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Using Old Plants for New Tricks?

Researchers have found a way we can find the best parent candidates for crop breeding to improve yield.

There are currently more than 1,700 gene banks in the world, housing the genetic materials of plants, from seed to stem and more, sampled from all types of crops, including ones that have not been cultivated in a century or longer! As plant diseases continue to evolve and the climate changes, these time capsules could help improve future crops with undesirable or unknown genes. However, an international study has found that there is a disconnect between the identification of candidate species and the management of gene bank data, which has hindered its practical application. The outcome is often a breed with less genetic diversity that cannot incorporate undiscovered resistance genes.

To address this, the researchers used genomic information to design a pre-breeding technique that predicts genomic data from both within and across gene banks, identifying the top parent choices for the desired plant traits in wheat. In several field trials, the team’s method produced plants that outyielded current wheat varieties.

“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 from the Wuhan Botanical Garden of the Chinese Academy of Sciences. Liu was working at the Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben in Germany at the time of the study.

Germplasm is the term used to describe the seeds and other samples of a plant useful in research and crop breeding. They typically represent a plant in time. On the other hand, plant genetic resources include all of plant’s variations across thousands of years, including the outcomes from human and natural selection. Germplasm that has adapted, either through natural or selective breeding, possess the physical and genetic resilience to better tolerate modern diseases or environmental challenges. Non-adapted germplasm may have unfavourable features for wheat, such as being taller, displacing more easily, and being more prone to diseases. According to Liu, in order to avoid using the non-adapted germplasm, which can be an expensive game of chance to find untapped genetic potential that could result in better crops, breeders instead rely on the adapted germplasm.

“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 per cent 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 per cent of the deployed genes are only partially effective or completely ineffective against virulent races in Germany.”

A possible solution is to integrate genome-wide marker profiles for full gene bank collections with a prediction of physical features from the identified genetics, called genomic prediction, in an algorithm that can swiftly sequence the data through association of known information. Liu says that precise knowledge of how the physical characteristics of non-adapted germplasm influence yield is still lacking.

“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 are genetically advantageous over the overall population for the current environment. PGR stands for plant genetic resources, which are the possible future variants of a species.

Liu explained that they could achieve a balance in possible genetic crosses by assembling a trait-customised core collection of diverse potential parents. For instance, 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. The 50 susceptible to yellow rust may have other genetic contributions to enhance the progeny, but they are close enough relations that the resistant genes in the 150 specimens would likely pass down.

By examining the genomes for pertinent correlations and using the same diverse selection to wheat hybrids, the researchers can swiftly modify the strategy to forecast breeding values from a small estimation set of ElitexPGR crosses. This aids in comprehending the physical characteristics of wildtype wheat that may have useful genes but were ignored because of undesirable traits, according to Liu. In one analysis, the method discovered functional genetic pipelines from 23 yellow rust-resistant sources, 16 of which are likely unique.

“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 adaptation 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.” [APBN]

Source: Schulthess et al. (2022). Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nature Genetics, 1-9.