Potato Breeders Went From Silencing Genes to Deleting Them — Here's What CRISPR Actually Changed

Gene-edited potatoes aren't a single technology or a single moment — they're a decade-long progression from one editing approach to a fundamentally more precise one, aimed at solving some of the crop's oldest, most economically damaging problems: bruising, browning, storage quality, and the disease that caused the Irish Potato Famine.

Before CRISPR entered commercial potato breeding, Simplot's Innate potato line was the first major gene-modified potato to reach the US market — approved by the USDA in 2014 and passing voluntary FDA safety review in 2015. Innate uses RNA interference (RNAi), a technique that switches off specific existing potato genes rather than introducing genetic material from another species. The goal: resistance to blackspot bruising and browning after cutting, plus reduced levels of asparagine, the amino acid that converts into acrylamide — a compound of health concern — during frying. Because Innate works entirely with genes potatoes already have, rather than genes borrowed from unrelated organisms, Simplot has positioned it as distinct from more conventional transgenic GMO crops, though it's still regulated in the US as a genetically engineered product. Two generations of Innate-branded varieties have now been commercialized using this approach.

Simplot has since licensed CRISPR-Cas9 gene editing technology — a deliberate strategic pivot toward a more precise tool for future potato development. The technical difference matters: CRISPR can directly edit the DNA sequence itself, including deleting a gene entirely, rather than only dialing down its expression at the RNA level the way RNAi does. That precision opens up editing strategies that weren't practically available before.

Peer-reviewed 2025 research published in the journal Biology developed non-GMO gene-edited potato lines using CRISPR/Cas9 specifically targeting cold-induced sweetening — a distinct problem from Innate's bruising/browning focus, affecting potatoes stored at low temperatures over extended periods. The results: gene-edited lines storable at low temperature for at least 120 days without losing quality, a genuinely significant improvement to the commercial storage window for harvested potatoes.

Late blight, caused by the pathogen Phytophthora infestans, remains one of potato's most economically damaging diseases worldwide — the same pathogen behind the Irish Potato Famine. Multiple independent CRISPR research efforts have targeted it through gene knockouts: disabling "susceptibility genes" like StDND1, StCHL1, and DMR6-1, whose normal function actually helps the pathogen infect the plant in the first place, rather than trying to add new resistance genes. Field evaluations of these CRISPR mutants over four consecutive growing seasons showed measurably increased late blight resistance without any yield penalty or tuber quality trade-off. That last detail matters more than it might sound: disease-resistant varieties have historically struggled with commercial adoption specifically because resistance often came bundled with a yield cost growers weren't willing to accept. A separate research track has also introduced the Rpi-amr3 and Rpi-amr1 resistance genes, sourced from the wild relative Solanum americanum, achieving field resistance through targeted gene introduction rather than knockout.

Susceptibility-gene knockout represents a conceptually different resistance strategy from traditional breeding, which typically works by introducing genes that actively fight a pathogen. Knockout instead disables the plant's own genes that a pathogen exploits to get in — and CRISPR has made that approach far more practically accessible than it was under older, slower breeding and mutagenesis methods. Combined with the storage-quality results, the shift from Innate's RNAi-based gene-silencing to CRISPR's direct gene-editing represents a genuine capability jump in potato breeding within roughly a decade — not just a rebranding of the same underlying technology.