intercedens and H. euclaston with perennial H. stenostachys and H. erectifolium. We have scored developmental and growth-related traits in the F1 plants and could show that perenniality is dominant in all these F1 crosses, whereas morphological and growth-related traits were intermediate. We have also conducted global transcriptome analyses in the parental and F1 plants to identify consistent cis- and trans-regulatory differences between the annual and perennial genomes. From the F1 plants, we have generated fertile BC1F1 and BC1F2 plants, which will be phenotyped during the next season in the Botanic Garden of the HHU.
Finally, we have started to generate Crispr/Cas transformants by either targeting the coding or regulatory regions for selected candidate genes. We have functionally analysed two candidate genes, which extended plant longevity by more than a year.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

While perennial rice and wheat cultivars have been recently commercialized, and their cultivation areas are increasing every year, breeding perennial crops is time-consuming and difficult because of hybridization barriers and poor yield of wild perennial species. We currently do not have a good understanding of the genetic underpinnings of annual versus perennial growth. Work in the Brassicaceae has revealed genetic factors that affect juvenility and seasonal flowering in perennial species but not the ability to maintain meristems and regrow the next season. We are confident that with our project, we will be able to detect major genes and genetic networks controlling plant longevity in the Hordeum clade. This knowledge will be crucial for the targeted and efficient generation of perennial cereals. Furthermore, we will be able to test experimentally, if plant longevity and reproductive output are genetically linked or can be modified at least to some extent independently. As such, this project will provide fundamental insights into the relationship between longevity and reproduction in plants (and the control of resource allocation).
Furthermore, with the generation of 22 de novo genome assemblies we have generated a valuable genomic resource for the identification of genetic variation underlying life-history traits. However, this resource is also valuable for mining allelic variation for adaptation to biotic and abiotic stress adaptation. Furthermore, the reference assemblies will be used for pangenomic analyses and mining for structural, genetic and regulatory variation in the Hordeum clade that includes the crop plant barley. Finally, the genomes will be valuable for studies on the evolution and adaptation of the diverse Hordeum species to a range of different environments.

Life cycle of annual cultivated barley and perennial Hordeum species with differences in the duratio