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Shigita G, Shimomura K, Dung TP, Haque NP, Duong TT, Imoh ON, Monden Y, Nishida H, Tanaka K, Sugiyama M, Kawazu Y, Tomooka N, Kato K. Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:174. [PMID: 38954043 PMCID: PMC11219412 DOI: 10.1007/s00122-024-04683-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
KEY MESSAGE Genotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia. The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber.
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Affiliation(s)
- Gentaro Shigita
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
- Department of Life Science Systems, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 2, 85354, Freising, Germany
| | - Koichiro Shimomura
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Tran Phuong Dung
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Naznin Pervin Haque
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Thuy Thanh Duong
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue, Vietnam
| | - Odirich Nnennaya Imoh
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Kenji Kato
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan.
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Chai CH, Hong CF, Huang JW. Identification and Characterization of a Multifunctional Biocontrol Agent, Streptomyces griseorubiginosus LJS06, Against Cucumber Anthracnose. Front Microbiol 2022; 13:923276. [PMID: 35722317 PMCID: PMC9201727 DOI: 10.3389/fmicb.2022.923276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
Twenty-eight bacterial strains isolated from Chinese herb extracts, beer fermentation waste, and raw oyster shells were evaluated for their efficacy in controlling cucumber anthracnose. Four bacterial strains, namely TG01, TG02, LJS06, and LJS08, were found to effectively reduce the mycelial growth of Colletotrichum orbiculare COC3 on PDA media. Spraying or drenching LJS06 spore suspension before inoculation significantly p < 0.05 reduced disease severity; thus, LJS06 was subject to further characterization. On the basis of the morphological, physiological, and biochemical characteristics and a multilocus sequence analysis of partial 16S rRNA, atpD, rpoB, and trpB genes, LJS06 was identified to be Streptomyces griseorubiginosus (Ryabova and Preobrazhenskaya) Pridham et al. Physiological and biochemical tests revealed that S. griseorubiginosus LJS06 can produce amylase, cellulase, chitinase, protease, siderophore, polyamines, and indole-3-acetic acid. Thus, a culture filtrate of LJS06 (specifically SL06) was formulated and evaluated for its efficacy against conidial germination, appressorium formation, and anthracnose management. Diluted SL06 was found to significantly (p < 0.05) inhibit conidial germination and appressorium formation, which can be attributed to impaired membrane integrity, accumulated reactive oxygen species (ROS), and impaired energy metabolism in the conidia. In addition, the spraying and drenching of diluted SL06 before inoculation consistently and significantly (p < 0.05) reduced anthracnose severity. These results jointly suggest that S. griseorubiginosus LJS06 can aid in the management of cucumber anthracnose by directly inhibiting conidial function and priming the plant defense system.
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Affiliation(s)
- Chien Hao Chai
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Fang Hong
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
- Innovative and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Cheng-Fang Hong,
| | - Jenn-Wen Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
- Innovative and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan
- Jenn-Wen Huang,
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Nguyen DV, Hoang TTH, Le NT, Tran HT, Nguyen CX, Moon YH, Chu HH, Do PT. An Efficient Hairy Root System for Validation of Plant Transformation Vector and CRISPR/Cas Construct Activities in Cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 12:770062. [PMID: 35222448 PMCID: PMC8874011 DOI: 10.3389/fpls.2021.770062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Hairy root induction system has been applied in various plant species as an effective method to study gene expression and function due to its fast-growing and high genetic stability. Recently, these systems have shown to be an effective tool to evaluate activities of CRISPR/Cas9 systems for genome editing. In this study, Rhizobium rhizogenes mediated hairy root induction was optimized to provide an effective tool for validation of plant transformation vector, CRISPR/Cas9 construct activities as well as selection of targeted gRNAs for gene editing in cucumber (Cucumis sativus L.). Under the optimized conditions including OD650 at 0.4 for infection and 5 days of co-cultivation, the highest hairy root induction frequency reached 100% for the cucumber variety Choka F1. This procedure was successfully utilized to overexpress a reporter gene (gus) and induce mutations in two Lotus japonicus ROOTHAIRLESS1 homolog genes CsbHLH66 and CsbHLH82 using CRISPR/Cas9 system. For induced mutation, about 78% of transgenic hairy roots exhibited mutant phenotypes including sparse root hair and root hair-less. The targeted mutations were obtained in individual CsbHLH66, CsbHLH82, or both CsbHLH66 and CsbHLH82 genes by heteroduplex analysis and sequencing. The hairy root transformation system established in this study is sufficient and potential for further research in genome editing of cucumber as well as other cucumis plants.
