Nearly 2,000 gene banks around the world hold the genetic resources of plants, from seed to stem and more, sampled from all crops — even those that were never cultivated or haven't grown in a century. These time capsules hold the potential to improve future crops with unknown or previously undesired genes as plant diseases evolve and climate changes. The practical implementation has fallen short, though, largely due to a disconnect between gene banks' data management and the identification of candidate species, according to an international research team. The result is typically a less diverse breed without the ability to incorporate untapped resistant genes.
To rectify this, the researchers developed a genomics-informed pre-breeding strategy that predicts genomic information within and across gene banks, pinpointing the best parent candidates for the desired plant characteristics in wheat. The team published their approach, which resulted in plants that outyielded current wheat varieties in multiple field trials, on October 4 in Nature Genetics.
"Genetic diversity is critical for crop improvement, and major yield gains have been achieved through sharing genetic information between species of novel germplasm into elite genotypes, but this has been largely serendipitous and represents only a tiny portion of diversity available in gene banks," said co-first author Liu Fang, currently with the Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences. At the time of the research, Liu was with the Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben in Germany.
Germplasm, or the seeds and other samples of a plant used for research and breeding, typically represent a plant in time. The plant genetic resources, on the other hand, comprise all the variations of a plant over millennia, including human and natural selection results. Germplasm that has adapted, either through natural or selective breeding, has the physical features and genetic hardiness to better withstand contemporary disease or environmental challenges. Non-adapted germplasm can be taller, displace more easily and be more susceptible to diseases — all undesirable traits for wheat. So, Liu said, breeders end up relying on the adapted germplasm and avoid planting non-adapted germplasm, which can be a pricey game of luck to discover untapped genetic potential that could produce better crops.
"Diverse plant genetic resources provide opportunity for plant breeders to develop new and improved cultivars with desirable characteristics," Liu said. "Take yellow rust — a fungal infection that thrives in winter and can reduce crop growth up to 100% in severe cases. Even though a lot of effort has been put into discovering, refining and deploying roughly 500 yellow rust-resistant genes for breeding, about 68% of the deployed genes are only partially effective or completely ineffective against virulent races in Germany."
A possible solution is to combine genome-wide marker profiles for full gene bank collections with a prediction of physical traits from the identified genetics, called genomic prediction, in an algorithm that can quickly sequence the data through association of known information. The missing link, according to Liu, is accurate information about how the unknown physical traits of non-adapted germplasm affect yield.
"We have proposed a hybrid strategy, in which performance is scored in an 'ElitexPGR' background to correct for the lack of agronomic adaption in gene bank materials," Liu said. The 'elite' part refers to genomes that have genetic advantage over the general population for the current environment. PGR is the plant genetic resources — the potential variations of a species over time.
Liu explained that by compiling a trait-customized core collection of diverse potential parents with, for example, 150 elite genotypes resistant to yellow rust and 50 from the plant genetic resources that were closely related to those 150 but still susceptible to yellow rust, they could strike a balance in possible genetic crosses. The 50 susceptible to yellow rust may have other genetic contributions to improve the offspring, but they are close enough relations that the resistant genes in the 150 specimens would likely pass down.
By scanning the genomes for relevant associations and applying the same diverse selection to wheat hybrids, the researchers can quickly adapt the method to predict breeding values from a small estimation set of ElitexPGR crosses. This helps with understanding physical traits of wildtype wheat that may have useful genes but were disregarded due to undesirable traits, Liu said. In one analysis, the approach found functional genetic pipelines from 23 yellow rust-resistant sources — 16 of which are likely novel, Liu said.
"Our parent selection approach holds the promise of improving input-to-output ratios in pre-breeding," Liu said. "We use the new hybrid scheme to overcome the challenges of growing and phenotyping wild relatives of wheat. Although it can be expensive to produce hybrids, this rapid adaption strategy can be useful to many crops. In all, this approach bridges plant genetic resources and elite cultivars effectively and has the potential to be applied to many other crops."
Other contributors include co-first author Albert W. Schulthess, co-first author Sandip M. Kale, Yusheng Zhao, Norman Philipp, Maximilian Rembe, Yong Jiang, Axel Himmelbach, Jörg Fuchs, Markus Oppermann, Stephan Weise, Matthias Lange, Uwe Scholz, Nils Stein and co-corresponding authors Martin Mascher and Jochen C. Reif, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben; Ulrike Beukert and Albrecht Serfling, Julius Kühn Institute (Federal Research Centre for Cultivated Plants); Philipp H.G. Boeven and Johannes Schact, Limagrain GmbH; C. Friedrich H. Longin, State Plant Breeding Institute, University of Hohenheim; Sonja Kollers and Viktor Korzun, KWS SAAT SE & Co.; and Nina Pfeiffer, KWS LOCHOW GmbH.
Kale is currently affiliated with the Carlsberg Research Laboratory in Copenhagen, Denmark. Stein is also affiliated with the Center for Integrated Breeding Research (CiBreed), and Mascher is also affiliated with the German Centre for Integrative Biodiversity Research (iDiv).
The German Federal Ministry of Education and Research, through the Project GeneBank 2.0, and the German Federal Ministry of Food and Agriculture, through the GenDiv-Project, funded this research.
