Quantification of potato glycoalkaloids (PGA) exerting toxicity to humans has some limits if applied to potato breeding populations on a large scale due to its high cost and time consumption. The aim of this study was to investigate key genes involved in PGA biosynthesis and their tuber expression patterns in two potato cultivars, Atlantic with low PGA content (18.6 mg/100g FW) and Haryoung with high PGA content (40.1 mg/100g FW), and to test the utility of these PGA gene transcript levels as selectable markers in potato breeding program. Pot grown potato plants of both ‘Atlantic’ and ‘Haryoung’ were exposed to drought stress where the transcript accumulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase 1 (Hmg1) and squalene synthase 1 (Pss1) gene was doubled in the tubers of ‘Haryoung’ at 5days after stress (DAS). The abundance of Hmg1, Pss1, solanidine galactosyl transferase, solanidine glucosyl transferase and rhamnosyl transferase gene transcripts increased at 10 DAS. Especially, the ratio of Hmg1 and Pss1 transcripts in tubers of ‘Haryoung’ to those in tubers of ‘Atlantic’ was higher at 5 DAS compared to that at 10 DAS. The results suggest that drought treatment for 5 days can make a distinct difference in the transcript levels of Hmg1 and Pss1 correlated to PGA levels in tubers of ‘Atlantic’ and ‘Haryoung’, and the mRNA level of Hmg1 and Pss1 can be used as selection markers for breeding potato cultivars with low PGA levels.

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