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Affiliation(s)
- Doai Van Nguyen
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Trang Thi-Huyen Hoang
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc Thu Le
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huyen Thi Tran
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Cuong Xuan Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Yong-Hwan Moon
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Department of Molecular Biology, Pusan National University, Busan, South Korea
| | - Ha Hoang Chu
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phat Tien Do
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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Pradeepkumara N, Sharma PK, Munshi AD, Behera TK, Bhatia R, Kumari K, Singh J, Jaiswal S, Iquebal MA, Arora A, Rai A, Kumar D, Bhattacharya RC, Dey SS. Fruit transcriptional profiling of the contrasting genotypes for shelf life reveals the key candidate genes and molecular pathways regulating post-harvest biology in cucumber. Genomics 2022; 114:110273. [PMID: 35092817 DOI: 10.1016/j.ygeno.2022.110273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Cucumber fruits are perishable in nature and become unfit for market within 2-3 days of harvesting. A natural variant, DC-48 with exceptionally high shelf life was developed and used to dissect the genetic architecture and molecular mechanism for extended shelf life through RNA-seq for first time. A total of 1364 DEGs were identified and cell wall degradation, chlorophyll and ethylene metabolism related genes played key role. Polygalacturunase (PG), Expansin (EXP) and xyloglucan were down regulated determining fruit firmness and retention of fresh green colour was mainly attributed to the low expression level of the chlorophyll catalytic enzymes (CCEs). Gene regulatory networks revealed the hub genes and cross-talk associated with wide variety of the biological processes. Large number of SSRs (21524), SNPs (545173) and InDels (126252) identified will be instrumental in cucumber improvement. A web genomic resource, CsExSLDb developed will provide a platform for future investigation on cucumber post-harvest biology.
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Affiliation(s)
- N Pradeepkumara
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A D Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jogendra Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - R C Bhattacharya
- ICAR-National Institute of Plant Biotechnology, New Delhi, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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5
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De Smet I, Vergauwen D. The Collaboration Between Art History and Genetics - An Unlikely Marriage of Disciplines. FRONTIERS IN PLANT SCIENCE 2021; 12:757439. [PMID: 34790214 PMCID: PMC8591120 DOI: 10.3389/fpls.2021.757439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Our fruits, vegetables, and cereal crops stem from a wild ancestor and have undergone major changes through millennia of domestication and selection. There are various ways to reveal plant diversity over time, and one of these is through the combination of art history and genetics (also known as #ArtGenetics). Here, we discuss this approach from the art historian's point of view and flag the advantages and caveats of such an approach. We also advocate for the development of an integrated, global art database to facilitate such analyses.
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Affiliation(s)
- Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Fahed C, Hayar S. Conventional vs. Organic Cucumber Production in Lebanon: Risk Assessment of the Recommended Agrochemicals on Consumer Health and the Environment. CHEMISTRY AFRICA 2021. [DOI: 10.1007/s42250-021-00238-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Flores-León A, García-Martínez S, González V, Garcés-Claver A, Martí R, Julián C, Sifres A, Pérez-de-Castro A, Díez MJ, López C, Ferriol M, Gisbert C, Ruiz JJ, Cebolla-Cornejo J, Picó B. Grafting Snake Melon [ Cucumis melo L. subsp. melo Var. flexuosus (L.) Naudin] in Organic Farming: Effects on Agronomic Performance; Resistance to Pathogens; Sugar, Acid, and VOC Profiles; and Consumer Acceptance. FRONTIERS IN PLANT SCIENCE 2021; 12:613845. [PMID: 33679829 PMCID: PMC7933694 DOI: 10.3389/fpls.2021.613845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/18/2021] [Indexed: 05/07/2023]
Abstract
