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Fang T, Wang M, He R, Chen Q, He D, Chen X, Li Y, Ren R, Yu W, Zeng L. A 224-bp Indel in the Promoter of PeMYB114 Accounts for Anthocyanin Accumulation of Skin in Passion Fruit ( Passiflora spp.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10138-10148. [PMID: 38637271 DOI: 10.1021/acs.jafc.4c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Passion fruit (Passiflora spp.) is an important fruit tree in the family Passifloraceae. The color of the fruit skin, a significant agricultural trait, is determined by the content of anthocyanin in passion fruit. However, the regulatory mechanisms behind the accumulation of anthocyanin in different passion fruit skin colors remain unclear. In the study, we identified and characterized a R2R3-MYB transcription factor, PeMYB114, which functions as a transcriptional activator in anthocyanin biosynthesis. Yeast one-hybrid system and dual-luciferase analysis showed that PeMYB114 could directly activate the expression of anthocyanin structural genes (PeCHS and PeDFR). Furthermore, a natural variation in the promoter region of PeMYB114 alters its expression. PeMYB114purple accessions with the 224-bp insertion have a higher anthocyanin level than PeMYB114yellow accessions with the 224-bp deletion. The findings enhance our understanding of anthocyanin accumulation in fruits and provide genetic resources for genome design for improving passion fruit quality.
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Affiliation(s)
- Ting Fang
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengzhen Wang
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruijie He
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiaowen Chen
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dayi He
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuerong Chen
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongkang Li
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Ren
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weijun Yu
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lihui Zeng
- College of Horticulture, Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Feng P, Wang Y, Wen J, Ren Y, Zhong Q, Li Q. Cloning and Analysis of Expression of Genes Related to Carotenoid Metabolism in Different Fruit Color Mutants of Pepper ( Capsicum annuum L.). Genes (Basel) 2024; 15:315. [PMID: 38540374 PMCID: PMC10970409 DOI: 10.3390/genes15030315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 06/14/2024] Open
Abstract
The formation of fruit color in pepper is closely related to the processes of carotenoid metabolism. In this study, red wild-type pepper XHB, SP01, PC01 and their corresponding mutants H0809 (orange), SP02 (yellow), and PC02 (orange) were used as research materials. The Ggps, Psy, Lcyb, Crtz, Zep, and Ccs genes involved in carotenoid biosynthesis were cloned, and bioinformatics and expression analyses were carried out. The results showed that the full lengths of the six genes were 1110 bp, 2844 bp, 1497 bp, 2025 bp, 510 bp, and 1497 bp, and they encoded 369, 419, 498, 315, 169, and 498 amino acids, respectively. Except for the full-length Ccs gene, which could not be amplified in the yellow mutant SP02 and the orange mutant PC02, the complete full-length sequences of the other genes could be amplified in different materials, indicating that the formation of fruit color in the SP02 and PC02 mutants could be closely related to the deletion or mutation of the Ccs gene. The analytical results of real-time quantitative reverse transcription PCR (qRT-PCR) showed that the Ggps, Psy, Lcyb, Crtz, and Zep genes were expressed at different developmental stages of three pairs of mature-fruit-colored materials, but their patterns of expression were not consistent. The orange mutant H0809 could be amplified to the full Ccs gene sequence, but its expression was maintained at a lower level. It showed a significant difference in expression compared with the wild-type XHB, indicating that the formation of orange mutant H0809 fruit color could be closely related to the different regulatory pattern of Ccs expression. The results provide a theoretical basis for in-depth understanding of the molecular regulatory mechanism of the formation of color in pepper fruit.
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Affiliation(s)
| | | | | | | | - Qiwen Zhong
- Academy of Agricultural and Forestry Sciences, Qinghai University/Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China; (P.F.); (Y.W.); (J.W.); (Y.R.); (Q.L.)
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Bashir T, Ul Haq SA, Masoom S, Ibdah M, Husaini AM. Quality trait improvement in horticultural crops: OMICS and modern biotechnological approaches. Mol Biol Rep 2023; 50:8729-8742. [PMID: 37642759 DOI: 10.1007/s11033-023-08728-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023]
Abstract
Horticultural crops are an essential part of food and nutritional security. Moreover, these form an integral part of the agricultural economy and have enormous economic potential. They are a rich source of nutrients that are beneficial to human health. Plant breeding of horticultural crops has focussed primarily on increasing the productivity and related traits of these crops. However, fruit and vegetable quality is paramount to their perishability, marketability, and consumer acceptance. The improved nutritional value is beneficial to underprivileged and undernourished communities. Due to a declining genetic base, conventional plant breeding does not contribute much to quality improvement as the existing natural allelic variations and crossing barriers between cultivated and wild species limit it. Over the past two decades, 'omics' and modern biotechnological approaches have made it possible to decode the complex genomes of crop plants, assign functions to the otherwise many unknown genes, and develop genome-wide DNA markers. Genetic engineering has enabled the validation of these genes and the introduction of crucial agronomic traits influencing various quality parameters directly or indirectly. This review discusses the significant advances in the quality improvement of horticultural crops, including shelf life, aroma, browning, nutritional value, colour, and many other related traits.
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Affiliation(s)
- Tanzeel Bashir
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Syed Anam Ul Haq
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Salsabeel Masoom
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Mwafaq Ibdah
- Newe Yaar Research Center, Agricultural Research Organization, Ramat Yishay, 30095, Israel
| | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India.
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Rosas-Saavedra C, Quiroz LF, Parra S, Gonzalez-Calquin C, Arias D, Ocarez N, Lopez F, Stange C. Putative Daucus carota Capsanthin-Capsorubin Synthase (DcCCS) Possesses Lycopene β-Cyclase Activity, Boosts Carotenoid Levels, and Increases Salt Tolerance in Heterologous Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2788. [PMID: 37570943 PMCID: PMC10421225 DOI: 10.3390/plants12152788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/08/2023] [Accepted: 07/17/2023] [Indexed: 08/13/2023]
Abstract
Plant carotenoids are synthesized and accumulated in plastids through a highly regulated pathway. Lycopene β-cyclase (LCYB) is a key enzyme involved directly in the synthesis of α-carotene and β-carotene through the cyclization of trans-lycopene. Daucus carota harbors two LCYB genes, of which DcLCYB2 (annotated as CCS-Like) is mostly expressed in mature storage roots, an organ that accumulates high α-carotene and β-carotene content. In this work, we determined that DcLCYB2 of the orange Nantes variety presents plastid localization and encodes for a functional LCYB enzyme determined by means of heterologous complementation in Escherichia coli. Also, ectopic expression of DcLCYB2 in tobacco (Nicotiana tabacum) and kiwi (Actinidia deliciosa) plants increases total carotenoid content showing its functional role in plants. In addition, transgenic tobacco T2 homozygous plants showed better performance under chronic salt treatment, while kiwi transgenic calli also presented a higher survival rate under salt treatments than control calli. Our results allow us to propose DcLCYB2 as a prime candidate to engineer carotenoid biofortified crops as well as crops resilient to saline environments.
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Affiliation(s)
- Carolina Rosas-Saavedra
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Luis Felipe Quiroz
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Samuel Parra
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Christian Gonzalez-Calquin
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Daniela Arias
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Nallat Ocarez
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
- Instituto de Investigaciones Agropecuarias (INIA), La Platina, Research Centre, Av. Santa Rosa 11610, Santiago 8820000, Chile
| | - Franco Lopez
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Claudia Stange
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
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De Mori G, Cipriani G. Marker-Assisted Selection in Breeding for Fruit Trait Improvement: A Review. Int J Mol Sci 2023; 24:ijms24108984. [PMID: 37240329 DOI: 10.3390/ijms24108984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst species to work with in terms of genetics and breeding. Most are characterized by large trees, long juvenile periods, and intensive agricultural practice, and environmental variability plays an important role in the heritability evaluations of every single important trait. Although vegetative propagation allows for the production of a significant number of clonal replicates for the evaluation of environmental effects and genotype × environment interactions, the spaces required for plant cultivation and the intensity of work necessary for phenotypic surveys slow down the work of researchers. Fruit breeders are very often interested in fruit traits: size, weight, sugar and acid content, ripening time, fruit storability, and post-harvest practices, among other traits relevant to each individual species. The translation of trait loci and whole-genome sequences into diagnostic genetic markers that are effective and affordable for use by breeders, who must choose genetically superior parents and subsequently choose genetically superior individuals among their progeny, is one of the most difficult tasks still facing tree fruit geneticists. The availability of updated sequencing techniques and powerful software tools offered the opportunity to mine tens of fruit genomes to find out sequence variants potentially useful as molecular markers. This review is devoted to analysing what has been the role of molecular markers in assisting breeders in selection processes, with an emphasis on the fruit traits of the most important fruit crops for which examples of trustworthy molecular markers have been developed, such as the MDo.chr9.4 marker for red skin colour in apples, the CCD4-based marker CPRFC1, and LG3_13.146 marker for flesh colour in peaches, papayas, and cherries, respectively.
