<i>FLOWERING LOCUS T</i> (<i>FT</i>) gene regulates short-day flowering in low latitude Xishuangbanna cucumber (<i>Cucumis sativus</i> var. <i>xishuangbannanesis</i>)

Xishuangbanna (XIS) cucumber is a semi-wild cucumber originating from a low latitude. XIS cucumbers are strictly short-day plants, while cultivated cucumbers are day-neutral plants. The length of the light phase has a dosage effect on flowering time and the day length requirement for flowering is 8h-11.5h. Out-of-range photoperiod conditions and weak light conditions are unfavorable for blooming. Transcriptomic and gene expression analysis indicate circadian pathway genes as well as CONSTANS (CO) did not show a differential response to photoperiod treatment between XIS and cultivated cucumbers. The FLOWERING LOCUS T (FT) gene is activated from 10:00 to 18:00, and long- (16h) and medium- (12h) day length suppressed this diurnal rhythm expression. We designed kompetitive allele specific PCR (KASP) markers based on genomic SNPs between the mapping parents (XIS49 and CL) to genetically map the short-day flowering gene. Field investigation was performed after long-day photoperiod (16h) treatment. Finally, we detected a strong quantitative trait locus (QTL) signal at a 540-kb segment (chr1:29.08Mb - 29.62Mb) that carries the FT gene. We found a 30-kb TE-rich insertion with a distance of 15kb to the FT gene in XIS49, which may contribute to the gain of the short-day flowering trait in XIS49. The 30-kb insertion endowed the FT gene and the inserted polygalacturonase (PG) gene with a photoperiod-dependent expression manner. Our study indicates that the FT gene, but not its upstream circadian clock genes, regulate short-day flowering in the XIS cucumber, and the cis-regulation of the FT gene is probably due to a TE insertion.