The performance of snake melon [Cucumis melo var. flexuosus (L.)] in organic farming was studied under high biotic and salt stress conditions. Soilborne diseases (mainly caused by Macrophomina phaseolina and Neocosmospora falciformis), combined with virus incidence [Watermelon mosaic virus (WMV), Zucchini yellow mosaic virus (ZYMV), and Tomato leaf curl New Delhi virus (ToLCNDV)] and Podosphaera xanthii attacks, reduced yield by more than 50%. Snake melon susceptibility to M. phaseolina and Monosporascus cannonballus was proved in pathogenicity tests, while it showed some degree of resistance to Neocosmospora keratoplastica and N. falciformis. On the contrary, salt stress had a minor impact, although a synergic effect was detected: yield losses caused by biotic stress increased dramatically when combined with salt stress. Under biotic stress, grafting onto the melon F1Pat81 and wild Cucumis rootstocks consistently reduced plant mortality in different agroecological conditions, with a better performance compared to classic Cucurbita commercial hybrids. Yield was even improved under saline conditions in grafted plants. A negative effect was detected, though, on consumer acceptability, especially with the use of Cucurbita rootstocks. Cucumis F1Pat81 rootstock minimized this side effect, which was probably related to changes in the profile of sugars, acids, and volatiles. Grafting affected sugars and organic acid contents, with this effect being more accentuated with the use of Cucurbita rootstocks than with Cucumis. In fact, the latter had a higher impact on the volatile organic compound profile than on sugar and acid profile, which may have resulted in a lower effect on consumer perception. The use of Cucumis rootstocks seems to be a strategy to enable organic farming production of snake melon targeted to high-quality markets in order to promote the cultivation of this neglected crop.
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Affiliation(s)
- Alejandro Flores-León
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | | | - Vicente González
- Plant Protection Unit/Instituto Agroalimentario de Aragón-IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Ana Garcés-Claver
- Horticulture Unit/Instituto Agroalimentario de Aragón-IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Raúl Martí
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Carmen Julián
- Plant Protection Unit/Instituto Agroalimentario de Aragón-IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Alicia Sifres
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Ana Pérez-de-Castro
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - María José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Carmelo López
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - María Ferriol
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | - Carmina Gisbert
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Juan José Ruiz
- Escuela Politécnica Superior de Orihuela, Universidad Miguel Hernández, Orihuela, Spain
| | - Jaime Cebolla-Cornejo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Belén Picó
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
- *Correspondence: Belén Picó,
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Wang Y, Jiang B, Dymerski R, Xu X, Weng Y. Quantitative trait loci for horticulturally important traits defining the Sikkim cucumber, Cucumis sativus var. sikkimensis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:229-247. [PMID: 32997165 DOI: 10.1007/s00122-020-03693-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
QTL mapping identified simply inherited genes and quantitative trait loci underlying morphologically characteristic traits of the Sikkim cucumber, which reveals their genetic basis during crop evolution. The data suggest the Sikkim cucumber as an ecotype of cultivated cucumber not worthy of formal taxonomic recognition. The Sikkim cucumber, Cucumis sativus var. sikkimensis, is featured with some morphological traits like black spine, brown fruit with fine and heavy netting, as well as large hollow in mature fruit. Despite its establishment as a botanical variety ~ 150 years ago, and its wide use as an important source of disease resistances in cucumber breeding, little is known about its taxonomic status and genetic basis of those characteristic traits. Here we reported QTL mapping with segregating populations derived from two Sikkim-type inbred lines, WI7088D and WI7120, and identification of 48 QTL underlying phenotypic variation for 18 horticulturally important traits. We found that the fruit spine and skin colors in the two populations were controlled by the previously cloned pleiotropic B (black spine) locus. The fruit netting in WI7088D and WI7120 was controlled by the well-known H (Heavy netting) and a novel Rs (Russet skin) locus, which was delimited to a 271-kb region on Chr5 and ~ 736-kb region on Chr1, respectively. A single major-effect QTL was detected for flowering time in each population (ft1.1 for WI7088D and ft6.2 for WI7120). Fifteen, six and five QTL were identified for fruit size, hollow size and flesh thickness variation in the two populations, respectively. No major structural changes were found between the Sikkim and cultivated cucumbers. Except for the rare allele at the Rs locus, there seem no private QTL/alleles identified from this study supporting the Sikkim cucumber as an ecotype of C. sativus, not worthy of formal taxonomic recognition.
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Affiliation(s)
- Yuhui Wang
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Biao Jiang
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ronald Dymerski
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Xuewen Xu
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, 53705, USA.
