Development of plant breeding innovations based on natural diversity - Mission impossible?

The discovery of Mendel’s laws of heredity in the 19th century transformed the ancient activity of selective methods from early plant-breeding procedures, dating to the very beginnings of agriculture, to a science. One of the major basic essentials that emerged during the history of scientific plant breeding is the knowledge about the tremendous wealth of genetic variability existing in plants. With an increased understanding of plant biology and plant genes, plant breeders have continuously improved their breeding tools for tapping the potential of genetic diversity to adapt plants to the ever-changing demands of farmers, consumers, and the environment. New Genomic Techniques (NGTs) are tools in plant breeding that make use of genetic diversity by induced mutagenesis directed to a defined genomic location, thus enabling editing of the genome with a precision not feasible before. NGTs render it possible to create genome alterations directly in elite germplasm and promise to shorten the development time for improved cultivars with desired phenotypes. Knowledge about causal sequence motifs for phenotypic variation is the indispensable prerequisite for changing the genetic material of a plant in the desired direction. The availability of high-quality reference genome sequences offers a state-of-the-art framework for identifying functional sequence motifs even in neglected crops like rye (Rabanus-Wallace et al. 2021). Indeed, a genome-wide association study (GWAS) has mapped 676 cross-validated SNPs associated with complex agronomic and quality traits to the Lo7 pseudomolecules with 206 SNPs residing in coding sequences (Siekmann et al. 2021). Followup studies are necessary to advance these GWAS results and to infer the exact causal variants. However, going from genetics to function is a challenging task in rye. For reverse-genetic tools to be functional, its active components have to be delivered to a cell for creating genetic modifications and observing the resulting phenotype. In rye, efficient procedures to investigate the impact of induced variation within a specific gene and to infer gene function by gene silencing, homologous recombination or nontargeted random disruptions (e.g. chemical mutagenesis or transposon mediated mutagenesis) followed by screening a library of individuals for mutations at a specific location are lacking. In a case study unlocking a major QTL controlling fertility restoration of Pampa-CMS in rye, methods to identify the candidate gene such as fine mapping of the mendelian factor underlying the QTL (Hackauf et al. 2012) as well as high-resolution genetic and physical mapping, and allele sequencing (Wilde et al. 2021) have been successfully applied. However, conclusive evidence for malefertility restoration of genetic variants in the identified candidate gene by specific functional assays is owing, as delivery mechanisms for gene-editing that bypass current challenges in tissue culture and regeneration procedures of rye need to be established. As plant-breeding innovations like NGTs seem to be not applicable at least in the short term, improved breeding efforts are crucial for enhancing the competitiveness of rye in agricultural production systems. The natural genetic diversity in rye was the fundamental basis to achieve a series of technological advances that ultimately facilitated the establishment of hybrid breeding, a cutting-edge technology to increase and secure cereal production on finite arable land without increasing water and fertilizer use (Hackauf et al. 2022). The recent implementation of the Gibberellin-sensitive dominant dwarfing gene Ddw1 in a commercial hybrid rye breeding program is paradigmatic for specific genes, and adaptive alleles that govern important agronomic traits in rye. The promising performance observed in extreme environments in 2021 and 2022 triggers an enhanced development of semidwarf hybrids and may initiate a new era of physiological rye breeding that aims to raise the yield potential of rye closer to its biological limit (Hackauf et al. 2022). To conclude, the successful integration of a Mendelian inheritance factor in hybrid rye breeding improves yield potential, lodging resistance, and drought tolerance and is an up-to-date example of reconciling food security and sustainability through plant breeding innovations based on natural diversity.