Mistaken Identity: Clarification of Rubus coreanus Miquel (Bokbunja)

Lee, Jungmin; Dossett, Michael; Finn, Chad E.

doi:10.3390/molecules190710524

Cited by 15 publications

(4 citation statements)

References 35 publications

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“…coreanus [ 6 ]. Unfortunately, contrary to what is reported in their paper [ 7 ], the species they studied was the commercially grown North American black raspberry R . occidentalis , often confused with R .…”

Section: Introductionmentioning

confidence: 73%

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Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

Chen

Liu

et al. 2018

International Journal of Genomics

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The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. coreanus reads (125 bp in length) generated by RNA sequencing from fruits at three representative developmental stages. We also used the recently released draft genome of R. occidentalis to perform reference-guided assembly. We inferred a final 95,845-transcript reference for R. coreanus. Of these genetic resources, 66,597 (69.5%) were annotated. Based on these results, we carried out a comprehensive analysis of differentially expressed genes. Flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis pathways were significantly enriched throughout the ripening process. We identified 23 transcripts involved in the flavonoid biosynthesis pathway whose expression perfectly paralleled changes in the metabolites. Additionally, we identified 119 nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-coding genes, involved in pathogen resistance, of which 74 were in the completely conserved domain. These results provide, for the first time, genome-wide genetic information for understanding developmental regulation of R. coreanus fruits. They have the potential for use in breeding through functional genetic approaches in the near future.

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Section: Introductionmentioning

confidence: 73%

“…occidentalis (which they mistook for R . coreanus [ 6 ]) from the perspective of fruit morphology and phenological traits [ 7 ], transcriptome analysis involved mRNA isolated only from fruits sampled 20 days after anthesis at an intermediate stage of ripening [ 6 ]. This may have underestimated the genetic information for the species.…”

Section: Resultsmentioning

confidence: 99%

Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

Chen

Liu

et al. 2018

International Journal of Genomics

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“…Phenolic and flavonoid compound profiles of RO extract (unripe, extract with 50% ethanol) were analyzed as previously described (Choi et al ., ): ellagic acid 6,352 µg/g; gallic acid 484 µg/g; rutin 160 µg/g; quercetin 114 µg/g; ferulic acid 100 µg/g; caffeic acid 82 µg/g; luteolin 42 µg/g; myricetin 22 µg/g; and kaempferol 12 µg/g. Definite anthocyanins levels of RO extract investigated in this study were not available, although molecular profiles were presented in several previous studies (Lee et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Effect ofRubus OccidentalisExtract on Metabolic Parameters in Subjects with Prediabetes: A Proof-of-concept, Randomized, Double-blind, Placebo-controlled Clinical Trial

Kim

Lee

et al. 2016

Phytother. Res.

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Rubus occidentalis (RO) has beneficial effects on glucose and lipid profiles in vitro. The aim of the study was to investigate RO extract effect on metabolic parameters in prediabetic patients, adopting a 12-week, randomized, double-blind, placebo-controlled trial. Forty-four patients (age 59.0 ± 8.2 years, 70.5% females, HbA1c 5.8 ± 0.4%) were divided into placebo (n = 13), low-dose RO extract (LRE; n = 14), or high-dose RO extract (HRE; n = 17) groups. Either 900 or 1800 mg per day of RO extract was administered orally. Area under the curve for glucose obtained 2 h after a 75-g oral glucose tolerance test was significantly decreased in the HRE group, compared with the placebo group (-28.1 ± 42.4 vs. +13.4 ± 52.6 mg/dL, p < 0.05). Homoeostasis model assessment-B was increased (+17.11 ± 10.69, +5.24 ± 4.10, and +0.86 ± 6.01 in HRE, LRE, and placebo, respectively, p < 0.05). Serum levels of monocyte chemoattractant protein-1 and oxidized low-density lipoprotein were significantly decreased by treatment in a dose-dependent manner (monocyte chemoattractant protein-1: -35.0 ± 21.2, +8.4 ± 18.1, and +24.2 ± 14.5; oxidized low-density lipoprotein: -19.7 ± 8.5, -13.1 ± 7.2, and -2.2 ± 11.0 in the HRE, LRE, and placebo, respectively, p < 0.05). The results support the beneficial effects of RO extract on the control of glycemia and vascular inflammation in prediabetic patients. (ClinicalTrials.gov: NCT01964703). Copyright © 2016 John Wiley & Sons, Ltd.

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“…The genes that were upregulated during fruit ripening consisted of those involved in hydrolase activity, cell wall degradation, sugar transport, and anthocyanin accumulation and biosynthesis, among others. Genes involved in anthocyanin accumulation during fruit ripening were also previously identified in what was erroneously labelled R. coreanus 103 and is, in fact, R. occidentalis 104 . A type I chalcone Isomerase, RcMCHI2 (Unigene 18325), from R. coreanus complemented an Arabidopsis testa 5–1 mutant and restored its ability to produce anthocyanin pigments in the cotyledon and hypocotyl and to accumulate delphinidin 3-O-rutinoside and cyaniding 3-O-rutinoside.…”

Section: Introductionmentioning

confidence: 93%

Genetic and genomic resources for Rubus breeding: a roadmap for the future

et al. 2019

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Rubus fruits are high-value crops that are sought after by consumers for their flavor, visual appeal, and health benefits. To meet this demand, production of red and black raspberries (R. idaeus L. and R. occidentalis L.), blackberries (R. subgenus Rubus), and hybrids, such as Boysenberry and marionberry, is growing worldwide. Rubus breeding programmes are continually striving to improve flavor, texture, machine harvestability, and yield, provide pest and disease resistance, improve storage and processing properties, and optimize fruits and plants for different production and harvest systems. Breeders face numerous challenges, such as polyploidy, the lack of genetic diversity in many of the elite cultivars, and until recently, the relative shortage of genetic and genomic resources available for Rubus. This review will highlight the development of continually improving genetic maps, the identification of Quantitative Trait Loci (QTL)s controlling key traits, draft genomes for red and black raspberry, and efforts to improve gene models. The development of genetic maps and markers, the molecular characterization of wild species and germplasm, and high-throughput genotyping platforms will expedite breeding of improved cultivars. Fully sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.

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Mistaken Identity: Clarification of Rubus coreanus Miquel (Bokbunja)

Cited by 15 publications

References 35 publications

Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

Effect ofRubus OccidentalisExtract on Metabolic Parameters in Subjects with Prediabetes: A Proof-of-concept, Randomized, Double-blind, Placebo-controlled Clinical Trial

Genetic and genomic resources for Rubus breeding: a roadmap for the future

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