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9
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Ottoni C, Guellil M, Ozga AT, Stone AC, Kersten O, Bramanti B, Porcier S, Van Neer W. Metagenomic analysis of dental calculus in ancient Egyptian baboons. Sci Rep 2019; 9:19637. [PMID: 31873124 PMCID: PMC6927955 DOI: 10.1038/s41598-019-56074-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.
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Affiliation(s)
- Claudio Ottoni
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway.
- Department of Oral and Maxillofacial Sciences, Diet and Ancient Technology Laboratory (DANTE), Sapienza University, Rome, Italy.
| | - Meriam Guellil
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
- University of Tartu, Institute of Genomics, Estonian Biocentre, 51010, Tartu, Estonia
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
| | - Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
- Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy, and Prevention, University of Ferrara, 35-441221, Ferrara, Italy
| | - Stéphanie Porcier
- Laboratoire CNRS ASM ≪ Archéologie des Sociétés Méditerranéennes (UMR 5140), Université Paul-Valéry, LabEx Archimede, F-34199, Montpellier, France
| | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, B-1000, Brussels, Belgium.
- KU Leuven-University of Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Center of Archaeological Sciences, B-3000, Leuven, Belgium.
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Wang X, Bao K, Reddy UK, Bai Y, Hammar SA, Jiao C, Wehner TC, Ramírez-Madera AO, Weng Y, Grumet R, Fei Z. The USDA cucumber ( Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development. HORTICULTURE RESEARCH 2018; 5:64. [PMID: 30302260 PMCID: PMC6165849 DOI: 10.1038/s41438-018-0080-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 05/19/2023]
Abstract
Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement. Optimal collection, preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection. Here we use the high-throughput genotyping-by-sequencing (GBS) technology to characterize the United States National Plant Germplasm System (NPGS) collection of cucumber (Cucumis sativus L.). The GBS data, derived from 1234 cucumber accessions, provided more than 23 K high-quality single-nucleotide polymorphisms (SNPs) that are well distributed at high density in the genome (~1 SNP/10.6 kb). The SNP markers were used to characterize genetic diversity, population structure, phylogenetic relationships, linkage disequilibrium, and population differentiation of the NPGS cucumber collection. These results, providing detailed genetic analysis of the U.S. cucumber collection, complement NPGS descriptive information regarding geographic origin and phenotypic characterization. We also identified genome regions significantly associated with 13 horticulturally important traits through genome-wide association studies (GWAS). Finally, we developed a molecularly informed, publicly accessible core collection of 395 accessions that represents at least 96% of the genetic variation present in the NPGS. Collectively, the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection, and will provide a valuable resource for genetic analyses, gene discovery, crop improvement, and germplasm preservation.
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Affiliation(s)
- Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, Virginia, WV 25112 USA
| | - Yang Bai
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Sue A. Hammar
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Todd C. Wehner
- Horticultural Science Department, North Carolina State University, Raleigh, NC 27695 USA
| | | | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- USDA-ARS Vegetable Crops Research Unit, Madison, WI 53706 USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
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Leibman D, Kravchik M, Wolf D, Haviv S, Weissberg M, Ophir R, Paris HS, Palukaitis P, Ding S, Gaba V, Gal‐On A. Differential expression of cucumber RNA-dependent RNA polymerase 1 genes during antiviral defence and resistance. MOLECULAR PLANT PATHOLOGY 2018; 19:300-312. [PMID: 27879040 PMCID: PMC6637986 DOI: 10.1111/mpp.12518] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/20/2016] [Accepted: 11/20/2016] [Indexed: 05/21/2023]
Abstract
RNA-dependent RNA polymerase 1 (RDR1) plays a crucial role in plant defence against viruses. In this study, it was observed that cucumber, Cucumis sativus, uniquely encodes a small gene family of four RDR1 genes. The cucumber RDR1 genes (CsRDR1a, CsRDR1b and duplicated CsRDR1c1/c2) shared 55%-60% homology in their encoded amino acid sequences. In healthy cucumber plants, RDR1a and RDR1b transcripts were expressed at higher levels than transcripts of RDR1c1/c2, which were barely detectable. The expression of all four CsRDR1 genes was induced by virus infection, after which the expression level of CsRDR1b increased 10-20-fold in several virus-resistant cucumber cultivars and in a broad virus-resistant transgenic cucumber line expressing a high level of transgene small RNAs, all without alteration in salicylic acid (SA) levels. By comparison, CsRDR1c1/c2 genes were highly induced (25-1300-fold) in susceptible cucumber cultivars infected with RNA or DNA viruses. Inhibition of RDR1c1/c2 expression led to increased virus accumulation. Ectopic application of SA induced the expression of cucumber RDR1a, RDR1b and RDRc1/c2 genes. A constitutive high level of RDR1b gene expression independent of SA was found to be associated with broad virus resistance. These findings show that multiple RDR1 genes are involved in virus resistance in cucumber and are regulated in a coordinated fashion with different expression profiles.
