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Title: Fine mapping, transcriptome analysis, and marker development for Y2, the gene that conditions beta-carotene accumulation in carrot (Daucus carota L.)

Author
item ELLISON, SHELBY - University Of Wisconsin
item Senalik, Douglas
item BOSTAN, HAMED - North Carolina State University
item Simon, Philipp
item IORIZZO, MASSIMO - North Carolina State University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2017
Publication Date: 6/29/2017
Publication URL: https://handle.nal.usda.gov/10113/5801834
Citation: Ellison, S., Senalik, D., Bostan, H., Iorizzo, M., Simon, P. 2017. Fine mapping, transcriptome analysis, and marker development for Y2, the gene that conditions beta-carotene accumulation in carrot (Daucus carota L.). G3, Genes/Genomes/Genetics. 7(8)2665-2675. doi: 10.1534/g3.117.043067.

Interpretive Summary: The first carrots ~1100 years ago were yellow in color, and orange carrots were only reported 500 years ago. The familiar orange color of carrots today is controlled by one gene, called Y2. The chromosomal location of the Y2 gene is known, but the specific DNA sequence responsible for this trait is not known. The purpose of this study was to identify possible DNA sequences in the region that are candidates for the Y2 gene. By evaluating the genetic map of the region of the carrot genome, 72 genes were identified. Since orange carrots accumulate orange carotenoid pigments not found in yellow carrots, it is hypothesized that orange carrots with the Y2 gene mutation have genes functioning that are not functioning in yellow carrots. To test that hypothesis, the function of the 72 genes in the Y2 region was evaluated and 13 of them were found to function differently in orange and yellow carrots, making them primary candidates for Y2. Of these 13 genes, two in particular have functions in other plants that might account for carotenoid accumulation controlled by the Y2 gene. Future studies will be needed to determine which of these candidate genes actually is Y2. This study is of interest to plant geneticists and molecular biologists, plant breeders, and nutritional scientists.

Technical Abstract: Domesticated carrots, Daucus carota subsp. sativus, are the richest source of beta-carotene in the US diet, which when consumed is converted into vitamin A, an essential component of eye health and immunity. The Y2 locus plays a significant role in beta-carotene accumulation in carrot roots, but a candidate gene has not been identified. To advance our understanding of this locus, the genetic basis of beta-carotene accumulation was explored by utilizing an advanced mapping population, transcriptome analysis, and nucleotide diversity in diverse carrot accessions with varying levels of beta-carotene. A single large effect Quantitative Trait Locus (QTL) on the distal arm of chromosome 7 overlapped with the previously identified beta-carotene accumulation QTL, Y2. Fine mapping efforts reduced the genomic region of interest to 650 kb including 72 genes. Transcriptome analysis within this fine mapped region identified four genes differentially expressed at two developmental time points and 13 genes differentially expressed at one time point. Differentially expressed genes, within the Y2 fine mapped region, included transcription factors and genes involved in light signaling and carotenoid flux, including a member of the Di19 gene family involved in Arabidopsis photomorphogenesis, and a homologue of the bHLH36 transcription factor involved in maize carotenoid metabolism. Analysis of nucleotide diversity in 25 resequenced carrot accessions revealed a drastic decrease in diversity of this fine-mapped region in orange cultivated accessions as compared to white and yellow cultivated and to white wild samples. The results presented in this study provide a foundation to identify and characterize the gene underlying beta-carotene accumulation in carrot.