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Affiliation(s)
- Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Guido Cipriani
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
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Zacarías-García J, Cronje PJ, Diretto G, Zacarías L, Rodrigo MJ. A comprehensive analysis of carotenoids metabolism in two red-fleshed mutants of Navel and Valencia sweet oranges ( Citrus sinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:1034204. [PMID: 36330241 PMCID: PMC9623303 DOI: 10.3389/fpls.2022.1034204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
Abstract
Kirkwood Navel and Ruby Valencia are two spontaneous bud mutations of the respective parental lines of sweet orange (Citrus sinensis) Palmer Navel and Olinda Valencia, showing an atypical red pigmentation of the pulp. These red-fleshed varieties are commercially available and highly attractive for consumers but their carotenoid metabolism and the basis of the mutation have not been investigated. The red colour of Kirkwood and Ruby pulp was observed from the very early stages of fruit development until full maturity and associated with an altered carotenoid profiling. The red-fleshed varieties accumulated from 6- up to 1000-times more total carotenoids compared to the standard oranges. Specifically, the pulp of Kirkwood and Ruby accumulated large amounts of phytoene and phytofluene, and moderate contents of lycopene. Moreover, the red-fleshed oranges contained other unusual carotenes as δ-carotene, and lower concentrations of downstream products such as β,β-xanthophylls, abscisic acid (ABA) and ABA-glucosyl ester. This peculiar profile was associated with chromoplasts with lycopene crystalloid structures and round vesicles likely containing colourless carotenes. The flavedo and leaves of Kirkwood and Ruby showed minor changes in carotenoids, mainly limited to higher levels of phytoene. The carotenoid composition in Kirkwood and Ruby fruits was not explained by differences in the transcriptional profile of 26 genes related to carotenoid metabolism, covering the main steps of biosynthesis, catabolism and other processes related to carotenoid accumulation. Moreover, sequence analysis of the lycopene cyclase genes revealed no alterations in those of the red-fleshed oranges compared to the genes of the standard varieties. A striking event observed in Kirkwood and Ruby trees was the reddish coloration of the inner side of the bark tissue, with larger amounts of phytoene, accumulation of lycopene and lower ABA content. These observation lead to the conclusion that the mutation is not only manifested in fruit, affecting other carotenogenic tissues of the mutant plants, but with different consequences in the carotenoid profile. Overall, the carotenoid composition in the red-fleshed mutants suggests a partial blockage of the lycopene β-cyclization in the carotenoid pathway, rendering a high accumulation of carotenes upstream lycopene and a reduced flow to downstream xanthophylls and ABA.
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Affiliation(s)
- Jaime Zacarías-García
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Paul J. Cronje
- Citrus Research International (CRI), Department of Horticultural Sciences, University of Stellenbosch, Stellenbosch, South Africa
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Biotechnology Laboratory, Casaccia Research Center, Roma, Italy
| | - Lorenzo Zacarías
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - María Jesús Rodrigo
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
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Advances in engineering the production of the natural red pigment lycopene: A systematic review from a biotechnology perspective. J Adv Res 2022; 46:31-47. [PMID: 35753652 PMCID: PMC10105081 DOI: 10.1016/j.jare.2022.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/31/2022] [Accepted: 06/20/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Lycopene is a natural red compound with potent antioxidant activity that can be utilized both as pigment and as a raw material in functional food, and so possesses good commercial prospects. The biosynthetic pathway has already been documented, which provides the foundation for lycopene production using biotechnology. AIM OF REVIEW Although lycopene production has begun to take shape, there is still an urgent need to alleviate the yield of lycopene. Progress in this area can provide useful reference for metabolic engineering of lycopene production utilizing multiple approaches. Key scientific concepts of review Using conventional microbial fermentation approaches, biotechnologists have enhanced the yield of lycopene by selecting suitable host strains, utilizing various additives, and optimizing culture conditions. With the development of modern biotechnology, genetic engineering, protein engineering, and metabolic engineering have been applied for lycopene production. Extraction from natural plants is the main way for lycopene production at present. Based on the molecular mechanism of lycopene accumulation, the production of lycopene by plant bioreactor through genetic engineering has a good prospect. Here we summarized common strategies for optimizing lycopene production engineering from a biotechnology perspective, which are mainly carried out by microbial cultivation. We reviewed the challenges and limitations of this approach, summarized the critical aspects, and provided suggestions with the aim of potential future breakthroughs for lycopene production in plants.
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Tian L, Shi J, Yang L, Wei A. Molecular Cloning and Functional Analysis of DXS and FPS Genes from Zanthoxylum bungeanum Maxim. Foods 2022; 11:foods11121746. [PMID: 35741944 PMCID: PMC9223008 DOI: 10.3390/foods11121746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/04/2023] Open
Abstract
Zanthoxylum bungeanum Maxim. (Z. bungeanum) has attracted attention for its rich aroma. The aroma of Z. bungeanum is mainly volatile terpenes synthesized by plant terpene metabolic pathways. However, there is little information on Z. bungeanum terpene metabolic gene. In this study, the coding sequence of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and farnesyl pyrophosphate synthase (FPS) were cloned from Z. bungeanum cv. 'Fengxiandahongpao.' ZbDXS and ZbFPS genes from Z. bungeanum with CDS lengths of 2172 bp and 1029 bp, respectively. The bioinformatics results showed that Z. bungeanum was closely related to citrus, and it was deduced that ZbFPS were hydrophilic proteins without the transmembrane domain. Subcellular localization prediction indicated that ZbDXS was most likely to be located in chloroplasts, and ZbFPS was most likely to be in mitochondria. Meanwhile, the 3D protein structure showed that ZbDXS and ZbFPS were mainly composed of α-helices, which were folded into a single domain. In vitro enzyme activity experiments showed that purified proteins ZbDXS and ZbFPS had the functions of DXS enzyme and FPS enzyme. Transient expression of ZbDXS and ZbFPS in tobacco significantly increased tobacco's terpene content. Moreover, ZbDXS and ZbFPS were expressed in different tissues of Z. bungeanum, and the relative expression of the two genes was the highest in fruits. Therefore, this suggests that ZbDXS and ZbFPS are positively related to terpene synthesis. This study could provide reference genes for improving Z. bungeanum breeding as well as for the Rutaceae research.
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Affiliation(s)
- Lu Tian
- College of Forestry, Northwest A&F University, Yangling, Xianyang 712100, China; (L.T.); (J.S.); (L.Y.)
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang 712100, China
| | - Jingwei Shi
- College of Forestry, Northwest A&F University, Yangling, Xianyang 712100, China; (L.T.); (J.S.); (L.Y.)
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang 712100, China
| | - Lin Yang
- College of Forestry, Northwest A&F University, Yangling, Xianyang 712100, China; (L.T.); (J.S.); (L.Y.)
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, Xianyang 712100, China; (L.T.); (J.S.); (L.Y.)
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang 712100, China
- Correspondence: ; Tel.: +86-029-8708-2211
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Shibaya T, Kuroda C, Tsuruoka H, Minami C, Obara A, Nakayama S, Kishida Y, Fujii T, Isobe S. Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F 2 populations. Sci Rep 2022; 12:8063. [PMID: 35577860 PMCID: PMC9110420 DOI: 10.1038/s41598-022-11544-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/18/2022] [Indexed: 11/21/2022] Open
Abstract
Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed an association analysis based on a general liner model using genome-wide single nucleotide polymorphism (SNPs) in two F2 populations, both derived from crosses of orange root carrots bred in Japan. The analysis revealed 21 significant quantitative trait loci (QTLs). To validate the detection of the QTLs, we also performed a QTL analysis based on a composite interval mapping of these populations and detected 32 QTLs. Eleven of the QTLs were detected by both the association and QTL analyses. The physical position of some QTLs suggested two possible candidate genes, an Orange (Or) gene for visual color evaluation, and the α- and β-carotene contents and a chromoplast-specific lycopene β-cyclase (CYC-B) gene for the β/α carotene ratio. A KASP marker developed on the Or distinguished a quantitative color difference in a different, related breeding line. The detected QTLs and the DNA marker will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots.
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Affiliation(s)
- Taeko Shibaya
- Fujii Seed Co. Ltd., Fujii Seed, 2-12-38 Juso-higashi, Yodogawa-ku, Osaka, 532-0023, Japan.
| | - Chika Kuroda
- Fujii Seed Co. Ltd., Fujii Seed, 2-12-38 Juso-higashi, Yodogawa-ku, Osaka, 532-0023, Japan
| | - Hisano Tsuruoka
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Chiharu Minami
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Akiko Obara
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | | | - Yoshie Kishida
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Takayoshi Fujii
- Fujii Seed Co. Ltd., Fujii Seed, 2-12-38 Juso-higashi, Yodogawa-ku, Osaka, 532-0023, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
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Mathiazhagan M, Chidambara B, Hunashikatti LR, Ravishankar KV. Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content. Genes (Basel) 2021; 12:1881. [PMID: 34946829 PMCID: PMC8701245 DOI: 10.3390/genes12121881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
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Affiliation(s)
| | | | | | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru 560089, India; (M.M.); (B.C.); (L.R.H.)
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Jo SH, Park HJ, Lee A, Jung H, Min SR, Lee HJ, Kim HS, Jung M, Hyun JY, Kim YS, Cho HS. A single amino acid insertion in LCYB2 deflects carotenoid biosynthesis in red carrot. PLANT CELL REPORTS 2021; 40:1793-1795. [PMID: 34268606 DOI: 10.1007/s00299-021-02741-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Sung Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Min Jung
- Department of Biotechnology, NongWoo Bio, Anseong, 17558, Korea
| | - Ji Young Hyun
- Department of Biotechnology, NongWoo Bio, Anseong, 17558, Korea
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo Bio, Anseong, 17558, Korea.
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea.
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12
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Zhu K, Sun Q, Chen H, Mei X, Lu S, Ye J, Chai L, Xu Q, Deng X. Ethylene activation of carotenoid biosynthesis by a novel transcription factor CsERF061. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3137-3154. [PMID: 33543285 DOI: 10.1093/jxb/erab047] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 02/01/2021] [Indexed: 05/24/2023]
Abstract
Chromoplast-specific lycopene β-cyclase (LCYb2) is a critical carotenogenic enzyme, which controls the massive accumulation of downstream carotenoids, especially provitamin A carotenoids, in citrus. Its regulatory metabolism is largely unknown. Here, we identified a group I ethylene response factor, CsERF061, in citrus by yeast one-hybrid screen with the promoter of LCYb2. The expression of CsERF061 was induced by ethylene. Transcript and protein levels of CsERF061 were increased during fruit development and coloration. CsERF061 is a nucleus-localized transcriptional activator, which directly binds to the promoter of LCYb2 and activates its expression. Overexpression of CsERF061 in citrus calli and tomato fruits enhanced carotenoid accumulation by increasing the expression of key carotenoid pathway genes, and increased the number of chromoplasts needed to sequester the elevated concentrations of carotenoids, which was accompanied by changes in the concentrations of abscisic acid and gibberellin. Electrophoretic mobility shift and dual-luciferase assays verified that CsERF061 activates the promoters of nine other key carotenoid pathway genes, PSY1, PDS, CRTISO, LCYb1, BCH, ZEP, NCED3, CCD1, and CCD4, revealing the multitargeted regulation of CsERF061. Collectively, our findings decipher a novel regulatory network of carotenoid enhancement by CsERF061, induced by ethylene, which will be useful for manipulating carotenoid accumulation in citrus and other plants.
