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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #352181

Research Project: Characterization, Systematics, and Acquisition of Genetic Resources of Carrot, Potato, and Related Wild Species

Location: Vegetable Crops Research

Title: Genome diversity of the potato

Author
item Huang, Binquan - University Of Oxford
item Spooner, David
item Liang, Qiqi - Novogene Bioinformatics Institue

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Other
Publication Acceptance Date: 6/12/2018
Publication Date: 7/10/2018
Citation: Huang, B., Spooner, D.M., Liang, Q. 2018. Genome diversity of the potato. Proceedings of the National Academy of Sciences. Vol. 115 no. 28. www.pnas.org/cgi/doi/10.1073/pnas.1805917115.
DOI: https://doi.org/10.1073/pnas.1805917115

Interpretive Summary:

Technical Abstract: A recent paper in the Proceedings of the National Academy of Sciences USA (PNAS) stated that the genetic diversity of potato is much greater than other major crops, based on 68.9 million single nucleotide polymorphisms (SNPs) identified from the resequencing of 67 accessions of wild and cultivated potatoes. We questioned this conclusion based on our own original analysis of wild and cultivated potato species. To explore this further, we re-analyzed the raw data from the PNAS paper using standard, stricter methods to filter SNPs and then reanalyzed the data from the PNAS paper and our prior paper with similar subsets of cultivated and wild species, focusing on only diploid germplasm. The PNAS paper identified 46,797,252 SNPs in 20 accessions of diploid wild species and 26,560,638 SNPs in 10 diploid landrace genotypes. We obtained many fewer; 10,473,482 SNPs from 20 diploid wild potatoes and 8,108,352 SNPs from 10 diploid landrace genotypes. Our stricter, and more standard filter deleted many false SNPs from the PNAS analysis, which led to overestimates of diversity. These results have broad implications for potato breeding because diploid cultivated potato wild and cultivated species have been used for base-broadening in potato breeding programs. High levels of genetic diversity in this germplasm would support this strategy but phenotypic variation does not necessarily require genetic diversity. Genetically similar individuals may be highly variable for traits of interest to breeders, such as tuber shape and color. Wild germplasm is generally used by breeders for specific traits, so genome-wide diversity is not as important as diversity at selected loci.