Background

Wheat, a staple food crop, faces challenges in maintaining productivity due to global warming and pests. This is because the genetic diversity of cultivated wheat has been drastically reduced through thousands of years of artificial selection, leading to the loss of beneficial traits for adapting to rapid climate change. In particular, tetraploid wheat, including durum wheat, is considered difficult to improve due to its complex genetic structure.

Previously, researchers have analyzed variations based on the reference genome information of a single cultivar. However, this approach has limitations in capturing broad genetic variations and differences between subgenomes. Consequently, the construction of a pangenome integrating multiple subspecies has emerged as a solution.

Key Findings

Creating a genomic map by integrating 12 genome datasets

A joint research team from the Beijing Academy of Agricultural Sciences and the Siberian Federal Scientific and Research Center for Agro-Biotechnologies decoded 12 representative cultivars of 10 subspecies using high-quality de novo assembly techniques. Based on this, they completed a graph-based tetraploid wheat pangenome map. This research was published in the online edition of the international journal 'Nature Genetics' on July 22.

Furthermore, they enhanced the research by combining the whole-genome resequencing data of 736 genetic resources collected from around the world with the pangenome map. This involved conducting a Genome-Wide Association Study (GWAS) to elucidate the correlation between traits and genetic variations using vast amounts of data. As a result, they identified an average of 250,000 structural variations per individual and demonstrated that chromosome rearrangements trigger asymmetric differentiation of subgenomes.

Discovery of key genes that will be the key to crop improvement

In this process, 287 gene loci associated with 32 major agricultural traits were revealed. In particular, the non-brittle rachis gene variant, which maximizes crop yield, is attracting attention. Wild wheat has a brittle rachis for reproduction, while cultivated wheat has a strong rachis, which is advantageous for human harvesting. The researchers clearly elucidated the process by which the non-brittle rachis trait was fixed through the insertion of a retrotransposon into the Btr1-A gene, leading to its loss of function.

The second is the HAT14-B gene variant, which controls the number and size of wheat grains. The research team revealed that this gene encodes a specific transcription factor, and the expression level determines the yield. In fact, cultivars with large and abundant grains showed higher activity of the gene.

Significance and Prospects

The completed tetraploid wheat pangenome map is considered a powerful foundation for molecular breeding aimed at overcoming climate change. This is because it restores the genetic diversity of wild subspecies that have survived in harsh environments. As a result, it is now possible to accurately identify genes specialized for drought and high temperatures and apply them to crop improvement. The scenario of introducing immune traits from wild species to develop cultivars resistant to climate stress has become even more concrete.

However, there are limitations in developing actual new crop varieties using pangenome information. This is because it is necessary to demonstrate that the target traits are expressed in the same way in the complex interaction with environmental factors. It is also necessary to overcome the technical challenges of correcting target sites using CRISPR gene editing.

The research team plans to dedicate itself to expanding the pangenome research of hexaploid bread wheat in the future, based on this data.