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Affiliation(s)
- Kaijie Zhu
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Quan Sun
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hongyan Chen
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xuehan Mei
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Suwen Lu
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
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13
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Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits. Sci Rep 2021; 11:292. [PMID: 33431939 PMCID: PMC7801719 DOI: 10.1038/s41598-020-79401-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
Papaya is a tropical and climacteric fruit that is recognized for its nutritional benefits and medicinal applications. Its fruits ripen quickly and show a drastic fruit softening, leading to great post-harvest losses. To overcome this scenario, breeding programs of papaya must invest in exploring the available genetic variation to continue developing superior cultivars with improved fruit quality traits. The objective of this study was to perform a whole-genome genotyping (WGG) of papaya, predict the effects of the identified variants, and develop a list of ripening-related genes (RRGs) with linked variants. The Formosa elite lines of papaya Sekati and JS-12 were submitted to WGG with an Illumina Miseq platform. The effects of variants were predicted using the snpEff program. A total of 28,451 SNPs having Ts/Tv (Transition/Transversion) ratio of 2.45 and 1,982 small insertions/deletions (InDels) were identified. Most variant effects were predicted in non-coding regions, with only 2,104 and 138 effects placed in exons and splice site regions, respectively. A total of 106 RRGs were found to be associated with 460 variants, which may be converted into PCR markers to facilitate genetic mapping and diversity studies and to apply marker-assisted selection (MAS) for specific traits in papaya breeding programs.
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14
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Zhao Z, Liu Z, Mao X. Biotechnological Advances in Lycopene β-Cyclases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11895-11907. [PMID: 33073992 DOI: 10.1021/acs.jafc.0c04814] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Lycopene β-cyclase is one of the key enzymes in the biosynthesis of carotenoids, which catalyzes the β-cyclization of both ends of lycopene to produce β-carotene. Lycopene β-cyclases are found in a wide range of sources, mainly plants and microorganisms. Lycopene β-cyclases have been extensively studied for their important catalytic activity, including for use in genetic engineering to modify plants and microorganisms, as a blocking target for lycopene industrial production strains, and for their genetic and physiological effects related to microorganic and plant biological traits. This review of lycopene β-cyclases summarizes the major studies on their basic classification, functional activity, metabolic engineering, and plant science.
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Affiliation(s)
- Zilong Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Zhen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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15
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Zhu K, Zheng X, Ye J, Jiang Q, Chen H, Mei X, Wurtzel ET, Deng X. Building the Synthetic Biology Toolbox with Enzyme Variants to Expand Opportunities for Biofortification of Provitamin A and Other Health-Promoting Carotenoids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12048-12057. [PMID: 33073979 DOI: 10.1021/acs.jafc.0c04740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Carotenoids are a large class of structures that are important in human health and include both provitamin A and nonprovitamin A compounds. Vitamin A deficiency is a global health problem that can be alleviated by enriching provitamin A carotenoids in a range of food crops. Suitable plants for biofortification are those with high levels of the provitamin A biosynthetic precursor, lycopene, which is enzymatically converted by lycopene β-cyclase (LCYB) to β-carotene, a provitamin A carotenoid. Crops, such as citrus, naturally accumulate high levels of provitamin A and other health-promoting carotenoids. Such plants may have useful genes to expand the synthetic biology toolbox for producing a range of phenotypes, including both high provitamin A crops and crops with unique compositions of health-promoting carotenoids. To examine enzyme variants having different activity levels, we introduced two citrus LCYB alleles into tomato, a plant with fruit rich in lycopene. Overexpression in tomato of the stronger allele of the citrus chromoplast-specific lycopene β-cyclase (CsLCYb2a) produced "golden" transgenic tomato fruits with 9.3-fold increased levels of β-carotene at up to 1.5 mg/g dry weight. The use of the weaker allele, CsLCYb2b, also led to enhanced levels of β-carotene but in the context of a more heterogeneous composition of carotenoids. From a synthetic biology standpoint, these allelic differences have value for producing cultivars with unique carotenoid profiles. Overexpression of the citrus LCYB genes was accompanied by increased expression of other genes encoding carotenoid biosynthetic enzymes and increased size and number of chromoplasts needed to sequester the elevated levels of carotenoids in the transgenic tomato fruits. The overexpression of the citrus LCYB genes also led to a pleiotropic effect on profiles of phytohormones and primary metabolites. Our findings show that enzyme variants are essential synthetic biology parts needed to create a wider range of metabolic engineering products. In this case, strong and weak variants of LCYB proved useful in creating dietary sources to alleviate vitamin A deficiency or, alternatively, to create crops with a heterogeneous composition including provitamin A and healthful, nonprovitamin A carotenoids.
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Affiliation(s)
- Kaijie Zhu
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Department of Biological Sciences, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York 10468, United States
| | - Xiongjie Zheng
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qihang Jiang
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hongyan Chen
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xuehan Mei
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Eleanore T Wurtzel
- Department of Biological Sciences, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York 10468, United States
- The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016-4309, United States
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of MOE (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
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16
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Jang SJ, Jeong HB, Jung A, Kang MY, Kim S, Ha SH, Kwon JK, Kang BC. Phytoene synthase 2 can compensate for the absence of PSY1 in the control of color in Capsicum fruit. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3417-3427. [PMID: 32219321 PMCID: PMC7475241 DOI: 10.1093/jxb/eraa155] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/25/2020] [Indexed: 05/22/2023]
Abstract
Phytoene synthase 1 (PSY1) and capsanthin-capsorubin synthase (CCS) are two major genes responsible for fruit color variation in pepper (Capsicum spp.). However, the role of PSY2 remains unknown. We used a systemic approach to examine the genetic factors responsible for the yellow fruit color of C. annuum 'MicroPep Yellow' (MY) and to determine the role of PSY2 in fruit color. We detected complete deletion of PSY1 and a retrotransposon insertion in CCS. Despite the loss of PSY1 and CCS function, both MY and mutant F2 plants from a cross between MY and the 'MicroPep Red' (MR) accumulated basal levels of carotenoids, indicating that other PSY genes may complement the loss of PSY1. qRT-PCR analysis indicated that PSY2 was constitutively expressed in both MR and MY fruits, and a color complementation assay using Escherichia coli revealed that PSY2 was capable of biosynthesizing a carotenoid. Virus-induced gene silencing of PSY2 in MY resulted in white fruits. These findings indicate that PSY2 can compensate for the absence of PSY1 in pepper fruit, resulting in the yellow color of MY fruits.
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Affiliation(s)
- So-Jeong Jang
- Department of Plant Science, Plant Genomics & Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Hyo-Bong Jeong
- Department of Plant Science, Plant Genomics & Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Ayoung Jung
- Department of Plant Science, Plant Genomics & Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Min-Young Kang
- Department of Plant Science, Plant Genomics & Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Suna Kim
- Food and Nutrition in Home Economics, Korea National Open University, Jongno-Gu, Seoul, Republic of Korea
| | - Sun-Hwa Ha
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics & Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics & Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
- Correspondence:
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Fang J, Wood AM, Chen Y, Yue J, Ming R. Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset. BMC Genomics 2020; 21:398. [PMID: 32532215 PMCID: PMC7291442 DOI: 10.1186/s12864-020-06804-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 06/05/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. RESULTS In this study, a total of more than 74 million Illumina reads for progenitor 'Sunset' were mapped onto transgenic papaya 'SunUp' reference genome. 310,364 single nucleotide polymorphisms (SNPs) and 34,071 small Inserts/deletions (InDels) were detected between 'Sunset' and 'SunUp'. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4 × 10- 4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. A total of 3430 nuclear plastid DNA (NUPT) and 2764 nuclear mitochondrial DNA (NUMT) junction sites have been found in 'SunUp', which is proportionally higher than the predicted total NUPT and NUMT junction sites in 'Sunset' (3346 and 2745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by 'SunUp' and 'Sunset'. The average identity between 'SunUp' specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by 'SunUp' and 'Sunset'. Six 'SunUp' organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18 ~ 100%). None of the paired-end spans of mapped 'Sunset' reads were elongated by any 'SunUp' transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions. CONCLUSIONS Comparative whole-genome analyses between 'SunUp' and 'Sunset' provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.
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Affiliation(s)
- Jingping Fang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.,Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, 350117, Fujian, China.,FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew Michael Wood
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.,Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Jingjing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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18
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Wei Z, Arazi T, Hod N, Zohar M, Isaacson T, Doron-Faigenboim A, Reznik N, Yedidia I. Transcriptome Profiling of Ornithogalum dubium Leaves and Flowers to Identify Key Carotenoid Genes for CRISPR Gene Editing. PLANTS 2020; 9:plants9040540. [PMID: 32326260 PMCID: PMC7238968 DOI: 10.3390/plants9040540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 11/16/2022]
Abstract
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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Affiliation(s)
- Zunzheng Wei
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Tzahi Arazi
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Nofar Hod
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Matat Zohar
- Newe Yaar Research Center, Agricultural Research Organization, Ramat Yishay 30095, Israel; (M.Z.); (T.I.)
| | - Tal Isaacson
- Newe Yaar Research Center, Agricultural Research Organization, Ramat Yishay 30095, Israel; (M.Z.); (T.I.)
| | - Adi Doron-Faigenboim
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Noam Reznik
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Iris Yedidia
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
- Correspondence:
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Wang Y, Singh R, Tong E, Tang M, Zheng L, Fang H, Li R, Guo L, Song J, Srinivasan R, Sharma A, Lin L, Trujillo JA, Manshardt R, Chen LY, Ming R, Yu Q. Positional cloning and characterization of the papaya diminutive mutant reveal a truncating mutation in the CpMMS19 gene. THE NEW PHYTOLOGIST 2020; 225:2006-2021. [PMID: 31733154 DOI: 10.1111/nph.16325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
The papaya diminutive mutant exhibits miniature stature, retarded growth and reduced fertility. This undesirable mutation appeared in the variety 'Sunset', the progenitor of the transgenic line 'SunUp', and was accidentally carried forward into breeding populations. The diminutive mutation was mapped to chromosome 2 and fine mapped to scaffold 25. Sequencing of a bacterial artificial chromosome in the fine mapped region led to the identification of the target gene responsible for the diminutive mutant, a gene orthologous to MMS19 with a 36.8 kb deletion co-segregating with the diminutive mutant. The genomic sequence of CpMMS19 is 62 kb, consisting of 20 exons and 19 introns. It encodes a protein of 1143 amino acids while the diminutive allele encodes a truncated protein of 287 amino acids. Expression of the full-length CpMMS19 was able to complement the thermosensitive growth of the yeast mms19 deletion mutant while expression of the diminutive allele resulted in increased thermosensitivity. Over-expression of the diminutive allele in Arabidopsis met18 mutant results in a high frequency of seed abortion. The papaya diminutive phenotype is caused by an alteration in gene function rather than a loss-of-function mutation. SCAR (sequence characterized amplified region) markers were developed for rapid detection of the diminutive allele in breeding populations.