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Affiliation(s)
- Diana Leibman
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, Volcani CenterBet Dagan50250Israel
| | - Michael Kravchik
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, Volcani CenterBet Dagan50250Israel
| | - Dalia Wolf
- Department of Vegetable and Field CropsAgricultural Research Organization, Volcani CenterBet Dagan50250Israel
| | - Sabrina Haviv
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, Volcani CenterBet Dagan50250Israel
| | - Mira Weissberg
- Department of Fruit Tree SciencesAgricultural Research Organization, Volcani CenterBet Dagan50250Israel
| | - Ron Ophir
- Department of Fruit Tree SciencesAgricultural Research Organization, Volcani CenterBet Dagan50250Israel
| | - Harry S. Paris
- Department of Vegetable Crops and Plant GeneticsAgricultural Research Organization, Newe Ya'ar Research Center, PO Box 1021RamatYishay30‐095Israel
| | - Peter Palukaitis
- Department of Horticultural SciencesSeoul Women's UniversityNowon‐guSeoul01797South Korea
| | - Shou‐Wei Ding
- Department of Plant Pathology and Microbiology & Institute for Integrative Genome BiologyUniversity of CaliforniaRiverside, CA92521USA
| | - Victor Gaba
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, Volcani CenterBet Dagan50250Israel
| | - Amit Gal‐On
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, Volcani CenterBet Dagan50250Israel
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12
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Pan Y, Liang X, Gao M, Liu H, Meng H, Weng Y, Cheng Z. Round fruit shape in WI7239 cucumber is controlled by two interacting quantitative trait loci with one putatively encoding a tomato SUN homolog. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:573-586. [PMID: 27915454 DOI: 10.1007/s00122-016-2836-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/26/2016] [Indexed: 05/10/2023]
Abstract
QTL analysis revealed two interacting loci, FS1.2 and FS2.1, underlying round fruit shape in WI7239 cucumber; CsSUN , a homolog of tomato fruit shape gene SUN , was a candidate for FS1.2. Fruit size is an important quality and yield trait in cucumber, but its genetic basis remains poorly understood. Here we reported QTL mapping results on fruit size with segregating populations derived from the cross between WI7238 (long fruit) and WI7239 (round fruit) inbred cucumber lines. Phenotypic data of fruit length and diameter were collected at anthesis, immature and mature fruit stages in four environments. Ten major-effect QTL were detected for six traits; synthesis of information from these QTL supported two genes, FS1.2 and FS2.1, underlying fruit size variation in the examined populations. Under the two-gene model, deviation from expected segregation ratio in fruit length and diameter among segregating populations was observed, which could be explained mainly by the interactions between FS1.2 and FS2.1, and segregation distortion in the FS2.1 region. Genome-wide candidate gene search identified CsSUN, a homolog of the tomato fruit shape gene SUN, as the candidate for FS1.2. The round-fruited WI7239 had a 161-bp deletion in the first exon of CsSUN, and its expression in WI7239 was significantly lower than that in WI7238. A marker derived from this deletion was mapped at the peak location of FS1.2 in QTL analysis. Comparative analysis suggested the melon gene CmSUN-14, a homolog of CsSUN as a candidate of the fl2/fd2/fw2 QTL in melon. This study revealed the unique genetic architecture of round fruit shape in WI7239 cucumber. It also highlights the power of QTL analysis for traits with a simple genetic basis but their expression is complicated by other factors.
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Affiliation(s)
- Yupeng Pan
- Horticulture College, Northwest A&F University, Yangling, 712100, China
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Xinjing Liang
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Meiling Gao
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Hanqiang Liu
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Huanwen Meng
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA.
| | - Zhihui Cheng
- Horticulture College, Northwest A&F University, Yangling, 712100, China.
