Watermelon lycopene β-cyclase: promoter characterization leads to the development of a PCR marker for allelic selection

Bang, Hyochoong; Yi, Gangman; Kim, Sunggil; Leskovar, Daniel I.; Patil, Bhimanagouda S.

doi:10.1007/s10681-014-1158-5

Cited by 13 publications

(15 citation statements)

References 49 publications

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“…In watermelon, to date, several functional fruit trait-related markers have been identified; fruit shape (SUN-Cla011257), stripe pattern (wsb6-11), and flesh color (Clcyb.600 and Lcyb) [29, 30, 52]. However, the development of functional markers requires time for their subsequent identification, cloning, and interpretation, as in the case of Clcyb.600 and Lcyb [29, 30]. In this study, the basic principle for identifying and developing genic markers through WGRS was similar to that of resequencing methods in other studies [10, 24].…”

Section: Resultsmentioning

confidence: 99%

“…Although evidence indicates that these loci are involved in flesh color, the regulatory mechanisms underlying flesh color formation in watermelon remain largely unknown. Bang et al [19, 29, 30] investigated flesh inheritance in watermelon through the characterization of a SNP mutation on the lycopene beta-cyclase ( LCYB ) gene, and its expression between red and canary yellow watermelon, and developed the Clcyb.600 marker, which perfectly co-segregated with flesh color phenotypes. Recently, Zhu et al [31] ruled out comparative transcriptional regulation between red and pale-yellow watermelons during fruit development and ripening stages and identified a large number of upregulated genes related to carotenoid biosynthesis and plant hormone pathways.…”

Section: Introductionmentioning

confidence: 99%

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Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content

et al. 2019

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Cultivated watermelon (Citrullus lanatus) is one of the most important food crops in the Cucurbitaceae family. Diversification after domestication has led cultivated watermelons to exhibit diverse fruit flesh colors, including red, yellow, and orange. Recently, there has been increased interest in red-fleshed watermelons because they contain the antioxidant cis-isomeric lycopene. We performed whole genome resequencing (WGRS) of 24 watermelons with different flesh colors to identify single-nucleotide polymorphisms (SNPs) related to high lycopene content. The resequencing data revealed 203,894–279,412 SNPs from read mapping between inbred lines and the 97103 reference genome. In total, 295,065 filtered SNPs were identified, which had an average polymorphism information content of 0.297. Most of these SNPs were intergenic (90.1%) and possessed a transversion (Tv) rate of 31.64%. Overall, 2,369 SNPs were chosen at 0.5 Mb physical intervals to analyze genetic diversity across the 24 inbred lines. A neighbor-joining dendrogram and principal coordinate analysis (PCA) based on the 2,369 SNPs revealed that the 24 inbred lines could be grouped into high and low lycopene-type watermelons. In addition, we analyzed SNPs that could discriminate high lycopene content, red-fleshed watermelon from low lycopene, yellow or orange watermelon inbred lines. For validation, 19 SNPs (designated as WMHL1–19) were chosen randomly, and cleavage amplified polymorphic sequence (CAPS) markers were designed. Genotyping of the above 24 lines and 12 additional commercial cultivars using WMHL1–19 CAPS markers resulted in match rates of over 0.92 for most validated markers in correlation with the flesh color phenotypes. Our results provide valuable genomic information regarding the high lycopene content phenotype of red-fleshed cultivated watermelons, and the identified SNPs will be useful for the development of molecular markers in the marker-assisted breeding of watermelons with high lycopene content.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content

et al. 2019

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“…It is an intermediate product which accumulates as a result of the activation of the first steps of the carotenoid biosynthesis pathway up to lycopene and the inhibition of the enzymatic steps that follow, namely the cyclization of lycopene, as was shown for tomato fruits [30,33]. In other plants, mutations associated with the decreased activity of LCYB were shown to cause lycopene accumulation, such as in red watermelons [34,35], papaya [36], red grapefruits [37] and red oranges [38]. In addition, tomato plants carrying a null mutation in the tomato chromoplasts-specific LCYB, or transgenic tomato plants in which this gene is silenced, showed an accumulation of lycopene in their flowers, a tissue that does not normally accumulate lycopene [30].…”