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Affiliation(s)
- Ying Wang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ratnesh Singh
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Eric Tong
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
| | - Min Tang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwei Zheng
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Hongkun Fang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruoyu Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Guo
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jinjin Song
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rajeswari Srinivasan
- Department of Tropical Plant & Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jorge A Trujillo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Richard Manshardt
- Department of Tropical Plant & Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
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Luo X, Xu L, Wang Y, Dong J, Chen Y, Tang M, Fan L, Zhu Y, Liu L. An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish (Raphanus sativus L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:274-286. [PMID: 31218798 PMCID: PMC6920339 DOI: 10.1111/pbi.13195] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 05/19/2023]
Abstract
High-density genetic map is a valuable tool for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery of economically agronomic traits in plant species. However, high-resolution genetic map applied to tag QTLs associated with important traits and to investigate genomic features underlying recombination landscape in radish (Raphanus sativus) remains largely unexplored. In this study, an ultra-high-density genetic map with 378 738 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole-genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin colour. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions (RHRs) were enriched near gene promoters and terminators. The recombination rate in RHRs was positively correlated with the density of SNPs and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the RHRs. The results provide novel insights into the radish genome evolution and recombination landscape, and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish.
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Affiliation(s)
- Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Guizhou Institute of BiotechnologyGuizhou Academy of Agricultural SciencesGuiyangChina
| | | | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yuelin Zhu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
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Expression of a Chromoplast-Specific Lycopene β-Cyclase Gene ( CYC- B) Is Implicated in Carotenoid Accumulation and Coloration in the Loquat. Biomolecules 2019; 9:biom9120874. [PMID: 31847172 PMCID: PMC6995616 DOI: 10.3390/biom9120874] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 01/24/2023] Open
Abstract
Carotenoids are the principal pigments in the loquat. Although the metabolic pathway of plant carotenoids has been extensively investigated, few studies have been explored the regulatory mechanisms of loquat carotenoids because knowledge of the loquat genome is incomplete. The chromoplast-specific lycopene β-cyclase gene (CYC-B) could catalyze cyclization of lycopene to β-carotene. In this study, the differential accumulation patterns of loquat with different colors were analyzed and virus-induced gene silencing (VIGS) was utilized in order to verify CYC-B gene function. Using a cloning strategy of homologous genes, a CYC-B gene orthologue was successfully identified from the loquat. At a later stage of maturation, CYC-B gene expression and carotenoids concentrations in the ‘Dawuxing’ variety were higher than in ‘Chuannong 1-5-9′, possibly leading to the difference in pulp coloration of loquat. Interference of CYC-B gene expression in the loquat demonstrated clear visual changes. The green color in negative control fruits became yellow, while TRV2-CYC-B silenced fruits remained green. CYC-B gene expression and total carotenoid content in the pulp decreased by 32.5% and 44.1%, respectively. Furthermore, multiple key genes in the carotenoid metabolic pathway synergistically responded to downregulation of CYC-B gene expression. In summary, we provide direct evidences that CYC-B gene is involved in carotenoid accumulation and coloration in the loquat.
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Xu C, Wei H, Movahedi A, Sun W, Ma X, Li D, Yin T, Zhuge Q. Evaluation, characterization, expression profiling, and functional analysis of DXS and DXR genes of Populus trichocarpa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:94-105. [PMID: 31279136 DOI: 10.1016/j.plaphy.2019.05.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 05/27/2023]
Abstract
1-Deoxy-D-xylulose-5-phosphate synthasse (DXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) are key enzymes in terpenoid biosynthesis. DXS catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate (DXP) from pyruvate and D-glyceraldehyde-3-phosphate. DXR catalyzes the formation of 2-C-methyl-D-erythritol 4-phosphate (MEP) from DXP. Previous studies of the DXS and DXR genes have focused on herbs, such as Arabidopsis thaliana, Salvia miltiorrhiza, and Amomum villosum, but few studies have been conducted on woody plants. For that reason, we chose Populus trichocarpa as a model woody plant for investigating the DXS and DXR genes. PtDXS exhibited the highest expression level in leaves and the lowest expression in roots. PtDXR showed maximum expression in young leaves, and the lowest expression in mature leaves. The expression profiles revealed by RT-PCR following different elicitor treatments such as abscisic acid, NaCl, PEG6000, H2O2, and cold stress showed that PtDXS and PtDXR were elicitor-responsive genes. Our results showed that the PtDXS gene exhibited diurnal changes, but PtDXR did not. Moreover, overexpression of PtDXR in transgenic poplars improved tolerance to abiotic and biotic stresses. Those results showed that the PtDXR encoded a functional protein, and widely participates in plant growth and development, stress physiological process.
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Affiliation(s)
- Chen Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China; Nanjing Key Laboratory of Quality and Safety of Agricultural Products, Nanjing Xiaozhuang University, Nanjing, 211171, China
| | - Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China
| | - Xiaoxing Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China.
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Fabi JP, do Prado SBR. Fast and Furious: Ethylene-Triggered Changes in the Metabolism of Papaya Fruit During Ripening. FRONTIERS IN PLANT SCIENCE 2019; 10:535. [PMID: 31105730 PMCID: PMC6497978 DOI: 10.3389/fpls.2019.00535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Papaya is a climacteric fleshy fruit characterized by fast ripening after harvest. During the relatively short postharvest period, papaya fruit undergoes several changes in metabolism that result in pulp softening and sweetening, as well as the development of a characteristic aroma. Since papaya is one of the most cultivated and appreciated tropical fruit crops worldwide, extensive research has been conducted to not only understand the formation of the quality and nutritional attributes of ripe fruit but also to develop methods for controlling the ripening process. However, most strategies to postpone papaya ripening, and therefore to increase shelf life, have failed to maintain fruit quality. Ethylene blockage precludes carotenoid biosynthesis, while cold storage can induce chilling injury and negatively affect the volatile profile of papaya. As a climacteric fruit, the fast ripening of papaya is triggered by ethylene biosynthesis. The generation of the climacteric ethylene positive feedback loop is elicited by the expression of a specific transcription factor that leads to an up-regulation of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC-oxidase (ACO) expression, triggering the system II ethylene biosynthesis. The ethylene burst occurs about 3 to 4 days after harvest and induces pectinase expression. The disassembling of the papaya cell wall appears to help in fruit sweetness, while glucose and fructose are also produced by acidic invertases. The increase in ethylene production also results in carotenoid accumulation due to the induction of cyclases and hydroxylases, leading to yellow and red/orange-colored pulp phenotypes. Moreover, the production of volatile terpene linalool, an important biological marker for papaya's sensorial quality, is also induced by ethylene. All these mentioned processes are related to papaya's sensorial and nutritional quality. We describe the understanding of ethylene-triggered events that influence papaya quality and nutritional traits, as these characteristics are a consequence of an accelerated metabolism during fruit ripening.