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13
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Skupień J, Wójtowicz J, Kowalewska Ł, Mazur R, Garstka M, Gieczewska K, Mostowska A. Dark-chilling induces substantial structural changes and modifies galactolipid and carotenoid composition during chloroplast biogenesis in cucumber (Cucumis sativus L.) cotyledons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 111:107-118. [PMID: 27915172 DOI: 10.1016/j.plaphy.2016.11.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/17/2016] [Accepted: 11/26/2016] [Indexed: 05/21/2023]
Abstract
Plants in a temperate climate are often subject to different environmental factors, chilling stress among them, which influence the growth especially during early stages of plant development. Chloroplasts are one of the first organelles affected by the chilling stress. Therefore the proper biogenesis of chloroplasts in early stages of plant growth is crucial for undertaking the photosynthetic activity. In this paper, the analysis of the cotyledon chloroplast biogenesis at different levels of plastid organization was performed in cucumber, one of the most popular chilling sensitive crops. Influence of low temperature on the ultrastructure was manifested by partial recrystallization of the prolamellar body, the formation of elongated grana thylakoids and a change of the prolamellar body structure from the compacted "closed" type to a more loose "open" type. Structural changes are strongly correlated with galactolipid and carotenoid content. Substantial changes in the galactolipid and the carotenoid composition in dark-chilled plants, especially a decrease of the monogalactosyldiacylglycerol to digalactosyldiacylglycerol ratio (MGDG/DGDG) and an increased level of lutein, responsible for a decrease in membrane fluidity, were registered together with a slower adaptation to higher light intensity and an increased level of non-photochemical reactions. Changes in the grana thylakoid fluidity, of their structure and photosynthetic efficiency in developing chloroplasts of dark-chilled plants, without significant changes in the PSI/PSII ratio, could distort the balance of photosystem rearrangements and be one of the reasons of cucumber sensitivity to chilling.
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Affiliation(s)
- Joanna Skupień
- Department of Plant Anatomy and Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Joanna Wójtowicz
- Department of Plant Anatomy and Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Łucja Kowalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Radosław Mazur
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Maciej Garstka
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Katarzyna Gieczewska
- Department of Plant Anatomy and Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agnieszka Mostowska
- Department of Plant Anatomy and Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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14
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Lust TA, Paris HS. Italian horticultural and culinary records of summer squash (Cucurbita pepo, Cucurbitaceae) and emergence of the zucchini in 19th-century Milan. ANNALS OF BOTANY 2016; 118:53-69. [PMID: 27343231 PMCID: PMC4934399 DOI: 10.1093/aob/mcw080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 03/17/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Summer squash, the young fruits of Cucurbita pepo, are a common, high-value fruit vegetable. Of the summer squash, the zucchini, C. pepo subsp. pepo Zucchini Group, is by far the most cosmopolitan. The zucchini is easily distinguished from other summer squash by its uniformly cylindrical shape and intense colour. The zucchini is a relatively new cultivar-group of C. pepo, the earliest known evidence for its existence having been a description in a book on horticulture published in Milan in 1901. For this study, Italian-language books on agriculture and cookery dating from the 16th to 19th centuries have been collected and searched in an effort to follow the horticultural development and culinary use of young Cucurbita fruits in Italy. FINDINGS The results indicate that Cucurbita fruits, both young and mature, entered Italian kitchens by the mid-16th century. A half-century later, round and elongate young fruits of C. pepo were addressed as separate cookery items and the latter had largely replaced the centuries-old culinary use of young, elongate bottle gourds, Lagenaria siceraria Allusion to a particular, extant cultivar of the longest fruited C. pepo, the Cocozelle Group, dates to 1811 and derives from the environs of Naples. The Italian diminutive word zucchini arose by the beginning of the 19th century in Tuscany and referred to small, mature, desiccated bottle gourds used as containers to store tobacco. By the 1840s, the Tuscan word zucchini was appropriated to young, primarily elongate fruits of C. pepo The Zucchini Group traces its origins to the environs of Milan, perhaps as early as 1850. The word zucchini and the horticultural product zucchini arose contemporaneously but independently. The results confirm that the Zucchini Group is the youngest of the four cultivar-groups of C. pepo subsp. pepo but it emerged approximately a half-century earlier than previously known.
