In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNA-seq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F₂ population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P₁ and P₃ genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P₃ only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.

中文翻译：

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胡萝卜根韧皮部组织特异性花青素色素沉着的遗传和转录谱分析

在紫胡萝卜中，花青素色素沉着可以在整个根部表现出来，也可以表现出组织特异性模式。在韧皮部内，可以在外韧皮部（OP）（也称为皮质）和内韧皮部（IP）中发现紫色色素沉着，也可以仅限于 OP。在这项工作中，通过连锁作图和转录组 (RNA-seq) 以及系统发育分析，研究了胡萝卜根 OP 和 IP 组织中组织特异性花青素色素沉着的遗传控制。随后在两个遗传背景、F ₂种群 (3242) 和近交 B7262 中进行基因表达 (RT-qPCR) 评估。“根外韧皮部花青素色素沉着”（ROPAP）和内韧皮部色素沉着（ RIPAP ）的遗传作图) 揭示了ROPAP与P ₁和P ₃基因组区域的共定位，以前已知这些区域可以调节不同遗传种群中的色素沉着，而RIPAP与P _3共定位只要。紫色 OP (POP) 与非紫色 IP (NPIP) 组织的转录组分析，以及连锁和系统发育数据，初步鉴定了 28 个候选基因，其中 19 个通过 RT-qPCR 在独立根样本中进一步评估3242 和 B7262，揭示了 15 个基因在两种遗传背景下的 POP 中持续上调，以及 2 个基因在特定背景下的 POP 中上调。其中包括七个转录因子、七个花青素结构基因和两个参与细胞转运的基因。总之，我们的结果指向DcMYB7、DcMYB113和一个 MADS-box (DCAR_010757) 作为 3242 中调节ROPAP的主要候选基因，而DcMYB7和 MADS-box 条件RIPAP在这样的背景下。在 7262 中，DcMYB113条件ROPAP。