1
|
Testone G, Lamprillo M, Gonnella M, Arnesi G, Sobolev AP, Aiese Cigliano R, Giannino D. The Chloroplast Genome of Endive ( Cichorium endivia L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events. Genes (Basel) 2023; 14:1829. [PMID: 37761969 PMCID: PMC10531310 DOI: 10.3390/genes14091829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
The chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (Cichorium endivia var. latifolium and var. crispum) are of nutritional and economic importance and are the target of ever-changing breeding programmes. A reference cp genome sequence was assembled and annotated (cultivar 'Confiance'), which was 152,809 base pairs long, organized into the angiosperm-typical quadripartite structure, harboring two inverted repeats separated by the large- and short- single copy regions. The annotation included 136 genes, 90 protein-coding genes, 38 transfer, and 8 ribosomal RNAs and the sequence generated a distinct phyletic group within Asteraceae with the well-separated C. endivia and intybus species. SSR variants within the reference genome were mostly of tri-nucleotide type, and the cytosine to uracil (C/U) RNA editing recurred. The cp genome was nearly fully transcribed, hence sequence polymorphism was investigated by RNA-Seq of seven cultivars, and the SNP number was higher in smooth- than curly-leafed ones. All cultivars maintained C/U changes in identical positions, suggesting that RNA editing patterns were conserved; most cultivars shared SNPs of moderate impact on protein changes in the ndhD, ndhA, and psbF genes, suggesting that their variability may have a potential role in adaptive response. The cp transcriptome expression was investigated in leaves of plants affected by pre-harvest rainfall and rainfall excess plus waterlogging events characterized by production loss, compared to those of a cycle not affected by extreme rainfall. Overall, the analyses evidenced stress- and cultivar-specific responses, and further revealed that genes of the Cytochrome b6/f, and PSI-PSII systems were commonly affected and likely to be among major targets of extreme rain-related stress.
Collapse
Affiliation(s)
- Giulio Testone
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (G.T.); (M.L.); (A.P.S.)
| | - Michele Lamprillo
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (G.T.); (M.L.); (A.P.S.)
| | - Maria Gonnella
- Institute of Sciences of Food Production, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy;
| | - Giuseppe Arnesi
- Enza Zaden Italia, Strada Statale Aurelia Km 96.400, Tarquinia, 01016 Viterbo, Italy;
| | - Anatoly Petrovich Sobolev
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (G.T.); (M.L.); (A.P.S.)
| | | | - Donato Giannino
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (G.T.); (M.L.); (A.P.S.)
| |
Collapse
|
2
|
El-Taher AM, Elzilal HA, Abd El-Raouf HS, Mady E, Alshallash KS, Alnefaie RM, Mahdy EMB, Ragab OG, Emam EA, Alaraidh IA, Randhir TO, Ibrahim MFM. Characterization of Some Cichorium Taxa Grown under Mediterranean Climate Using Morphological Traits and Molecular Markers. Plants (Basel) 2023; 12:388. [PMID: 36679101 PMCID: PMC9866365 DOI: 10.3390/plants12020388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
The verification of taxonomic identities is of the highest significance in the field of biological study and categorization. Morpho-molecular characterization can clarify uncertainties in distinguishing between taxonomic groups. In this study, we characterized five local taxa of the genus Cichorium using morphological and molecular markers for taxonomic authentication and probably future genetic improvement. The five Cichorium taxa grown under the Mediterranean climate using morphological traits and molecular markers showed variations. The examined taxa showed a widespread range of variations in leaf characteristics, i.e., shape, type, texture, margin, and apex and cypsela characteristics i.e., shape, color, and surface pattern. The phylogenetic tree categorized the Cichorium intybus var. intybus and C. intybus var. foliosum in a single group, whereas C. endivia var. endivia was grouped separately. However, C. endivia var. crispum and C. endivia subsp. pumilum were classified as a cluster. The recorded variance between classes using the molecular markers SCoT, ISSR, and RAPD was documented at 34.43%, 36.62%, and 40.34%, respectively. Authentication using molecular tools proved the usefulness of a dichotomous indented key, as revealed by morphological identification. The integrated methodology using morphological and molecular assessment could support improved verification and authentication of the various taxa of chicory. It seems likely that the Egyptian chicory belongs to C. endivia subsp. pumilum.
Collapse
Affiliation(s)
- Ahmed M. El-Taher
- Department of Agricultural Botany, Faculty of Agriculture, Al-Azhar University, Cairo 11884, Egypt
| | - Hala A. Elzilal
- Department of Science and Technology, College of Ranyah, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Hany S. Abd El-Raouf
- Department of Agricultural Botany, Faculty of Agriculture, Al-Azhar University, Cairo 11884, Egypt
- Biology Department, University College, Taif University, Turaba 29731, Saudi Arabia
| | - Emad Mady
- Horticulture Department, Faculty of Agriculture, Al-Azhar University, Cairo 11884, Egypt
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA
| | - Khalid S. Alshallash
- College of Science and Humanities-Huraymila, Imam Mohammed Bin Saud Islamic University (IMSIU), Riyadh 11432, Saudi Arabia
| | - Rasha M. Alnefaie
- Biology Department, Faculty of Science Albaha University, Albaha 65779, Saudi Arabia
| | - Ehab M. B. Mahdy
- National Gene Bank (NGB), Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Osama G. Ragab
- Botany and Microbiology Department, Faculty of Science (Boys Branch), Al-Azhar University, Cairo 11884, Egypt
| | - Elhassan A. Emam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Ibrahim A. Alaraidh
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh 11362, Saudi Arabia
| | - Timothy O. Randhir
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA
| | - Mohamed F. M. Ibrahim
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| |
Collapse
|
3
|
Guarino F, Castiglione S, Improta G, Triassi M, Cicatelli A. Ecotype-Level Genetic Biodiversity of Five Italian Traditional Crops. Scientifica (Cairo) 2019; 2019:4652769. [PMID: 31355045 PMCID: PMC6636500 DOI: 10.1155/2019/4652769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/05/2019] [Accepted: 05/22/2019] [Indexed: 06/10/2023]
Abstract
Italy displays a high level of agrobiodiversity due to its diversified pedoclimatic zones. The Administrative Region of Campania includes several and divergent biomes, occurring close to each other. In fact, the distance between a sea level environment and that of high mountains can be less than 20 km. These environmental conditions allow the cultivation of many different crops and vegetables, represented by diverse ecotypes and varieties that are well adapted to the distribution range where they have been selected and grown. Efforts to maintain and further increase biodiversity in farming systems require a better understanding of the existing diversity created by traditional farming practices. The aim of our study was to identify and molecularly characterize several ecotypes belonging to five horticultural species commonly cultivated in Campania. In particular, we analysed five ecotypes of maize, two of garlic, four of onion, one of escarole, and two of courgette by means of simple sequence repeat (SSR) markers in order to evaluate their level of genetic biodiversity. The results reveal, for the first time, the high genetic biodiversity of horticultural ecotypes of the Campania Region. This feature is very important to improve the quality and productivity of agroecosystems.
Collapse
Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “Adolfo Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano (SA), Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “Adolfo Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano (SA), Italy
| | - Giovanni Improta
- Dipartimento di Sanità Pubblica, Università degli Studi di Napoli Federico II, Via Pansini, 5, 80125 Napoli (NA), Italy
| | - Maria Triassi
- Dipartimento di Sanità Pubblica, Università degli Studi di Napoli Federico II, Via Pansini, 5, 80125 Napoli (NA), Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “Adolfo Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano (SA), Italy
| |
Collapse
|