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Affiliation(s)
- Teresa A Lust
- Dartmouth College, Rassias Center for World Languages and Cultures, 6071 Blunt, Suite 315, Hanover, NH 03755-3526, USA
| | - Harry S Paris
- Agricultural Research Organization, Newe Ya'ar Research Center, PO Box 1021, Ramat Yishay 3009500, Israel
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15
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Weng Y, Colle M, Wang Y, Yang L, Rubinstein M, Sherman A, Ophir R, Grumet R. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1747-63. [PMID: 26048092 DOI: 10.1007/s00122-015-2544-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/18/2015] [Indexed: 05/06/2023]
Abstract
QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.
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Affiliation(s)
- Yiqun Weng
- Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA,
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16
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Paris HS. Origin and emergence of the sweet dessert watermelon, Citrullus lanatus. ANNALS OF BOTANY 2015; 116:133-48. [PMID: 26141130 PMCID: PMC4512189 DOI: 10.1093/aob/mcv077] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/16/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Watermelons, Citrullus species (Cucurbitaceae), are native to Africa and have been cultivated since ancient times. The fruit flesh of wild watermelons is watery, but typically hard-textured, pale-coloured and bland or bitter. The familiar sweet dessert watermelons, C. lanatus, featuring non-bitter, tender, well-coloured flesh, have a narrow genetic base, suggesting that they originated from a series of selection events in a single ancestral population. The objective of the present investigation was to determine where dessert watermelons originated and the time frame during which sweet dessert watermelons emerged. KEY FINDINGS Archaeological remains of watermelons, mostly seeds, that date from 5000 years ago have been found in northeastern Africa. An image of a large, striped, oblong fruit on a tray has been found in an Egyptian tomb that dates to at least 4000 years ago. The Greek word pepon, Latin pepo and Hebrew avattiah of the first centuries CE were used for the same large, thick-rinded, wet fruit which, evidently, was the watermelon. Hebrew literature from the end of the second century CE and Latin literature from the beginning of the sixth century CE present watermelons together with three sweet fruits: figs, table grapes and pomegranates. Wild and primitive watermelons have been observed repeatedly in Sudan and neighbouring countries of northeastern Africa. CONCLUSIONS The diverse evidence, combined, indicates that northeastern Africa is the centre of origin of the dessert watermelon, that watermelons were domesticated for water and food there over 4000 years ago, and that sweet dessert watermelons emerged in Mediterranean lands by approximately 2000 years ago. Next-generation ancient-DNA sequencing and state-of-the-art genomic analysis offer opportunities to rigorously assess the relationships among ancient and living wild and primitive watermelons from northeastern Africa, modern sweet dessert watermelons and other Citrullus taxa.
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Affiliation(s)
- Harry S Paris
- Institute of Plant Sciences, Agricultural Research Organization, Newe Ya'ar Research Center, P. O. Box 1021, Ramat Yishay 30-095, Israel
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Avital A, Paris HS. Cucurbits depicted in Byzantine mosaics from Israel, 350-600 ce. ANNALS OF BOTANY 2014; 114:203-22. [PMID: 24948671 PMCID: PMC4111391 DOI: 10.1093/aob/mcu106] [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] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Thousands of floor mosaics were produced in lands across the Roman and Byzantine empires. Some mosaics contain depictions of agricultural produce, potentially providing useful information concerning the contemporary presence and popularity of crop plants in a particular geographical region. Hundreds of floor mosaics produced in Israel during the Byzantine period have survived. The objective of the present work was to search these mosaics for Cucurbitaceae in order to obtain a more complete picture of cucurbit crop history in the eastern Mediterranean region. RESULTS AND CONCLUSIONS Twenty-three mosaics dating from 350-600 ce were found that had images positively identifiable as cucurbits. The morphological diversity of the cucurbit fruits in the mosaics of Israel is greater than that appearing in mosaics from any other Roman or Byzantine provincial area. The depicted fruits vary in shape from oblate to extremely long, and some are furrowed, others are striped and others lack definite markings. The cucurbit taxa depicted in the mosaics are Cucumis melo (melon), Citrullus lanatus (watermelon), Luffa aegyptiaca (sponge gourd) and Lagenaria siceraria (bottle gourd). Cucumis melo is the most frequently found taxon in the mosaics and is represented by round dessert melons and long snake melons. Fruits of at least two cultivars of snake melons and of watermelons are represented. To our knowledge, images of sponge gourds have not been found in Roman and Byzantine mosaics elsewhere. Indeed, the mosaics of Israel contain what are probably the oldest depictions of Luffa aegyptiaca in Mediterranean lands. Sponge gourds are depicted often, in 11 of the mosaics at eight localities, and the images include both mature fruits, which are useful for cleaning and washing, and immature fruits, which are edible. Only one mosaic has images positively identifiable as of bottle gourds, and these were round-pyriform and probably used as vessels.
