Identification of an SCPL gene controlling anthocyanin acylation in carrot (Daucus carota L.) root

Authors: CURABA, JULIEN - North Carolina State University; BOSTAN, HAMED - North Carolina State University; CAVAGNARO, PABLO - Consejo Nacional De Investigaciones Científicas Y Técnicas(CONICET); Senalik, Douglas; MENGIST, MOLLA FENTIE - North Carolina State University; ZHAO, YUNYANG - North Carolina State University; Simon, Philipp; IORIZZO, MASSIMO - North Carolina State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/18/2019
Publication Date: 1/31/2020
Citation: Curaba, J., Bostan, H., Cavagnaro, P., Senalik, D.A., Mengist, M., Zhao, Y., Simon, P.W., Iorizzo, M. 2020. Identification of an SCPL gene controlling anthocyanin acylation in carrot (Daucus carota L.) root. Frontiers in Plant Science. 10(1770):1-17. https://doi.org/10.3389/fpls.2019.01770.
DOI: https://doi.org/10.3389/fpls.2019.01770

Interpretive Summary: The purple or red pigments of many vegetables and fruits including red potatoes, onions, grapes, apples and purple carrots are anthocyanins which not only impart appealing colors but also dietary antioxidants that confer several health benefits. There are five different anthocyanin pigments in purple carrots of which three include a chemical moiety called an acyl group, and are said to be acylated while the other two carrot anthocyanins are non-acylated. While all five carrot anthocyanins have a similar purple color the non-acylated anthocyanins are readily absorbed during digestion and consequently able to confer health benefits while the three acylated anthocyanins are not well-absorbed and confer minimal health benefits. Interestingly the acylated anthocyanins of carrot are much more stable when exposed to heat and light so they make excellent natural food coloring while the non-acylated anthocyanins are much more readily broken down and consequently not widely usable as natural colorants. Within the last decade we discovered that a gene in carrot controls the relative amount or balance of acylated to non-acylated anthocyanins of carrot. We knew where that gene resides on carrot chromosomes but it was not know exactly how it controlled acylation. Since we recently published the carrot genome, this study was undertaken to identify the specific gene controlling carrot anthocyanin acylation. We evaluated several large carrot populations and sequenced genes in each to discover a mutation in a gene called SCPL (Serine Carboxypeptidase-Like) that controls acylation. SCPL genes control acylation in some other plants but this was the first discovery of a functioning SCPL gene in carrot. This study is of interest to biochemists and molecular biologists studying plant metabolism and also to plant breeders, food scientists and nutritionists developing new pigments to replace carcinogenic coal-tar dyes currently used to color foods, and also developing new functional foods.

Technical Abstract: Anthocyanins are natural health promoting pigments that can be produced in large quantities in some purple carrot cultivars. Decoration patterns of anthocyanins, such as acylation, can greatly influence their stability and biological properties and use in the food industry as nutraceuticals and natural colorants. Despite recent advances made towards understanding the genetic control of anthocyanin accumulation in purple carrot, the genetic mechanism controlling acylation of anthocyanin in carrot root have not been studied yet. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify the genetic factor conditioning the accumulation of non-acylated (Cy3XGG) versus acylated (Cy3XFGG and Cy3XSGG) cyanidin derivatives, in three carrot populations. Segregation and mapping analysis pointed to a single gene with dominant effect controlling anthocyanin acylation in the root, located in a 576kb region containing 29 predicted genes. Orthologous and phylogenetic analyses enabled the identification of a cluster of three SCPL-acyltransferases coding genes within this region. Comparative transcriptome analysis indicated that only one of these three genes, DcSCPL1, was always expressed in association with anthocyanin pigmentation in the root and was co-expressed with DcMYB7, a gene known to activate anthocyanin biosynthetic genes in carrot. DcSCPL1 sequence analysis, in root tissue containing a low level of acylated anthocyanins, demonstrated the presence of an insertion causing an abnormal splicing of the 3rd exon during mRNA editing, likely resulting in the production of a non-functional acyltransferase and explaining the reduced acylation phenotype. This study provides strong linkage-mapping and functional evidences for the candidacy of DcSCPL1 as a primary regulator of anthocyanin acylation in carrot storage root.