Identifying candidate genes involved in trichome formation on carrot stems by transcriptome profiling and resequencing

Trichomes are specialized structures developed from epidermal cells and can protect plants against biotic and abiotic stresses. Trichomes cover carrots during the generative phase. However, the morphology of the carrot trichomes and candidate genes controlling the formation of trichomes are still unclear. This study found that carrot trichomes were non-glandular and unbranched hairs distributed on the stem, leaf, petiole, pedicel, and seed of carrot. Resequencing analysis of a trichome mutant with sparse and short trichomes (sst) and a wild type (wt) with long and dense trichomes on carrot stems was conducted. A total of 15 396 genes containing nonsynonymous mutations in sst were obtained, including 42 trichome-related genes. We also analyzed the transcriptome of the trichomes on secondary branches when these secondary branches were 10 cm long between wt and sst and obtained 6 576 differentially expressed genes (DEGs), including 24 trichome-related genes. qRT-PCR validation exhibited three significantly up-regulated DEGs, 20 significantly down-regulated, and one with no difference. We considered both the resequencing and transcriptome sequencing analyses and found that 12 trichome-related genes that were grouped into five transcription factor families containing nonsynonymous mutations and significantly down-regulated in sst. Therefore, these genes are potentially promising candidate genes whose nonsynonymous mutations and down-regulation may result in scarce and short trichomes mutation on carrot stems in sst.