Grapes are one of the most important crops in the world, producing wine, juice, raisins, and other products.
But they are also vulnerable to pests, diseases, and environmental stresses, such as drought and salinity.
To improve the resilience and adaptability of grape varieties, researchers are looking for new sources of genetic diversity in their wild relatives.
A Super-Pangenome of Wild North American Grapes
ROBYN BECK/AFP via Getty Images
Wild North American grapes are now less of a mystery after an international team of researchers led by the University of California, Davis, decoded and cataloged the genetic diversity of nine species of this valuable wine crop.
The researchers sequenced, assembled, and annotated the genomes of nine wild grape species, which were phased and scaffolded at chromosome scale.
They then generated a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level.
The super-pangenome is a comprehensive representation of the genetic variation within and across the wild grape species, capturing both common and rare alleles.
It also accurately assesses the similarity of hybrids to their parents, as well as the evolutionary relationships among the species.
The super-pangenome includes known allelic variants in the sex-determining region and for Pierce's disease resistance loci, which are important for grape breeding.
The Potential of Wild Grapes for Crop Improvement
The super-pangenome is not only a valuable resource for understanding the biology and evolution of wild grapes, but also a powerful tool for identifying genes and traits that can enhance the performance and quality of cultivated grapes.
Using pangenome-wide association analysis, the researchers demonstrated the utility of the super-pangenome by effectively mapping short-reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes.
Salt tolerance is a crucial trait for grape cultivation, as salinity can reduce plant growth, yield, and fruit quality.
The researchers found that salt tolerance in wild grapes is associated with genes involved in ion transport, osmotic adjustment, and stress response.
These genes could be used to improve the salt tolerance of domesticated grapes, which could help them cope with climate change and water scarcity.
The super-pangenome of wild North American grapes is a milestone for the field of grape genomics and breeding, as it reveals the genetic basis of adaptive traits from wild relatives and potentially accelerates crop improvement.
The researchers hope that their work will inspire similar efforts for other crops and their wild relatives, which could help us secure a sustainable, clean-energy future.
The Challenges and Opportunities of Grape Genomics
Grape genomics is a challenging field, as grapes have a complex genome structure, with high heterozygosity, polyploidy, and structural variation.
Moreover, grapes have a long generation time and a large genome size, which make breeding and sequencing difficult.
However, advances in sequencing technologies and bioinformatics have enabled researchers to overcome some of these challenges and generate high-quality genome assemblies and annotations for several grape species and varieties.
Grape genomics also offers many opportunities for improving grape quality and productivity, as well as understanding the evolution and domestication of this crop.
By comparing the genomes of wild and cultivated grapes, researchers can identify the genes and mutations that are responsible for the phenotypic differences and the adaptation to different environments and human selection.
By analyzing the genetic diversity and population structure of grapes, researchers can also trace the origin and migration of grape varieties and their relationships with other crops.
The Future of Grape Breeding and Research
The super-pangenome of wild North American grapes is a valuable resource for grape breeding and research, as it provides a comprehensive and accurate view of the genetic variation within and across the wild grape species.
It also enables the discovery of novel genes and alleles that can improve the traits of interest for grape cultivation, such as disease resistance, stress tolerance, and fruit quality.
The super-pangenome can also facilitate the development of new breeding strategies and tools, such as genomic selection, gene editing, and marker-assisted selection.
The super-pangenome is not the end of the story, but rather the beginning of a new era of grape genomics and breeding.
The researchers plan to expand the super-pangenome by adding more wild and cultivated grape genomes from different regions and backgrounds, as well as integrating other types of genomic data, such as transcriptomics, epigenomics, and metabolomics.
The ultimate goal is to create a comprehensive and dynamic grape pangenome that can capture the full spectrum of the grape diversity and evolution, and provide a powerful tool for improving the grape crop and its products.
