Genome of Aegilops ventricosa Reveals Its Contribution to Wheat Genetic Improvement

Aegilops ventricosa (2n=4X=28, D^vD^vN^vN^v) is a species of allotetraploid wheat, mainly distributed in the Mediterranean and its neighboring regions. It has been considered an important germplasm resource for wheat genetic improvement because of its good resistance to biotic stress. As early as the 1990s, wheat breeders had successfully used the chromosome fragment of Ae. ventricosa 2N^vS in common wheat to create the world-famous wheat line VPM1. On this basis, a series of wheat varieties containing the resistance gene cluster Yr17-Lr37-Sr38-Cre5 were cultivated, such as Jagger and Renan. In recent years, introgression fragments derived from the genome of Ae. ventricosa have been detected in more wheat materials. However, due to the lack of a reference genome of Ae. ventricosa, the original state of these introgression fragments in Ae. ventricosa remains unknown, limiting the in-depth study and application of introgression fragments.

On September 10, 2024, Plant communications published an article titled "Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement" by Wuyun Yang's team and their collaborators. This study successfully assembled a high-quality reference genome at the chromosome level of Ae. ventricosa material RM271, with a genome size of 8.67 Gb, the longest contigs and contigs N50 were 255.18 Mb and 54.71 Mb, respectively, and a BUSCO completeness of 99.18%. The deciphering of the Ae. ventricosa reference genome has laid the foundation for cloning excellent genes such as disease resistance and stress resistance from Ae. ventricosa, and is of great significance for further using Ae. ventricosa to carry out genetic improvement of hexaploid common wheat.

Figure 1. Genome features of RM271. (Liu, et al., 2024)

Phylogenetic analysis shows that the ancestral donor of the D^v subgenome of Ae. ventricosa is Ae. tauschii ssp. tauschii (genome DD), which is different from the ancestral donor of the D subgenome of common wheat Ae. tauschii ssp. strangulata (genome DD). This discovery has laid a theoretical foundation for using the D^v subgenome of Ae. ventricosa to broaden the genetic diversity of the D subgenome of wheat in future wheat genetic improvement. Molecular evolutionary evidence shows that the origin of Ae. ventricosa was at the latest about 0.7Mya (700,000 years ago), which is earlier than the hybridization of Ae. tauschii ssp. strangulata and tetraploid wheat (T. turgidum, genome AABB) to form hexaploid common wheat; of course, this estimate may be too small, and a larger population is needed to estimate the formation time more accurately in the future.

Based on the analysis of genomic chromosome structure, the authors found that the D^v subgenome of Ae. ventricosa has more structural rearrangements than the D subgenome of common wheat. The structural rearrangement of the genome of Ae. ventricosa exists both between the D^v and N^v subgenomes and within the subgenomes, and the chromosome rearrangement within the D^v and N^v subgenomes is more than the chromosome rearrangement between the subgenomes. The largest chromosome rearrangement is the exchange of chromosome arms between the D^v and N^v subgenomes, forming chimeric 1N^v and 3D^v chromosomes. In addition, a 6N^vL-2N^vS translocation of about 37Mbp in length is included. This fragment is the 2N^vS fragment in the famous wheat material VPM1 and its derivatives (the homologous segment in this study material is 6N^vL), which allows researchers to further study the ancestral state of this segment. By constructing a Graph-based pan-genome of 24 2AS/6N^vL homologous segments (including 6 6N^vL segments and 18 2AS segments), the authors identified 6 disease resistance-related candidate genes with complete R gene structures. These genes have different genotypes in the 6N^vL segment and the 2AS segment, which laid a certain foundation for the later cloning of disease resistance genes.

Based on the genome assembly sequence, the authors identified three new introgression fragments from chromosome 7D^vL in common wheat, proving the feasibility of using Ae. ventricosa to broaden the genetic diversity of the D subgenome of common wheat. In addition, based on the high-quality genome of RM271, the authors analyzed 664 wheat whole genome resequencing data and identified 12 non-redundant introgression fragments from the D^v and N^v subgenomes. In European wheat varieties, the frequency of detecting these introgression fragments was the highest, up to 29.40%, proving that Ae. ventricosa has made an important contribution to the genetic improvement of European wheat.

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Reference

1. Liu, Z., et al. Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement. Plant Commun. 2024, 101131.