Section: Plant Materialsmentioning

confidence: 99%

“…All of these transcript data were used to query public genomic databases, including The Arabidopsis Information Resource (TAIR), Rice and non-redundant proteins (NR) databases (Figure 1c), using the BLASTX (Basic Local Alignment Search Tool). The results showed significant hits in three databases, revealing a general similarity of 9.9-10.1% (35,014) with O. dubium contigs (File S2). Most of the contigs (34,595, 89.3%) were found in all three databases.…”

Section: Transcriptome Sequencing De Novo Assembly and Functional Anmentioning

confidence: 99%

Transcriptome Profiling of Ornithogalum dubium Leaves and Flowers to Identify Key Carotenoid Genes for CRISPR Gene Editing

Wei

Arazi

Hod

et al. 2020

Plants

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Ornithogalum dubium is a popular ornamental monocot native to South Africa with flower colors ranging from pure white to deep orange. Gene editing based on the CRISPR/Cas9 system has recently been shown to hold potential for color improvement in ornamental flower crops. To apply this approach to Ornithogalum color manipulation, genomic or transcriptomic data must first be collected. Here, cDNA libraries of O. dubium leaves and flowers were constructed and sequenced using the Illumina HiSeq 2500. Over 155 million 100-bp paired-end reads were assembled into a transcriptome database of 360,689 contigs, of which 18,660 contigs were differentially expressed between leaves and flowers. Carotenoids are the main pigment imparting spectrum of orange hues to O. dubium flowers. By querying our database, we identified a total of 16 unique transcripts (unigenes) predicted to be involved in the carotenoid biosynthesis pathway of Ornithogalum. Combining carotenoid profiles, we further inferred several key unigenes responsible for floral coloration and accumulation in O. dubium, of which the gene LCYB/comp146645_c0 was found as a suitable target to generate potentially red flower varieties of O. dubium. Our research thus provides a framework for the application of CRISPR/Cas9 technology to improve this ornamental crop.

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“…Additionally, since LCYb1 is nearly present in all plant species and is an evolutionarily ancient and conserved gene, study of citrus LCYb1 promoter will not only help us to understand the transcriptional regulatory mechanism of LCYb1 in citrus, but also promote the understanding of LCYb1 in other species. Although the promoters of LCYb2 have been isolated and functionally analyzed in tomato ( Dalal et al, 2010 ) and watermelon ( Bang et al, 2014 ), little information is available regarding the LCYb1 promoter.…”

Section: Introductionmentioning

confidence: 99%

Isolation and Functional Characterization of a Lycopene β-cyclase Gene Promoter from Citrus

Zhang

Zheng

et al. 2016

Front. Plant Sci.

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Lycopene β-cyclases are key enzymes located at the branch point of the carotenoid biosynthesis pathway. However, the transcriptional regulatory mechanisms of LCYb1 in citrus with abundant carotenoid accumulation are still unclear. To understand the molecular basis of CsLCYb1 expression, we isolated and functionally characterized the 5′ upstream sequences of CsLCYb1 from citrus. The full-length CsLCYb1 promoter and a series of its 5′ deletions were fused to the β-glucuronidase (GUS) reporter gene and transferred into different plants (tomato, Arabidopsis and citrus callus) to test the promoter activities. The results of all transgenic species showed that the 1584 bp upstream region from the translational start site displayed maximal promoter activity, and the minimal promoter containing 746 bp upstream sequences was sufficient for strong basal promoter activity. Furthermore, the CsLCYb1 promoter activity was developmentally and tissue-specially regulated in transgenic Arabidopsis, and it was affected by multiple hormones and environmental cues in transgenic citrus callus under various treatments. Finer deletion analysis identified an enhancer element existing as a tandem repeat in the promoter region between -574 to -513 bp and conferring strong promoter activity. The copy numbers of the enhancer element differed among various citrus species, leading to the development of a derived simple sequence repeat marker to distinguish different species. In conclusion, this study elucidates the expression characteristics of the LCYb1 promoter from citrus and further identifies a novel enhancer element required for the promoter activity. The characterized promoter fragment would be an ideal candidate for genetic engineering and seeking of upstream trans-acting elements.

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Watermelon lycopene β-cyclase: promoter characterization leads to the development of a PCR marker for allelic selection

Cited by 13 publications

References 49 publications

Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content

Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content

Transcriptome Profiling of Ornithogalum dubium Leaves and Flowers to Identify Key Carotenoid Genes for CRISPR Gene Editing

Isolation and Functional Characterization of a Lycopene β-cyclase Gene Promoter from Citrus

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