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Affiliation(s)
- João Paulo Fabi
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, Brazil
| | - Samira Bernardino Ramos do Prado
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, Brazil
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High hydrostatic pressure treatments trigger de novo carotenoid biosynthesis in papaya fruit (Carica papaya cv. Maradol). Food Chem 2019; 277:362-372. [DOI: 10.1016/j.foodchem.2018.10.102] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/17/2018] [Accepted: 10/22/2018] [Indexed: 11/22/2022]
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Shen YH, Yang FY, Lu BG, Zhao WW, Jiang T, Feng L, Chen XJ, Ming R. Exploring the differential mechanisms of carotenoid biosynthesis in the yellow peel and red flesh of papaya. BMC Genomics 2019; 20:49. [PMID: 30651061 PMCID: PMC6335806 DOI: 10.1186/s12864-018-5388-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/18/2018] [Indexed: 12/31/2022] Open
Abstract
Background Red-fleshed papaya is a good material to study the different carotenoids accumulation mechanism in the peel and flesh. Although the peel and flesh of papaya closely integrated into one body, the flesh coloration changing from white to red, while the exocarp coloration changing from green to yellow. In this study, the major carotenoids accumulation and the expression patterns of key carotenoid biosynthesis pathway genes in the process of papaya fruit ripening were studied, and the carotenoid biosynthetic pathways in the yellow peel and red flesh of papaya were investigated. Results The carotenoid composition in papaya flesh and peel were different. The major carotenoids were lutein and β-carotene in the peel, while lycopene in the flesh. The accumulation of carotenoids, including lycopene, β-carotene, and β-cryptoxanthin were considered to cause the orange-red color of papaya cv. ‘Daqing No.10’ flesh. The color of peel changed from green to yellow because of the fast degradation of chlorophyll and the appearance of carotenoids such as lutein and β-carotene. Thirteen genes that encode enzymes in the carotenoid biosynthetic pathway were detected in papaya fruit transcriptome: two phytoene synthase (PSY1, PSY2), two phytoene desaturase (PDS1, PDS2), one ζ-carotene desaturase (ZDS), four lycopene cyclase (CYCB, LCYB1, LCYB2, LCYE), one β-carotene hydroxylase (CHYB), one carotene ε-monooxygenase (LUT1), one violaxanthin de-epoxidase (VDE), and one zeaxanthin epoxidase (ZEP). The results of RNA-Seq and RT-qPCR showed the expression of carotenoid biosynthetic pathway genes was consistent with the change of carotenoid content. Carotenoid biosynthetic pathways in the yellow peel and red flesh of papaya were analysed based on the major carotenoids accumulation and the expression patterns of key carotenoid biosynthesis pathway genes. There was only a β-branch of carotenoid biosynthesis in the flesh of papaya, while there were both α- and β-branch of carotenoid biosynthesis in papaya peel. In the process of papaya fruit ripening, the α-branch was inhibited and the β-branch was enhanced in the peel. Conclusions The differential carotenoid accumulation and biosynthesis pathway genes expression in peel and flesh, lay a foundation for further study and provide further insights to control fruit color and improve fruit quality and appearance. Electronic supplementary material The online version of this article (10.1186/s12864-018-5388-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Hong Shen
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, Hebei, China. .,College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Fei Ying Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Bing Guo Lu
- College of Life Science, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Wan Wan Zhao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tao Jiang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, Hebei, China
| | - Li Feng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiao Jing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Zhou D, Shen Y, Zhou P, Fatima M, Lin J, Yue J, Zhang X, Chen LY, Ming R. Papaya CpbHLH1/2 regulate carotenoid biosynthesis-related genes during papaya fruit ripening. HORTICULTURE RESEARCH 2019; 6:80. [PMID: 31263564 PMCID: PMC6588581 DOI: 10.1038/s41438-019-0162-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 05/03/2023]
Abstract
The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids, alternation of flesh color and flavor, which depending on genotype and external factors such as light and hormone. Transcription factors regulating carotenoid biosynthesis have not been analyzed during papaya fruit ripening. RNA-Seq experiments were implemented using different ripening stages of papaya fruit from two papaya varieties. Cis-elements in lycopene β-cyclase genes (CpCYC-B and CpLCY-B) were identified, and followed by genome-wide analysis to identify transcription factors binding to these cis-elements, resulting in the identification of CpbHLH1 and CpbHLH2, two bHLH genes. The expressions of CpbHLH1/2 were changed during fruit development, coupled with transcript increase of carotenoid biosynthesis-related genes including CpCYC-B, CpLCY-B, CpPDS2, CpZDS, CpLCY-E, and CpCHY-B. Yeast one-hybrid (Y1H) and transient expression assay revealed that CpbHLH1/2 could bind to the promoters of CpCYC-B and CpLCY-B, and regulate their transcriptions. In response to strong light, the results of elevated expression of carotenoid biosynthesis-related genes and the changed expression of CpbHLH1/2 indicated that CpbHLH1/2 were involved in light-mediated mechanisms of regulating critical genes in the carotenoid biosynthesis pathway. Collectively, our findings demonstrated several TF family members participating in the regulation of carotenoid genes and proved that CpbHLH1 and CpbHLH2 individually regulated the transcription of lycopene β-cyclase genes (CpCYC-B and CpLCY-B). This study yielded novel findings on regulatory mechanism of carotenoid biosynthesis during papaya fruit ripening.
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Affiliation(s)
- Dong Zhou
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yanhong Shen
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Ping Zhou
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Mahpara Fatima
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Jishan Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Jingjing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Xingtan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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Yan F, Shi M, He Z, Wu L, Xu X, He M, Chen J, Deng X, Cheng Y, Xu J. Largely different carotenogenesis in two pummelo fruits with different flesh colors. PLoS One 2018; 13:e0200320. [PMID: 29985936 PMCID: PMC6037374 DOI: 10.1371/journal.pone.0200320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/23/2018] [Indexed: 02/03/2023] Open
Abstract
Carotenoids in citrus fruits have health benefits and make the fruits visually attractive. Red-fleshed ‘Chuhong’ (‘CH’) and pale green-fleshed ‘Feicui’ (‘FC’) pummelo (Citrus maxima (Burm) Merr.) fruits are interesting materials for studying the mechanisms of carotenoid accumulation. In this study, particularly high contents of linear carotenes were observed in the albedo tissue, segment membranes and juice sacs of ‘CH’. However, carotenoids, especially β-carotene and xanthophylls, accumulated more in the flavedo tissue of ‘FC’ than in that of ‘CH’. Additionally, the contents of other terpenoids such as limonin, nomilin and abscisic acid significantly differed in the juice sacs at 150 days postanthesis. A dramatic increase in carotenoid production was observed at 45 to 75 days postanthesis in the segment membranes and juice sacs of ‘CH’. Different expression levels of carotenogenesis genes, especially the ζ-carotene desaturase (CmZDS), β-carotenoid hydroxylase (CmBCH) and zeaxanthin epoxidase (CmZEP) genes, in combination are directly responsible for the largely different carotenoid profiles between these two pummelo fruits. The sequences of eleven genes involved in carotenoid synthesis were investigated; different alleles of seven of eleven genes might also explain the largely different carotenogenesis observed between ‘CH’ and ‘FC’. These results enhance our understanding of carotenogenesis in pummelo fruits.
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Affiliation(s)
- Fuhua Yan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
- Forestry Science Academy of Lishui, Lishui, Zhejiang, P.R. China
| | - Meiyan Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Zhenyu He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Lianhai Wu
- Forestry Science Academy of Lishui, Lishui, Zhejiang, P.R. China
| | - Xianghua Xu
- Forestry Science Academy of Lishui, Lishui, Zhejiang, P.R. China
| | - Min He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Jiajing Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
- * E-mail:
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Sun T, Yuan H, Cao H, Yazdani M, Tadmor Y, Li L. Carotenoid Metabolism in Plants: The Role of Plastids. MOLECULAR PLANT 2018; 11:58-74. [PMID: 28958604 DOI: 10.1016/j.molp.2017.09.010] [Citation(s) in RCA: 298] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/02/2017] [Accepted: 09/13/2017] [Indexed: 05/17/2023]
Abstract
Carotenoids are indispensable to plants and critical in human diets. Plastids are the organelles for carotenoid biosynthesis and storage in plant cells. They exist in various types, which include proplastids, etioplasts, chloroplasts, amyloplasts, and chromoplasts. These plastids have dramatic differences in their capacity to synthesize and sequester carotenoids. Clearly, plastids play a central role in governing carotenogenic activity, carotenoid stability, and pigment diversity. Understanding of carotenoid metabolism and accumulation in various plastids expands our view on the multifaceted regulation of carotenogenesis and facilitates our efforts toward developing nutrient-enriched food crops. In this review, we provide a comprehensive overview of the impact of various types of plastids on carotenoid biosynthesis and accumulation, and discuss recent advances in our understanding of the regulatory control of carotenogenesis and metabolic engineering of carotenoids in light of plastid types in plants.
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Affiliation(s)
- Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Hui Yuan
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Hongbo Cao
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA; College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Mohammad Yazdani
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Yaakov Tadmor
- Plant Science Institute, Israeli Agricultural Research Organization, Newe Yaar Research Center, P.O. Box 1021, Ramat Yishai 30095, Israel
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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29
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Fu CC, Han YC, Kuang JF, Chen JY, Lu WJ. Papaya CpEIN3a and CpNAC2 Co-operatively Regulate Carotenoid Biosynthesis-Related Genes CpPDS2/4, CpLCY-e and CpCHY-b During Fruit Ripening. PLANT & CELL PHYSIOLOGY 2017; 58:2155-2165. [PMID: 29040739 DOI: 10.1093/pcp/pcx149] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 09/26/2017] [Indexed: 05/08/2023]
Abstract
Papaya is an important tropical fruit with a rich source of carotenoids. The ripening of papaya is a physiological and metabolic process with remarkable changes including accumulation of carotenoids, which depends primarily on the action of ethylene. Ethylene response is mediated by a transcriptional cascade involving the transcription factor families of EIN3/EILs and ERFs. Although ERF members have been reported to control carotenoid production in Arabidopsis and tomato, whether EIN3/EILs are also involved in carotenoid biosynthesis during fruit ripening remains unclear. In this work, two EIN3 genes from papaya fruit, namely CpEIN3a and CpEIN3b, were studied, of which CpEIN3a was increased during fruit ripening, concomitant with the increase of transcripts of carotenoid biosynthesis-related genes including CpPDS2/4, CpZDS, CpLCY-e and CpCHY-b, and carotenoid content. Electrophoretic mobility shift assays (EMSAs) and transient expression analyses revealed that CpEIN3a was able to bind to the promoters of CpPDS4 and CpCHY-b, and promoted their transcription. Protein-protein interaction assays indicated that CpEIN3a physically interacted with another transcription factor CpNAC2, which acted as a transcriptional activator of CpPDS2/4, CpZDS, CpLCY-e and CpCHY-b by directly binding to their promoters. More importantly, the transcriptional activation abilities of CpPDS2/4, CpLCY-e and CpCHY-b were more pronounced following their interaction. Collectively, our findings suggest that CpEIN3a interacts with CpNAC2 and, individually or co-operatively, activates the transcription of a subset of carotenoid biosynthesis-related genes, providing new insights into the regulatory networks of carotenoid biosynthesis during papaya fruit ripening.
