Mutations in SGT2 & Game 4 altered GA content and its biosynthesis gene expression in diploid potatoes

Potato is the third most consumed food crop by humans after rice and wheat. In the potato breeding continuum, breeders face the challenge of reducing anti-nutritional factors such as steroidal glycoalkaloids (SGAs) through recurrent crosses. Despite all efforts, and depending on variety and postharvest handling conditions, some released potato varieties still show high levels of SGA. We developed an EMS mutagenized diploid potato population of which 246 mutant lines, 21 wild types and 3 commercial varieties were phenotyped for the SGA trait. Of the 246 mutant lines characterized, 16% showed lower SGA content compared to the wild type potato lines and the commercial varieties. The current study was conducted to gain a better understanding of mutational events underlying the low SGA phenotypes in the mutant lines. An ampliseq sequencing was performed using a panel of 9 target genes including SGT1, SGT2, SGT3, Game 4a, Game 4b, Game 6, Game 7, Game 11, and Game12 in 112 lines. To identify SGA biosynthetic genes whose expression might be altered in mutant lines, an RNAseq transcriptomic analysis was further conducted in a mutant line showing a low SGA content and in its wild type counterpart. Here, we report that frame shift and missense mutations in SGT2 and Game 4 genes lead to loss-of-function, significantly reduce glycoalkaloid content, and altered expression of SGA biosynthesis genes was observed in the mutant potato line. The data will be presented and further discussed in the context of generating a large potato pre-breeding germplasm.