Wild relatives of domesticated plants have long been recognized as important sources of beneficial traits for crop improvement. Having diverged millions of years ago from the domesticate, they have evolved adaptations to more diverse habitats, potentially representing a much wider genetic diversity than could be captured by intraspecific diversity in a crop and its direct wild progenitor. However, concomitant sequence and karyotype divergence have made crop-wild relatives inaccessible to the cross-and-select cycles of traditional breeding. Thus, the main obstacles to transferring beneficial traits from wild relatives have been the lack of effective methods for gene isolation and fertility barriers. The technological breakthroughs in high-throughput sequencing, genome mapping and genotyping have brought to wild species a full-fledged toolkit for linking genotype and phenotype, namely quantitative trait locus mapping and genome scans in natural population. At the same time, new biotechnological approaches have obliterated the need for overcoming crossing barriers: discrete genetic factors controlling adaptive traits can be isolated in the wild relatives and then transferred into the domesticate by gene editing. Exploiting these innovations, this project aims at understanding speciation and edaphic adaptation in three closely related wild relative of barley from South America. We will elucidate the genetic basis of salt tolerance and transfer it into the domesticate. Our specific aims are to (i) develop a genomics toolbox for a complex of three Hordeum species from Patagonia; (ii) understand the interplay of speciation, adaptation and patterns of sequence diversity by population genomic analyses; and (iii) isolate genes involved in adaptation to saline soils and transform them into domesticated barley.

The root cortex is a primary ground tissue of the root organ and plays an important and adaptive role in plant growth and function. Root cortical parenchyma, thin-walled cells in the cortex, have great potential to change both in structure and function during plant development, even after cell differentiation. Root cortical cells can have many different post-differentiation fates that form different cortical tissues (e.g. aerenchyma, exodermis) in succession, or even simultaneously through the deposition or degradation of lignin and suberin and programmed cell death. The formation of these different cortical tissues have the potential to influence stress adaptation and plant performance, for example by altering the radial movement of water and solutes, the metabolic efficiency required for nutrient exploitation, and the synthesis and deposition of exudates. I will investigate the developmental transition of cortical cells into different cell fates and the extent to which root cortical parenchyma have different cell fate trajectories to form simultaneous or successive cortical tissues. I will discover the potential of tissues for synergistic interactions to capture soil resources and modify of rhizosphere properties, and the genes that control these processes at a single-cell resolution to discover when and where signals occur in the cortex. I will use a combination of breakthrough technologies and interdisciplinary expertise including state-of-the-art imaging, analytical chemistry, microbial ecology, and cutting-edge molecular biology methods to tackle the fundamental questions of how and why root cortical parenchyma have different post-differentiation cell fates. FATE will enable us to engineer crop roots to optimize soil foraging and resource capture. The payoffs of this project will be significant for European agriculture, as nutrient limitation is a primary constraint on crop growth and will become an increasing challenge due to climate change.

Progress in plant breeding towards superior varieties relies on selecting favourable traits after creating genetically diverse material. This is primarily achieved by homologous recombination (HR) during meiosis, when programmed DNA double strand breaks (DSBs) are alternatively repaired as crossover (CO, resulting in new parental chromosome combinations) or as non-crossover (NCO, restoring the previous situation). In cereal crops such as barley, recombination by CO occurs mainly near chromosome ends leaving the main body of genetic material untouched. NCO repair can also result in NCO gene conversion (NCO-GC), non-reciprocal exchange of short DNA stretches between alleles. More than 90% of meiotic DSB repair results in NCO, and NCO-GCs are typically not considered in breeding practices as little is known about their tract length, frequency or formation mechanism. MEIOBARMIX aims at uncovering new strategies and developing novel tools to increase and redirect meiotic HR outcome to improve and accelerate plant breeding. Based on novel and high throughput single pollen nuclei genotyping tools, NCO-GC frequency, length, and sequence context and their potential as natural source of genetic variation will be determined. Using the power of a forward genetic approach in Arabidopsis, components regulating the formation of a NCO-GC and/or CO will be identified and genome editing tools will be used to explore novel strategies for site-specific DSB induction as trigger for targeted meiotic recombination. Moreover, novel virus-based tools and ‘stresses’ will be employed to modify the barley recombination landscape. This study will provide ground-breaking results regarding the role of NCO-GCs for genome diversity, explore the feasibility of novel targeted meiotic recombination approaches and uncover novel tools to develop new strategies to harness and influence the outcome, frequency and/or distribution of meiotic recombination in barley ultimately boosting plant breeding.

Meeting the forecasted world demand for food remains a crucial challenge for plant scientists in this century. One promising avenue for improving grain yield of cereal crops, including wheat and barley, involves reducing spikelet mortality. Spikelets, the grain-bearing units of cereal spikes, usually form in excess and subsequently abort during development; increased spikelet survival is linked to increased numbers of grains per spike. Therefore, reducing spikelet mortality is an intriguing approach to improve grain yield. In barley, the number of spikelets per spike at the awn primordium (AP) stage represents the maximum yield potential per spike. After the AP stage, significant spikelet mortality results in fewer grains per spike. Our previous results clearly indicated that spikelet survival in barley is highly genetically controlled (broad-sense heritability >0.80) and that the period from AP to tipping represents the most critical pre-anthesis phase related to spikelet reduction and grain yield per spike. However, the underlying genetic and molecular determinants of spikelet survival remain to be discovered. I therefore propose this ambitious research program with an emphasis on using available genetic resources. Our specific aims during the LUSH SPIKE project are to: (i) discover quantitative trait loci (QTL) for spikelet survival and grain number per spike and validate these QTL in bi-parental doubled-haploid mapping populations, (ii) isolate and functionally characterize Mendelized QTL using a map-based approach, (iii) reveal gene regulatory networks determining spikelet survival during the critical spike growth period from AP to heading, and (iv) elucidate spatio-temporal patterns of metabolite and phytohormone distributions in spike and spikelet sections during the critical growth period, using mass spectrometric imaging. The results we obtain will advance our understanding of how to improve yields of cereal crops.