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Affiliation(s)
- Chang-Chun Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, PR China
| | - Yan-Chao Han
- Institute of Food Science, Zhejiang Academy of Agricultural Science/Key Laboratory of Post-Harvest Handing of Fruits, Ministry of Agriculture, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of China Light Industry, Hangzhou 310021, PR China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, PR China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, PR China
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Shen YH, Lu BG, Feng L, Yang FY, Geng JJ, Ming R, Chen XJ. Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq. BMC Genomics 2017; 18:671. [PMID: 28859626 PMCID: PMC5580268 DOI: 10.1186/s12864-017-4072-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 08/16/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Since papaya is a typical climacteric fruit, exogenous ethylene (ETH) applications can induce premature and quicker ripening, while 1-methylcyclopropene (1-MCP) slows down the ripening processes. Differential gene expression in ETH or 1-MCP-treated papaya fruits accounts for the ripening processes. To isolate the key ripening-related genes and better understand fruit ripening mechanisms, transcriptomes of ETH or 1-MCP-treated, and non-treated (Control Group, CG) papaya fruits were sequenced using Illumina Hiseq2500. RESULTS A total of 18,648 (1-MCP), 19,093 (CG), and 15,321 (ETH) genes were detected, with the genes detected in the ETH-treatment being the least. This suggests that ETH may inhibit the expression of some genes. Based on the differential gene expression (DGE) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, 53 fruit ripening-related genes were selected: 20 cell wall-related genes, 18 chlorophyll and carotenoid metabolism-related genes, four proteinases and their inhibitors, six plant hormone signal transduction pathway genes, four transcription factors, and one senescence-associated gene. Reverse transcription quantitative PCR (RT-qPCR) analyses confirmed the results of RNA-seq and verified that the expression pattern of six genes is consistent with the fruit senescence process. Based on the expression profiling of genes in carbohydrate metabolic process, chlorophyll metabolism pathway, and carotenoid metabolism pathway, the mechanism of pulp softening and coloration of papaya was deduced and discussed. We illustrate that papaya fruit softening is a complex process with significant cell wall hydrolases, such as pectinases, cellulases, and hemicellulases involved in the process. Exogenous ethylene accelerates the coloration of papaya changing from green to yellow. This is likely due to the inhibition of chlorophyll biosynthesis and the α-branch of carotenoid metabolism. Chy-b may play an important role in the yellow color of papaya fruit. CONCLUSIONS Comparing the differential gene expression in ETH/1-MCP-treated papaya using RNA-seq is a sound approach to isolate ripening-related genes. The results of this study can improve our understanding of papaya fruit ripening molecular mechanism and reveal candidate fruit ripening-related genes for further research.
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Affiliation(s)
- Yan Hong Shen
- College of Horticulture, Fijian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Bing Guo Lu
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117 China
| | - Li Feng
- College of Horticulture, Fijian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Fei Ying Yang
- College of Horticulture, Fijian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Jiao Jiao Geng
- College of Horticulture, Fijian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801 USA
| | - Xiao Jing Chen
- College of Horticulture, Fijian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
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Chan-León AC, Estrella-Maldonado H, Dubé P, Fuentes Ortiz G, Espadas-Gil F, Talavera May C, Ramírez Prado J, Desjardins Y, Santamaría JM. The high content of β-carotene present in orange-pulp fruits of Carica papaya L. is not correlated with a high expression of the CpLCY-β2 gene. Food Res Int 2017; 100:45-56. [PMID: 28888458 DOI: 10.1016/j.foodres.2017.08.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/04/2017] [Accepted: 08/05/2017] [Indexed: 01/25/2023]
Abstract
We investigated the transcriptional regulation of six genes involved in carotenoid biosynthesis, together with the carotenoid accumulation during postharvest ripening of three different papaya genotypes of contrasting pulp color. Red-pulp genotype (RPG) showed the lowest content of yellow pigments (YP), such as β-cryptoxanthin, zeaxanthin, and violaxanthin, together with the lowest relative expression levels (REL) of CpLCY-β2 and CpCHX-β genes. On the contrary, the yellow-pulp genotype (YPG) showed the highest content of YP and the highest REL of CpLCY-β2 and CpCHX-β genes. Interestingly, the orange-pulp genotype (OPG) showed intermediate content of YP and intermediate REL of CpLCY-β2 and CpCHX-β genes. The highest content of β-carotene shown by OPG despite having an intermediate REL of the CpLCY-β2 genes, suggests a post-transcriptional regulation. Thus, the transcriptional level of the genes, directing the carotenoid biosynthesis pathway, can partially explain the accumulation of carotenoids during the postharvest ripening in C. papaya genotypes of contrasting pulp color.
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Affiliation(s)
- Arianna C Chan-León
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34. Colonia Chuburná de Hidalgo, CP 97205 Mérida, Yucatán, Mexico
| | - Humberto Estrella-Maldonado
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34. Colonia Chuburná de Hidalgo, CP 97205 Mérida, Yucatán, Mexico
| | - Pascal Dubé
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Boulevard Hochelaga, Québec, QC G1V 0A6, Canada
| | - Gabriela Fuentes Ortiz
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34. Colonia Chuburná de Hidalgo, CP 97205 Mérida, Yucatán, Mexico
| | - Francisco Espadas-Gil
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34. Colonia Chuburná de Hidalgo, CP 97205 Mérida, Yucatán, Mexico
| | - Carlos Talavera May
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34. Colonia Chuburná de Hidalgo, CP 97205 Mérida, Yucatán, Mexico
| | - Jorge Ramírez Prado
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34. Colonia Chuburná de Hidalgo, CP 97205 Mérida, Yucatán, Mexico
| | - Yves Desjardins
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Boulevard Hochelaga, Québec, QC G1V 0A6, Canada
| | - Jorge M Santamaría
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34. Colonia Chuburná de Hidalgo, CP 97205 Mérida, Yucatán, Mexico.
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Wu M, Lewis J, Moore RC. A wild origin of the loss-of-function lycopene beta cyclase (CYC-b) allele in cultivated, red-fleshed papaya (Carica papaya). AMERICAN JOURNAL OF BOTANY 2017; 104:116-126. [PMID: 28082282 DOI: 10.3732/ajb.1600301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The red flesh of some papaya cultivars is caused by a recessive loss-of-function mutation in the coding region of the chromoplast-specific lycopene beta cyclase gene (CYC-b). We performed an evolutionary genetic analysis of the CYC-b locus in wild and cultivated papaya to uncover the origin of this loss-of-function allele in cultivated papaya. METHODS We analyzed the levels and patterns of genetic diversity at the CYC-b locus and six loci in a 100-kb region flanking CYC-b and compared these to genetic diversity levels at neutral autosomal loci. The evolutionary relationships of CYC-b haplotypes were assessed using haplotype network analysis of the CYC-b locus and the 100-kb CYC-b region. KEY RESULTS Genetic diversity at the recessive CYC-b allele (y) was much lower relative to the dominant Y allele found in yellow-fleshed wild and cultivated papaya due to a strong selective sweep. Haplotype network analyses suggest the y allele most likely arose in the wild and was introduced into domesticated varieties after the first papaya domestication event. The shared haplotype structure between some wild, feral, and cultivated haplotypes around the y allele supports subsequent escape of this allele from red cultivars back into wild populations through feral intermediates. CONCLUSIONS Our study supports a protracted domestication process of papaya through the introgression of wild-derived traits and gene flow from cultivars to wild populations. Evidence of gene flow from cultivars to wild populations through feral intermediates has implications for the introduction of transgenic papaya into Central American countries.
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Affiliation(s)
- Meng Wu
- Miami University, Department of Biology, 212 Pearson Hall, Oxford, Ohio 45056 USA
| | - Jamicia Lewis
- Department of Biological Sciences, Alabama State University, Montgomery, Alabama 36104 USA
| | - Richard C Moore
- Miami University, Department of Biology, 212 Pearson Hall, Oxford, Ohio 45056 USA
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Fu CC, Han YC, Fan ZQ, Chen JY, Chen WX, Lu WJ, Kuang JF. The Papaya Transcription Factor CpNAC1 Modulates Carotenoid Biosynthesis through Activating Phytoene Desaturase Genes CpPDS2/4 during Fruit Ripening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:5454-63. [PMID: 27327494 DOI: 10.1021/acs.jafc.6b01020] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Papaya fruits accumulate carotenoids during fruit ripening. Although many papaya carotenoid biosynthesis pathway genes have been identified, the transcriptional regulators of these genes have not been characterized. In this study, a NAC transcription factor, designated as CpNAC1, was characterized from papaya fruit. CpNAC1 was localized exclusively in nucleus and possessed transcriptional activation activity. Expression of carotenoid biosynthesis genes phytoene desaturases (CpPDSs) and CpNAC1 was increased during fruit ripening and by propylene treatment, which correlates well with the elevated carotenoid content in papaya. The gel mobility shift assays and transient expression analyses demonstrated that CpNAC1 directly binds to the NAC binding site (NACBS) motifs in CpPDS2/4 promoters and activates them. Collectively, these data suggest that CpNAC1 may act as a positive regulator of carotenoid biosynthesis during papaya fruit ripening possibly via transcriptional activation of CpPDSs such as CpPDS2/4.
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Affiliation(s)
- Chang-Chun Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou 510642, China
| | - Yan-Chao Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou 510642, China
| | - Zhong-Qi Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou 510642, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou 510642, China
| | - Wei-Xin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou 510642, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou 510642, China
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Martins GF, Fabi JP, Mercadante AZ, de Rosso VV. The ripening influence of two papaya cultivars on carotenoid biosynthesis and radical scavenging capacity. Food Res Int 2016. [DOI: 10.1016/j.foodres.2015.11.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Carotenoids are recognized as the main pigments in most fruit crops, providing colours that range from yellow and pink to deep orange and red. Moreover, the edible portion of widely consumed fruits or their derived products represent a major dietary source of carotenoids for animals and humans. Therefore, these pigments are crucial compounds contributing to fruit aesthetic and nutritional quality but may also have protecting and ecophysiological functions in coloured fruits. Among plant organs, fruits display one of the most heterogeneous carotenoids patterns in terms of diversity and abundance. In this chapter a comprehensive list of the carotenoid content and profile in the most commonly cultivated fleshy fruits is reported. The proposed fruit classification systems attending to carotenoid composition are revised and discussed. The regulation of carotenoids in fruits can be rather complex due to the dramatic changes in content and composition during ripening, which are also dependent on the fruit tissue and the developmental stage. In addition, carotenoid accumulation is a dynamic process, associated with the development of chromoplasts during ripening. As a general rule, carotenoid accumulation is highly controlled at the transcriptional level of the structural and accessory proteins of the biosynthetic and degradation pathways, but other mechanisms such as post-transcriptional modifications or the development of sink structures have been recently revealed as crucial factors in determining the levels and stability of these pigments. In this chapter common key metabolic reactions regulating carotenoid composition in fruit tissues are described in addition to others that are restricted to certain species and generate unique carotenoids patterns. The existence of fruit-specific isoforms for key steps such as the phytoene synthase, lycopene β-cyclases or catabolic carotenoid cleavage dioxygenases has allowed an independent regulation of the pathway in fruit tissues and a source of variability to create novel activities or different catalytic properties. Besides key genes of the carotenoid pathway, changes in carotenoid accumulation could be also directly influenced by differences in gene expression or protein activity in the pathway of carotenoid precursors and some relevant examples are discussed. The objective of this chapter is to provide an updated review of the main carotenoid profiles in fleshy fruits, their pattern of changes during ripening and our current understanding of the different regulatory levels responsible for the diversity of carotenoid accumulation in fruit tissues.
