Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (12): 3589-3599.DOI: 10.1016/j.jia.2022.08.032

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  • 收稿日期:2022-03-10 接受日期:2022-05-25 出版日期:2022-12-01 发布日期:2022-05-25

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

WU Zhe1*, YANG Xuan1*, ZHAO Yu-xuan1, JIA Li2   

  1. 1 College of Horticulture, Shanxi Agricultural University, Taigu 030801, P.R.China
    2 Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, P.R.China
  • Received:2022-03-10 Accepted:2022-05-25 Online:2022-12-01 Published:2022-05-25
  • About author:Correspondence WU Zhe, E-mail: wzz0618@163.com; JIA Li, Tel: +86-551-65160817, E-mail: jiali820@aaas.org.cn * These authors contributed equally to this study.
  • Supported by:
    This study was sponsored by the Research Project Supported by Shanxi Scholarship Council of China (2021–066), the National Natural Science Foundation of China (31601751), the Key Research and Development Plan of Shanxi Province, China (201903D221063), the Fundamental Research Program of Shanxi Province, China (20210302123412), and the Science and Technology Innovation Project of Shanxi Agricultural University, China (2016ZZ02).

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摘要：

表皮毛是由表皮细胞发育而来的特殊结构，可以保护植物免受生物和非生物胁迫。胡萝卜在生殖阶段被表皮毛覆盖，但胡萝卜表皮毛的形态和控制表皮毛形成的候选基因仍未知。研究结果表明，胡萝卜表皮毛是非腺毛且不分枝，分布在胡萝卜的茎、叶、叶柄、花梗和种子上。本研究对1个胡萝卜花茎上分布稀而短的表皮突变体（sst）和1个花茎上分布长而密的表皮毛野生型（wt）进行了重测序分析，在sst上共检测到15, 396个非同义突变，包含42个与表皮毛相关的基因。对wt和sst长度为10cm的一级侧枝进行了转录组分析，获得了6, 576个差异表达基因（DEG），包括24个表皮毛相关的基因。qRT-PCR验证的这些差异表达基因中，有3个显著上调，20个显著下调，1个没有差异。综合重测序和转录组测序分析发现，12个表皮毛相关的基因含有非同义突变且在sst中显著下调表达，可归类为5个转录因子家族。因此，这些基因是可能的候选基因，他们的非同义突变和下调表达可能是导致sst中胡萝卜花茎的表皮毛短且稀少的突变。

Abstract:

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.

Key words: carrot , trichome ,  resequencing ,  transcriptome ,  candidate genes