Coloring Outside the Lines

Potato tuber skin and flesh color matter; do we know where it comes from?

Published online: May 03, 2019 Articles Csaba Hornyik
Viewed 313 time(s)

This article appears in the May 2019 issue of Potato Grower

One of the most important and eye-catching potato tuber traits is tuber color. Skin and flesh color are equally important for consumers in different countries and continents. Some people prefer red-skinned potatoes, while other eat nearly exclusively yellow-skinned varieties. There is an increasing importance placed in understanding tuber color formation in order to support breeding programs to establish modern varieties that meet consumers’ requirements.

The presence of anthocyanins in tuber skin and flesh can strongly influence their color and appearance. Additionally, anthocyanins and polyphenols accumulating in tubers are potent sources of antioxidants. Being bioactive compounds, they have potential health benefits. Anthocyanin accumulation is influenced by the balance between biosynthesis and degradation; a conserved network of activators and repressors were identified in several plant species. A common set of transcription factors including MYB, MYC and WD40 family members were described previously. In 1955, research proved that in diploid potato, three genetic loci—P, R and I—describe anthocyanin accumulation in tuber skin. Later, these genes were identified by Walter De Jong, a potato breeder at Cornell University, and other scientists. Anthocyanin development is a complex process, and not everything could be explained by the identified factors. Diploid and tetraploid potatoes have an incredible variation in primary and secondary skin color and distribution. Also, tuber flesh pigmentation varies well among cultivars. Recently, MYB transcription factors have come into prominence and widened our knowledge about anthocyanin production.

A new layer of gene regulation describing the role of short, non-coding, single stranded RNA molecules has emerged in the 21st century. These molecules are conserved in eukaryotes; some are species-specific, and many of them are conserved influencing similar biological processes in different species. The International Potato Genome Sequencing Consortium helped to understand the genetic load of potato in 2011. In 2013, a species of small RNAs, called micro-RNAs (miRNAs) were characterized for the first time in tetraploid potato by a team at The James Hutton Institute led by Csaba Hornyik. This allowed researchers to perform detailed studies aiming at finding key factors of potato development and tuber formation. miRNAs can suppress gene function at the RNA level: They can cut long RNA molecules, which will be degraded or cause translational inhibition, both of which prevent the action of certain genes.

In potato tuber skin and flesh, it was found that a conserved miRNA is associated with purple color formation: miR828 accumulates in high levels in purple tissues where anthocyanin level is high. Diploid and tetraploid potato varieties (DB22670, IVP48, Desiree and Congo) were used for this study with contrasting tuber skin and flesh color. This finding, achieved by molecular biology and bioinformatics methods, allowed researchers to identify key transcription factors (MYB), which might have a role in anthocyanin formation, as their targets. These MYB factors could suppress anthocyanin production, representing new repressors of the pathway. Additionally, a conserved small RNA was characterized in potato (TAS4 D4-) for the first time, and its target was described as being a different MYB transcription factor. The active role of miRNAs shades light on the complex regulation of anthocyanin production has a strong impact on tuber color formation.

Novel potato breeding programs that utilize the knowledge of potato genome and marker-assisted breeding greatly help breeding efforts to select desired traits early in the process. Genome selection is still a new approach that takes markers into account genome-wide and predicts trait appearance with high confidence. Using these approaches, breeders can identify the genes and genomic regions that are important for certain traits.

However, these methods have a disadvantage: Key regulatory factors could be missed during the selection—factors that might have strong impact on phenotypes. One example is the previously described regulatory miRNAs. Even if the best genes and their alleles are present in a potato variety that can support the trait of interest, we might miss the potential regulatory factors, as they were not selected during the process. miRNAs are regulators playing a role in many essential pathways including plant development, leaf morphology, flower development and tissue color formation, as well as regulating key genes under abiotic or biotic stresses. It is important to understand that selecting for favorable alleles of genes might not be enough. In parallel, we must consider regulatory elements as well. This regulation can impact breeders, producers and, ultimately, consumers determining which product to buy with their desired traits, including skin and flesh color.

Micro-RNAs have an increasing role in gene regulation in crops. Our understanding of trait development has improved, but it is far from complete. The one associated with purple color formation, miR828, is just one example; many miRNAs that may improve potato production in the future are likely still undiscovered. In the future, we need to focus on complex understanding of biological pathways for potato traits.


Author Csaba Hornyik is a senior research scientist at The James Hutton Institute in Dundee, Scotland. He specializes in analysis of genetic pathways that regulate tuber formation. Hornyik can be contacted at