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Affiliation(s)
- Joanna Lado
- Instituto de Agroquimica y Tecnologia de Alimentos (IATA), Consejo Superior de Investigaciones Cientificas (CSIC), Avenida Agustin Escardino 7, 46980, Paterna, Valencia, Spain.
- Instituto Nacional de Investigacion Agropecuaria (INIA), Camino a la Represa s/n, Salto, Uruguay.
| | - Lorenzo Zacarías
- Instituto de Agroquimica y Tecnologia de Alimentos (IATA), Consejo Superior de Investigaciones Cientificas (CSIC), Avenida Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - María Jesús Rodrigo
- Instituto de Agroquimica y Tecnologia de Alimentos (IATA), Consejo Superior de Investigaciones Cientificas (CSIC), Avenida Agustin Escardino 7, 46980, Paterna, Valencia, Spain
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Abstract
Carotenoids are the most important biocolor isoprenoids responsible for yellow, orange and red colors found in nature. In plants, they are synthesized in plastids of photosynthetic and sink organs and are essential molecules for photosynthesis, photo-oxidative damage protection and phytohormone synthesis. Carotenoids also play important roles in human health and nutrition acting as vitamin A precursors and antioxidants. Biochemical and biophysical approaches in different plants models have provided significant advances in understanding the structural and functional roles of carotenoids in plants as well as the key points of regulation in their biosynthesis. To date, different plant models have been used to characterize the key genes and their regulation, which has increased the knowledge of the carotenoid metabolic pathway in plants. In this chapter a description of each step in the carotenoid synthesis pathway is presented and discussed.
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Affiliation(s)
| | - Claudia Stange
- Centro de Biología Molecular Vegetal, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
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Tong Y, Su P, Zhao Y, Zhang M, Wang X, Liu Y, Zhang X, Gao W, Huang L. Molecular Cloning and Characterization of DXS and DXR Genes in the Terpenoid Biosynthetic Pathway of Tripterygium wilfordii. Int J Mol Sci 2015; 16:25516-35. [PMID: 26512659 PMCID: PMC4632813 DOI: 10.3390/ijms161025516] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
1-Deoxy-d-xylulose-5-phosphate synthase (DXS) and 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) genes are the key enzyme genes of terpenoid biosynthesis but still unknown in Tripterygium wilfordii Hook. f. Here, three full-length cDNA encoding DXS1, DXS2 and DXR were cloned from suspension cells of T. wilfordii with ORF sizes of 2154 bp (TwDXS1, GenBank accession no.KM879187), 2148 bp (TwDXS2, GenBank accession no.KM879186), 1410 bp (TwDXR, GenBank accession no.KM879185). And, the TwDXS1, TwDXS2 and TwDXR were characterized by color complementation in lycopene accumulating strains of Escherichia coli, which indicated that they encoded functional proteins and promoted lycopene pathway flux. TwDXS1 and TwDXS2 are constitutively expressed in the roots, stems and leaves and the expression level showed an order of roots > stems > leaves. After the suspension cells were induced by methyl jasmonate, the mRNA expression level of TwDXS1, TwDXS2, and TwDXR increased, and triptophenolide was rapidly accumulated to 149.52 µg·g−1, a 5.88-fold increase compared with the control. So the TwDXS1, TwDXS2, and TwDXR could be important genes involved in terpenoid biosynthesis in Tripterygium wilfordii Hook. f.
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Affiliation(s)
- Yuru Tong
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Ping Su
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Yujun Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Meng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Xiujuan Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Yujia Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Xianan Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Yuan H, Zhang J, Nageswaran D, Li L. Carotenoid metabolism and regulation in horticultural crops. HORTICULTURE RESEARCH 2015; 2:15036. [PMID: 26504578 PMCID: PMC4591682 DOI: 10.1038/hortres.2015.36] [Citation(s) in RCA: 260] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/07/2015] [Accepted: 07/11/2015] [Indexed: 05/05/2023]
Abstract
Carotenoids are a diverse group of pigments widely distributed in nature. The vivid yellow, orange, and red colors of many horticultural crops are attributed to the overaccumulation of carotenoids, which contribute to a critical agronomic trait for flowers and an important quality trait for fruits and vegetables. Not only do carotenoids give horticultural crops their visual appeal, they also enhance nutritional value and health benefits for humans. As a result, carotenoid research in horticultural crops has grown exponentially over the last decade. These investigations have advanced our fundamental understanding of carotenoid metabolism and regulation in plants. In this review, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in horticultural crops and highlight recent achievements in our understanding of carotenoid metabolic regulation in vegetables, fruits, and flowers.
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Affiliation(s)
- Hui Yuan
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Junxiang Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Divyashree Nageswaran
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Li Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
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Zou Y, Zhang L, Rao S, Zhu X, Ye L, Chen W, Li X. The relationship between the expression of ethylene-related genes and papaya fruit ripening disorder caused by chilling injury. PLoS One 2014; 9:e116002. [PMID: 25542021 PMCID: PMC4277447 DOI: 10.1371/journal.pone.0116002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/02/2014] [Indexed: 01/30/2023] Open
Abstract
Papaya (Carica papaya L.) is sensitive to low temperature and easy to be subjected to chilling injury, which causes fruit ripening disorder. This study aimed to investigate the relationship between the expression of genes related to ethylene and fruit ripening disorder caused by chilling injury. Papaya fruits were firstly stored at 7°C and 12°C for 25 and 30 days, respectively, then treated with exogenous ethylene and followed by ripening at 25°C for 5 days. Chilling injury symptoms such as pulp water soaking were observed in fruit stored at 7°C on 20 days, whereas the coloration and softening were completely blocked after 25 days, Large differences in the changes in the expression levels of twenty two genes involved in ethylene were seen during 7°C-storage with chilling injury. Those genes with altered expression could be divided into three groups: the group of genes that were up-regulated, including ACS1/2/3, EIN2, EIN3s/EIL1, CTR1/2/3, and ERF1/3/4; the group of genes that were down-regulated, including ACO3, ETR1, CTR4, EBF2, and ERF2; and the group of genes that were un-regulated, including ACO1/2, ERS, and EBF1. The results also showed that pulp firmness had a significantly positive correlation with the expression of ACS2, ACO1, CTR1/4, EIN3a/b, and EBF1/2 in fruit without chilling injury. This positive correlation was changed to negative one in fruit after storage at 7°C for 25 days with chilling injury. The coloring index displayed significantly negative correlations with the expression levels of ACS2, ACO1/2, CTR4, EIN3a/b, ERF3 in fruit without chilling injury, but these correlations were changed into the positive ones in fruit after storage at 7°C for 25 days with chilling injury. All together, these results indicate that these genes may play important roles in the abnormal softening and coloration with chilling injury in papaya.
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Affiliation(s)
- Yuan Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory for Postharvest Science and Technology of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Lin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory for Postharvest Science and Technology of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Shen Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory for Postharvest Science and Technology of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Xiaoyang Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory for Postharvest Science and Technology of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Lanlan Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory for Postharvest Science and Technology of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Weixin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory for Postharvest Science and Technology of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Xueping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory for Postharvest Science and Technology of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou, 510642, P.R. China
- * E-mail:
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Na JK, Wang J, Ming R. Accumulation of interspersed and sex-specific repeats in the non-recombining region of papaya sex chromosomes. BMC Genomics 2014; 15:335. [PMID: 24885930 PMCID: PMC4035066 DOI: 10.1186/1471-2164-15-335] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 04/22/2014] [Indexed: 12/26/2022] Open
Abstract
Background The papaya Y chromosome has undergone a degenerative expansion from its ancestral autosome, as a consequence of recombination suppression in the sex determining region of the sex chromosomes. The non-recombining feature led to the accumulation of repetitive sequences in the male- or hermaphrodite-specific regions of the Y or the Yh chromosome (MSY or HSY). Therefore, repeat composition and distribution in the sex determining region of papaya sex chromosomes would be informative to understand how these repetitive sequences might be involved in the early stages of sex chromosome evolution. Results Detailed composition of interspersed, sex-specific, and tandem repeats was analyzed from 8.1 megabases (Mb) HSY and 5.3 Mb corresponding X chromosomal regions. Approximately 77% of the HSY and 64% of the corresponding X region were occupied by repetitive sequences. Ty3-gypsy retrotransposons were the most abundant interspersed repeats in both regions. Comparative analysis of repetitive sequences between the sex determining region of papaya X chromosome and orthologous autosomal sequences of Vasconcellea monoica, a close relative of papaya lacking sex chromosomes, revealed distinctive differences in the accumulation of Ty3-Gypsy, suggesting that the evolution of the papaya sex determining region may accompany Ty3-Gypsy element accumulation. In total, 21 sex-specific repeats were identified from the sex determining region; 20 from the HSY and one from the X. Interestingly, most HSY-specific repeats were detected in two regions where the HSY expansion occurred, suggesting that the HSY expansion may result in the accumulation of sex-specific repeats or that HSY-specific repeats might play an important role in the HSY expansion. The analysis of simple sequence repeats (SSRs) revealed that longer SSRs were less abundant in the papaya sex determining region than the other chromosomal regions. Conclusion Major repetitive elements were Ty3-gypsy retrotransposons in both the HSY and the corresponding X. Accumulation of Ty3-Gypsy retrotransposons in the sex determining region of papaya X chromosome was significantly higher than that in the corresponding region of V. monoica, suggesting that Ty3-Gypsy could be crucial for the expansion and evolution of the sex determining region in papaya. Most sex-specific repeats were located in the two HSY expansion regions. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-335) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Xu J, Tao N, Cao H, Liu Q, Deng X. Presence of Two Variants of Lycopene β-Cyclase Gene in Genomes of Citrus and its Relatives. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Molecular cloning, characterizing, and expression analysis of CTR1 genes in harvested papaya fruit. Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-2131-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Falchi R, Vendramin E, Zanon L, Scalabrin S, Cipriani G, Verde I, Vizzotto G, Morgante M. Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:175-87. [PMID: 23855972 PMCID: PMC4223380 DOI: 10.1111/tpj.12283] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 06/27/2013] [Accepted: 07/04/2013] [Indexed: 05/18/2023]
Abstract
Peach flesh color (white or yellow) is among the most popular commercial criteria for peach classification, and has implications for consumer acceptance and fruit nutritional quality. Despite the increasing interest in improving cultivars of both flesh types, little is known about the genetic basis for the carotenoid content diversity in peach. Here we describe the association between genotypes at a locus encoding the carotenoid cleavage dioxygenase 4 (PpCCD4), localized in pseudomolecule 1 of the Prunus persica reference genome sequence, and the flesh color for 37 peach varieties, including two somatic revertants, and three ancestral relatives of peach, providing definitive evidence that this locus is responsible for flesh color phenotype. We show that yellow peach alleles have arisen from various ancestral haplotypes by at least three independent mutational events involving nucleotide substitutions, small insertions and transposable element insertions, and that these mutations, despite being located within the transcribed portion of the gene, also result in marked differences in transcript levels, presumably as a consequence of differential transcript stability involving nonsense-mediated mRNA decay. The PpCCD4 gene provides a unique example of a gene for which humans, in their quest to diversify phenotypic appearance and qualitative characteristics of a fruit, have been able to select and exploit multiple mutations resulting from a variety of mechanisms.