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Affiliation(s)
- Anat Avital
- Department of Land of Israel Studies and Archaeology, Bar-Ilan University, Ramat Gan 52-900, Israel
| | - Harry S Paris
- Department of Vegetable Crops and Plant Genetics, Agricultural Research Organization, Newe Ya'ar Research Center, PO Box 1021, Ramat Yishay 30-095, Israel
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18
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Yang L, Koo DH, Li Y, Zhang X, Luan F, Havey MJ, Jiang J, Weng Y. Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:895-906. [PMID: 22487099 DOI: 10.1111/j.1365-313x.2012.05017.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cucumber, Cucumis sativus L. is the only taxon with 2n = 2x = 14 chromosomes in the genus Cucumis. It consists of two cross-compatible botanical varieties: the cultivated C. sativus var. sativus and the wild C. sativus var. hardwickii. There is no consensus on the evolutionary relationship between the two taxa. Whole-genome sequencing of the cucumber genome provides a new opportunity to advance our understanding of chromosome evolution and the domestication history of cucumber. In this study, a high-density genetic map for cultivated cucumber was developed that contained 735 marker loci in seven linkage groups spanning 707.8 cM. Integration of genetic and physical maps resulted in a chromosome-level draft genome assembly comprising 193 Mbp, or 53% of the 367 Mbp cucumber genome. Strategically selected markers from the genetic map and draft genome assembly were employed to screen for fosmid clones for use as probes in comparative fluorescence in situ hybridization analysis of pachytene chromosomes to investigate genetic differentiation between wild and cultivated cucumbers. Significant differences in the amount and distribution of heterochromatins, as well as chromosomal rearrangements, were uncovered between the two taxa. In particular, six inversions, five paracentric and one pericentric, were revealed in chromosomes 4, 5 and 7. Comparison of the order of fosmid loci on chromosome 7 of cultivated and wild cucumbers, and the syntenic melon chromosome I suggested that the paracentric inversion in this chromosome occurred during domestication of cucumber. The results support the sub-species status of these two cucumber taxa, and suggest that C. sativus var. hardwickii is the progenitor of cultivated cucumber.
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Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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19
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Paris HS, Amar Z, Lev E. Medieval emergence of sweet melons, Cucumis melo (Cucurbitaceae). ANNALS OF BOTANY 2012; 110:23-33. [PMID: 22648880 PMCID: PMC3380595 DOI: 10.1093/aob/mcs098] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 03/27/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sweet melons, Cucumis melo, are a widely grown and highly prized crop. While melons were familiar in antiquity, they were grown mostly for use of the young fruits, which are similar in appearance and taste to cucumbers, C. sativus. The time and place of emergence of sweet melons is obscure, but they are generally thought to have reached Europe from the east near the end of the 15th century. The objective of the present work was to determine where and when truly sweet melons were first developed. METHODS Given their large size and sweetness, melons are often confounded with watermelons, Citrullus lanatus, so a list was prepared of the characteristics distinguishing between them. An extensive search of literature from the Roman and medieval periods was conducted and the findings were considered in their context against this list and particularly in regard to the use of the word 'melon' and of adjectives for sweetness and colour. FINDINGS Medieval lexicographies and an illustrated Arabic translation of Dioscorides' herbal suggest that sweet melons were present in Central Asia in the mid-9th century. A travelogue description indicates the presence of sweet melons in Khorasan and Persia by the mid-10th century. Agricultural literature from Andalusia documents the growing of sweet melons, evidently casabas (Inodorous Group), there by the second half of the 11th century, which probably arrived from Central Asia as a consequence of Islamic conquest, trade and agricultural development. Climate and geopolitical boundaries were the likely causes of the delay in the spread of sweet melons into the rest of Europe.
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Affiliation(s)
- Harry S Paris
- Department of Vegetable Crops & Plant Genetics, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishay, Israel.
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