Journal
G3-GENES GENOMES GENETICS
Volume 7, Issue 8, Pages 2665-2675Publisher
OXFORD UNIV PRESS INC
DOI: 10.1534/g3.117.043067
Keywords
carotenoids; Daucus carota L.; genotyping-by-sequencing; RNA-sequencing; QTL
Categories
Funding
- National Science Foundation [1202666]
- United States Department of Agriculture National Institute of Food and Agriculture, Hatch project [1008691]
- NIFA [912916, 1008691] Funding Source: Federal RePORTER
- Direct For Biological Sciences
- Division Of Integrative Organismal Systems [1202666] Funding Source: National Science Foundation
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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. These differentially expressed genes 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 homolog 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 finemapped 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.
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