Genetic and Transcription Profile Analysis of Tissue-Specific Anthocyanin Pigmentation in Carrot Root Phloem

Abstract

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.

Morphological and Biochemical Variation in Carrot Genetic Resources Grown under Open Field Conditions: The Selection of Functional Genotypes for a Breeding Program

“…The different root color was conferred by the Y and Y 2 loci in the chromosomes 5 and 7, respectively, in which Y_Y 2 _, yyY 2 _, Y_y 2 y 2 , and yyy 2 y 2 genotypes represent white, yellow, pale orange, and orange root color, respectively [38,39]. Moreover, the purple root color was due to the deposition of anthocyanin, which was regulated by the genes in the P 1 and P 3 regions of chromosome 3 [40,41]. The majority of the genotypes were orange (n = 142), whereas the least dominant root color was purple (n = 8).…”

A Survey of Enhanced Cold Tolerance and Low-Temperature-Induced Anthocyanin Accumulation in a Novel Zoysia japonica Biotype

“…Anthocyanins are synthesized in cytosol and endoplasmic reticulum membrane system, then transported into vacuoles via ABC transporters located in tonoplast [ 39 , 88 , 89 , 90 , 91 , 92 ]. In this study, three genes that were uniquely up-regulated in YN-9 lay in the overlap of auxin transport and pigmentation accumulation GOs.…”

Genome-Wide Identification and Evolution Analysis of R2R3-MYB Gene Family Reveals S6 Subfamily R2R3-MYB Transcription Factors Involved in Anthocyanin Biosynthesis in Carrot

“…In addition, celery and water dropwort and coriander also belong to common Apiaceae plants [ 4 , 48 , 49 ]. In addition to having rich anthocyanins [ 7 , 11 , 50 ], carrot has many active compounds, including carotenoids, volatile oil, vitamins, dietary fiber [ 4 , 48 ] and other nutrients.…”

“…DcMYB6 ( DCAR_000385 ) can induce anthocyanin biosynthesis of A. thaliana [ 9 ]. DcMYB7 ( DCAR_010745 ), designated as the DcMYB113-like gene in the carrot genome, was always associated with purple root pigmentation of all purple carrots [ 6 , 7 , 11 , 17 , 58 , 62 , 63 ]. This corresponds to our transcriptional and heatmap values.…”

“…Non-purple carrots are well known for their orange pigmentation and carotenoid accumulation [ 5 ]. Purple carrot can be divided into solid purple carrot type and tissue-specific purple carrot types [ 6 , 7 , 8 , 9 ]. Nowadays, purple carrots are popular among consumers because they are an excellent source of anthocyanins.…”