Unlocking the Potential of Plant Genetic Resources with Genome-Wide Prediction

The International Day of Biological Diversity 2024,’ themed “Be part of the plan”, reflects how ICARDA’s genebanks are bio-digital resource centers where useful traits within plant genetic resources are selected according to predictions of their performance.

Genebanks around the world conserve precious and unique samples of the natural biodiversity that are vital for developing crops that can withstand tomorrow’s climate impacts. Yet, connecting the dots between these genetic resources and their climate-smart performance in the field often remains challenging and slow, making it difficult to develop varieties that are more efficient, more resistant to pests and diseases, and more tolerant to climate change before the challenges have further evolved.

On 22 May, as the world marks the International Day for Biological Diversity 2024 under the theme “Be part of the plan”, ICARDA is actively working on bridging information gaps in genebanks to speed up and laser-focus crop research.

Playing a crucial role in the implementation of the Biodiversity Plan, designed to halt and reverse the loss of biodiversity, ICARDA is turning its genebanks from bank-like depositories for germplasm, into active bio-digital resource centers where scientists and breeders can now select genetic resources according to predictions of their performance.

In a new journal article to which ICARDA contributed, Genomic predictions to leverage phenotypic data across genebanks, scientists detail how genome-wide prediction can help better comprehend the genetic diversity and phenotypic wealth in genebanks collections.

“By gaining a deeper and more nuanced understanding of growth habits in genebank accessions, genome-wide prediction can help foster significant progress in breeding and crop management strategies”, says Dr. Zakaria Kehel, co-author and Research Team Leader - Genetic Resources, Conservation, Characterization, and Use (GRS), ICARDA

Mine the gaps

Established in Lebanon and Morocco, ICARDA’s genebanks contain 152,223 accessions (plant genetic resources) that are vital for identifying climate-smart traits in crops.  By breeding these traits into existing crop varieties, ICARDA enhances the adaptability and resilience of agricultural systems, particularly in places, such as the hot, dry CWANA region, vulnerable to climate change. Every year, ICARDA distributes between 6,000 and 8,000 to national partners and global research institutes.

Unfortunately, selecting suitable accessions with specific desired traits for breeding presents many difficulties: the vast genebank holdings make it challenging to pinpoint specific germplasm, passport information remains limited, phenotypic characterization can be slow, and robust and cost-efficient phenotyping capacities are insufficient.

In response, large-scale sequencing, and genotyping datasets for entire genebank collections are underway. By combining genomic profiles with genebanks' comprehensive historical phenotypic data accumulated over the years, scientists get better insights into information gaps in collections.

Those gaps, argue the article's authors, can now be bridged by genome-wide prediction. This powerful tool, which aims to forecast germplasm’s genomic values and phenotypes, can attribute phenotypic information to entire genebank collections based on representative samples of collections for which genotypes and phenotypes have already been recorded.

The authors used comprehensive historical phenotypic and genomic data of 9,344 barley accessions from the Leibniz Institute of Plant Genetics and Crop Plant Research in Germany, and 1,089 barley accessions from ICARDA’s genebanks. Focusing on three traits – heading date, plant height, and thousand kernel weight – they then ran data models to evaluate prediction abilities according to different scenarios.

Results suggest that genome-wide prediction offers a cost- and time-effective alternative to populating genebanks with phenotypic estimates. “This will help bridge gaps between genebanks, enrich genebank information, and help in capturing the genetic diversity and richness present across genebank collections”, say the authors.

The scientists also demonstrated how genome-wide prediction can help foresee the facultative type across genebanks using the pooled spring and winter barley populations.

 

“This is particularly interesting for barley, which is a globally significant staple crop, because it could unlock the diversity of this unique growth habit that provides the flexibility to be sown either in the fall as winter or even as a spring crop”, adds Dr. Zakaria Kehel

Optimizing genebank management for a sustainable agricultural development

Through this study and in line with its collaborative approach and strategic research priorities on the conservation and availability of plant genetic diversity for the development of climate-smart crops, ICARDA is leveraging genome-wide prediction to unlock the potential of plants' genetic resources stored in its genebanks.

The study shows the tremendous potential of genome-wide prediction to optimize genebank management and contribute to sustainable agricultural development. Moreover, precision in predicting growth habits is supported by the steady progress of genomic technologies and functional marker applications that are used for breeding selection, and ICARDA is embracing wholesale. 

READ THE RESEARCH PAPER