Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in the carrot root phloem

Authors: BANNOUD, FLORENCIA - Consejo Nacional De Investigaciones Científicas Y Técnicas(CONICET); CARVAJAL, SOFIA - Consejo Nacional De Investigaciones Científicas Y Técnicas(CONICET); SHELBY, ELLISON - University Of Wisconsin; Senalik, Douglas; GOMEZ TALQUENCA, SEBASTIAN - National Institute Of Agricultural Technology(INTA); MASSIMO, IORIZZO - North Carolina State University; Simon, Philipp; CAVAGNARO, PABLO - National Institute Of Agricultural Technology(INTA)

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2021
Publication Date: 9/22/2021
Citation: Bannoud, F., Carvajal, S., Ellison, S., Senalik, D.A., Gomez Talquenca, S., Massimo, I., Simon, P.W., Cavagnaro, P. 2021. Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in the carrot root phloem. Genes. 12(10), 1464. https://doi.org/10.3390/genes12101464.
DOI: https://doi.org/10.3390/genes12101464

Interpretive Summary: Purple carrots are relatively unknown today, but purple and yellow, not orange, were the colors of the first known carrots about 1100 years ago in Central Asia. The purple pigments of carrots are anthocyanins, a category of chemicals found in most purple vegetables and fruits, and known for their health properties as powerful antioxidants. The distribution of anthocyanins, and consequently purple color in carrot roots, varies widely among carrot varieties or cultivars. Color ranges from a thin purple layer only on root surface; to purple color in the outer, or cortical, root tissue; to solid purple color throughout the entire root. These color patterns vary with carrot cultivars, and a genetic basis for presence of absence of anthocyanin pigmentation has been studied, but distribution of pigment has not. In this study carrot populations varying in the distribution of pigment were studied to identify genes that control the trait. Gene expression was also studied to identify the genes underlying this trait. Two genes controlling distribution of pigment in the root cortex were located on chromosome 3 and genetic variation for three genes was identified as controlling the presence of absence of purple color in that tissue. This study is of interest to vegetable seed companies breeding for novel carrot colors, to plant molecular biologists, and for nutritionists.

Technical Abstract: Purple carrots can accumulate large quantities of anthocyanins in their roots. Depending on the genetic background, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns, confined to the root phloem or xylem tissues. Within the phloem, the main tissue contributing to the overall anthocyanin concentration in the carrot root, purple pigmentation can be found in the outer phloem (OP) (also called cortex) and inner phloem (IP) tissues, or it can be confined exclusively to the OP. The latter is a fairly-common phenotype in many purple carrot cultivars. 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, transcriptome (RNA-seq), phylogenetic, and gene expression (RT-qPCR) analyses in two genetic backgrounds; an F2 mapping population (3242) and the inbred line B7262. Genetic mapping of the ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed co-localization 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) versus 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 (4 MYBs, 1 bHLH, 1 MADS-box, 1 ERF), 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, which roots present purple pigmentation only in the outer phloem, DcMYB113 conditions ROPAP.