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Affiliation(s)
- Rachele Falchi
- Dipartimento di Scienze Agrarie e Ambientali, University of UdineVia delle Scienze 206, 33100, Udine, Italy
| | - Elisa Vendramin
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA) – Centro di Ricerca per la FrutticolturaVia di Fioranello 52, 00134, Rome, Italy
| | - Laura Zanon
- Dipartimento di Scienze Agrarie e Ambientali, University of UdineVia delle Scienze 206, 33100, Udine, Italy
| | - Simone Scalabrin
- Istituto di Genomica Applicata (IGA)Via J. Linussio 51, 33100, Udine, Italy
| | - Guido Cipriani
- Dipartimento di Scienze Agrarie e Ambientali, University of UdineVia delle Scienze 206, 33100, Udine, Italy
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA) – Centro di Ricerca per la FrutticolturaVia di Fioranello 52, 00134, Rome, Italy
| | - Ignazio Verde
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA) – Centro di Ricerca per la FrutticolturaVia di Fioranello 52, 00134, Rome, Italy
| | - Giannina Vizzotto
- Dipartimento di Scienze Agrarie e Ambientali, University of UdineVia delle Scienze 206, 33100, Udine, Italy
- *For correspondence (e-mail or )
| | - Michele Morgante
- Dipartimento di Scienze Agrarie e Ambientali, University of UdineVia delle Scienze 206, 33100, Udine, Italy
- Istituto di Genomica Applicata (IGA)Via J. Linussio 51, 33100, Udine, Italy
- *For correspondence (e-mail or )
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Li X, Zhu X, Mao J, Zou Y, Fu D, Chen W, Lu W. Isolation and characterization of ethylene response factor family genes during development, ethylene regulation and stress treatments in papaya fruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 70:81-92. [PMID: 23770597 DOI: 10.1016/j.plaphy.2013.05.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/13/2013] [Indexed: 05/08/2023]
Abstract
Ethylene response factors (ERFs) play important roles in fruit development, ripening, defense responses and stress signaling pathways. After harvest, climacteric fruit such as papaya are subject to a range of problems associated with postharvest handling and storage treatments. There have been few attempts to evaluate the role of ERFs in fruit's responses to environmental stimuli. To investigate the transcriptional mechanisms underlying fruit developmental, ripening and stresses, we cloned four ERFs from papaya. The deduced amino acid sequence of CpERFs contained the conserved apetalous (AP2)/ERF domain, which shared high similarity with other reported AP2/ERF domains. The phylogeny, gene structures, and putatively conserved motifs in papaya ERF proteins were analyzed, and compared with those of Arabidopsis. Expression patterns of CpERFs were examined during fruit development, under 1-MCP treatment, ethephon treatment, biotic stress (temperature stress) and pathogen stress. CpERFs displayed differential expression patterns and expression levels under different experimental conditions. CpERF2 and CpERF3 showed a close association with fruit ripening and CpERFs had a high expression level in the earlier stages during the fruit development period. The expression of CpERFs strongly associated with stress response. These results support the role for papaya ERFs in transcriptional regulation of ripening-related or stress-respond genes and thus, in the regulation of papaya fruit-ripening processes and stress responses.
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Affiliation(s)
- Xueping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Provincial Key Laboratory for Postharvest Science and Technology of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, PR China.
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Ramos-Parra PA, García-Salinas C, Hernández-Brenes C, de la Garza RID. Folate levels and polyglutamylation profiles of papaya (Carica papaya cv. Maradol) during fruit development and ripening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:3949-3956. [PMID: 23574547 DOI: 10.1021/jf305364x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Folates are essential micronutrients for humans, and their deficiency causes several detrimental effects on human health. Papaya fruit is an important natural source of some micronutrients. This paper presents a first complete characterization of folate derivatives accumulated in cv. Maradol papaya during fruit development and ripening processes. During postharvest ripening, the fruit accumulated up to 24.5% of the daily folate recommended dietary allowance (RDA) for an adult in a 1 cup (145 g) portion. Tetrahydrofolate (THF) and 5-methyl-THF were the predominant folate classes observed. Surprisingly, an unusually long polyglutamylation profile of tentatively up to 17 glutamates linked to 5-methyl-THF was detected; to the authors' knowledge, this very long polyglutamyl tail has not been reported for any organism, and it is probably characteristic of this plant species. This polyglutamylation degree changed throughout fruit development and ripening, showing the largest differences at the onset of ripening. This work raises questions about the functional role of folate derivatives in fruit development.
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Affiliation(s)
- Perla A Ramos-Parra
- Escuela de Biotecnología y Alimentos, Centro de Biotechnologı́a - FEMSA, Tecnológico de Monterrey , Campus-Monterrey 64849, Mexico
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Levels of lycopene β-cyclase 1 modulate carotenoid gene expression and accumulation in Daucus carota. PLoS One 2013; 8:e58144. [PMID: 23555569 PMCID: PMC3612080 DOI: 10.1371/journal.pone.0058144] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 01/30/2013] [Indexed: 12/03/2022] Open
Abstract
Plant carotenoids are synthesized and accumulated in plastids through a highly regulated pathway. Lycopene β-cyclase (LCYB) is a key enzyme involved directly in the synthesis of α-carotene and β-carotene through the cyclization of lycopene. Carotenoids are produced in both carrot (Daucus carota) leaves and reserve roots, and high amounts of α-carotene and β-carotene accumulate in the latter. In some plant models, the presence of different isoforms of carotenogenic genes is associated with an organ-specific function. D. carota harbors two Lcyb genes, of which DcLcyb1 is expressed in leaves and storage roots during carrot development, correlating with an increase in carotenoid levels. In this work, we show that DcLCYB1 is localized in the plastid and that it is a functional enzyme, as demonstrated by heterologous complementation in Escherichia coli and over expression and post transcriptional gene silencing in carrot. Transgenic plants with higher or reduced levels of DcLcyb1 had incremented or reduced levels of chlorophyll, total carotenoids and β-carotene in leaves and in the storage roots, respectively. In addition, changes in the expression of DcLcyb1 are accompanied by a modulation in the expression of key endogenous carotenogenic genes. Our results indicate that DcLcyb1 does not possess an organ specific function and modulate carotenoid gene expression and accumulation in carrot leaves and storage roots.
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Sivakumar D, Wall MM. Papaya Fruit Quality Management during the Postharvest Supply Chain. FOOD REVIEWS INTERNATIONAL 2013. [DOI: 10.1080/87559129.2012.692138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Zhu X, Li X, Zou Y, Chen W, Lu W. Cloning, characterization and expression analysis of Δ1-pyrroline-5-carboxylate synthetase (P5CS) gene in harvested papaya (Carica papaya) fruit under temperature stress. Food Res Int 2012. [DOI: 10.1016/j.foodres.2012.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
X chromosomes have long been thought to conserve the structure and gene content of the ancestral autosome from which the sex chromosomes evolved. We compared the recently evolved papaya sex chromosomes with a homologous autosome of a close relative, the monoecious Vasconcellea monoica, to infer changes since recombination stopped between the papaya sex chromosomes. We sequenced 12 V. monoica bacterial artificial chromosomes, 11 corresponding to the papaya X-specific region, and 1 to a papaya autosomal region. The combined V. monoica X-orthologous sequences are much shorter (1.10 Mb) than the corresponding papaya region (2.56 Mb). Given that the V. monoica genome is 41% larger than that of papaya, this finding suggests considerable expansion of the papaya X; expansion is supported by a higher repetitive sequence content of the X compared with the papaya autosomal sequence. The alignable regions include 27 transcript-encoding sequences, only 6 of which are functional X/V. monoica gene pairs. Sequence divergence from the V. monoica orthologs is almost identical for papaya X and Y alleles; the Carica-Vasconcellea split therefore occurred before the papaya sex chromosomes stopped recombining, making V. monoica a suitable outgroup for inferring changes in papaya sex chromosomes. The papaya X and the hermaphrodite-specific region of the Y(h) chromosome and V. monoica have all gained and lost genes, including a surprising amount of changes in the X.
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Yang Q, Yuan D, Shi L, Capell T, Bai C, Wen N, Lu X, Sandmann G, Christou P, Zhu C. Functional characterization of the Gentiana lutea zeaxanthin epoxidase (GlZEP) promoter in transgenic tomato plants. Transgenic Res 2012; 21:1043-56. [DOI: 10.1007/s11248-012-9591-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 01/12/2012] [Indexed: 12/23/2022]
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