Genetic Sequencing Sheds New Light on Potato and Sweetpotato Diversity

The collections of potato and sweetpotato biodiversity that the CIP genebank safeguards for humanity are among the world’s most important for those crops. As part of an effort to improve the management of those genetic resources, the genebank undertook DNA fingerprinting for the entire collections of cultivated potato and sweetpotato, and the results have the potential to improve scientists’ understanding of those crops.

Genebank Head David Ellis explained that for the more than 4,500 accessions of cultivated potatoes in the genebank, DNA fingerprints were established using thousands of genetic markers called single nucleotide polymorphisms (SNP) that can be used to identify individuals and understand their relatedness. The identification of species, subspecies and varieties has traditionally been based on morphological traits such as tubers, flowers and leaves, but genetic fingerprints can yield new insight into crop diversity, and the decreasing cost of sequencing is making that tool more accessible.

DNA fingerprints have helped genetic resources manager Ana Panta improve the fidelity of the genebank’s cultivated potato and sweetpotato collections.
The genetic data could help scientists better understand the origins and relatedness of potato and sweetpotato taxa.

“Our main goal was to better understand our collection and build information that will make it more useful for current and future users,” David said. He explained that the SNP data revealed that approximately 20 percent of CIP’s potato accessions were misidentified, which he believes is a common, yet unstated, problem in genebanks. CIP genebank personnel corrected the misidentified accessions to ensure all users receive the material they need. The genebank will continue to use the fingerprints in a quality management system where randomly selected samples are genotyped to ensure fidelity of the collection.

While these corrections have improved the genebank’s collection management, David and his colleagues quickly realized that the SNP data had many other applications. For example, the ability to identify genetically unique accessions will help the genebank make its field collection process more efficient and cost effective. The genotyping data have also provided a new understanding of cultivated potato taxonomic relationships, which suggests that further examination of the taxonomy of cultivated potato is warranted.

While the genetic fingerprinting of potato was based on between 4,000 and 6,000 SNP markers, a comparable analysis of cultivated sweetpotato used as many as 55,000 markers, which allowed researchers to map distinct populations of cultivated sweetpotato in the collection to different regions of the world. Researchers then collaborated with Diversity Arrays Technology to narrow those markers down to approximately 5000 that can be used for comparably accurate identification at a cost of less than $10 per accession. This opens the door for more widespread uses of genetic fingerprinting, such as tracking parental lines in the breeding process, or determining which varieties farmers are growing.

 “We will be mining these data for years to come,” David predicted.

Related research:

Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection

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