1
|
Asadi A, Shariati V, Mousavi S, Mariotti R, Hosseini Mazinani M. Meta-analysis of transcriptome reveals key genes relating to oil quality in olive. BMC Genomics 2023; 24:566. [PMID: 37740234 PMCID: PMC10517554 DOI: 10.1186/s12864-023-09673-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Olive oil contains monounsaturated oleic acid up to 83% and phenolic compounds, making it an excellent source of fat. Due to its economic importance, the quantity and quality of olive oil should be improved in parallel with international standards. In this study, we analyzed the raw RNA-seq data with a meta-analysis approach to identify important genes and their metabolic pathways involved in olive oil quality. RESULTS A deep search of RNA-seq published data shed light on thirty-nine experiments associated with the olive transcriptome, four of these proved to be ideal for meta-analysis. Meta-analysis confirmed the genes identified in previous studies and released new genes, which were not identified before. According to the IDR index, the meta-analysis had good power to identify new differentially expressed genes. The key genes were investigated in the metabolic pathways and were grouped into four classes based on the biosynthetic cycle of fatty acids and factors that affect oil quality. Galactose metabolism, glycolysis pathway, pyruvate metabolism, fatty acid biosynthesis, glycerolipid metabolism, and terpenoid backbone biosynthesis were the main pathways in olive oil quality. In galactose metabolism, raffinose is a suitable source of carbon along with other available sources for carbon in fruit development. The results showed that the biosynthesis of acetyl-CoA in glycolysis and pyruvate metabolism is a stable pathway to begin the biosynthesis of fatty acids. Key genes in oleic acid production as an indicator of oil quality and critical genes that played an important role in production of triacylglycerols were identified in different developmental stages. In the minor compound, the terpenoid backbone biosynthesis was investigated and important enzymes were identified as an interconnected network that produces important precursors for the synthesis of a monoterpene, diterpene, triterpene, tetraterpene, and sesquiterpene biosynthesis. CONCLUSIONS The results of the current investigation can produce functional data related to the quality of olive oil and would be a useful step in reducing the time of cultivar screening by developing gene specific markers in olive breeding programs, releasing also new genes that could be applied in the genome editing approach.
Collapse
Affiliation(s)
- AliAkbar Asadi
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
| | - Vahid Shariati
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran.
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, 06128, Perugia, Italy
| | - Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, 06128, Perugia, Italy
| | - Mehdi Hosseini Mazinani
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran.
| |
Collapse
|
2
|
Cultrera NGM. Genetics of Plant Metabolism. Int J Mol Sci 2023; 24:ijms24086890. [PMID: 37108054 PMCID: PMC10138566 DOI: 10.3390/ijms24086890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/20/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
This Special Issue is aimed to collect scientific papers that support holistic methodological approaches, both top-down and horizontal, for the correct application of various omics sciences because, when well-integrated, they can contribute to our understanding of the genotypic plasticity of plant species [...].
Collapse
Affiliation(s)
- Nicolò G M Cultrera
- CNR-IBBR Institute of Biosciences and Bioresources, National Research Council, 70126 Bari, Italy
| |
Collapse
|
3
|
Choi BS, Choi SK, Kim NS, Choi IY. NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer. Genomics Inform 2022; 20:e40. [PMID: 36239113 PMCID: PMC9576473 DOI: 10.5808/gi.21075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 12/31/2022] Open
Abstract
BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as "query" or "target" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.
Collapse
Affiliation(s)
| | - Seon Kang Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Soo Kim
- BIT Institute NBIT Co., Ltd., Chuncheon 24341, Korea
| | - Ik-Young Choi
- BIT Institute NBIT Co., Ltd., Chuncheon 24341, Korea
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| |
Collapse
|
4
|
Wu Z, Huang L, Huang F, Lu G, Wei S, Liu C, Deng H, Liang G. Temporal transcriptome analysis provides molecular insights into flower development in red-flesh pitaya. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
5
|
Alagna F, Cirilli M, Galla G, Carbone F, Daddiego L, Facella P, Lopez L, Colao C, Mariotti R, Cultrera N, Rossi M, Barcaccia G, Baldoni L, Muleo R, Perrotta G. Correction: Transcript Analysis and Regulative Events during Flower Development in Olive (Olea europaea L.). PLoS One 2022; 17:e0263101. [PMID: 35061857 PMCID: PMC8782328 DOI: 10.1371/journal.pone.0263101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
6
|
De Pascali M, Vergine M, Negro C, Greco D, Vita F, Sabella E, De Bellis L, Luvisi A. Xylella fastidiosa and Drought Stress in Olive Trees: A Complex Relationship Mediated by Soluble Sugars. BIOLOGY 2022; 11:biology11010112. [PMID: 35053110 PMCID: PMC8773346 DOI: 10.3390/biology11010112] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/02/2022] [Accepted: 01/07/2022] [Indexed: 12/19/2022]
Abstract
Simple Summary Carbohydrates play important roles in tolerance to both biotic and abiotic stressors. Xylella fastidiosa, the causal agent of “Olive Quick Decline Syndrome”, is a quarantine pathogen that induces drought stress in the host, aggravated by eventual water shortage, which is a frequent environmental condition in Mediterranean olive groves. At present, the resistance mechanisms shown by few resistant olive cultivars (e.g., cv Leccino) are not completely known; therefore, the aim of this research is to understand whether sugar metabolism is involved in the cross-talk mechanisms of biotic and abiotic responses. The results show that drought stress response induces effects beneficial to resistance of Xylella fastidiosa in cv Leccino. In the current context of global climate change, this study supports the importance of investigating the complex drought–disease interaction to detect resistance traits and thus find ways to counter the threat of this pathogen in the future. Abstract Xylella fastidiosa (Xf) subsp. pauca “De Donno” is the etiological agent of “Olive Quick Decline Syndrome” (OQDS) on olive trees (Olea europaea L.); the presence of the bacterium causes xylem vessel occlusions inducing a drought stress and the development of leaf scorch symptoms, which may be worsened by water shortage in summer. In order to evaluate how the two stress factors overlap each other, the carbohydrate content and the expression patterns of genes related to carbohydrate metabolism have been evaluated in two olive cvs trees (Cellina di Nardò, susceptible to Xf, and Leccino, resistant to Xf) reporting transcriptional dynamics elicited by Xf infection, drought, or combined stress (drought/Xf). In the Xf-susceptible Cellina di Nardò plants, Xf and its combination with drought significantly decrease total sugars compared to control (−27.0% and −25.7%, respectively). In contrast, the Xf-resistant Leccino plants show a more limited reduction in sugar content in Xf-positive conditions (−20.1%) and combined stresses (−11.1%). Furthermore, while the amount of glucose decreases significantly in stressed Cellina di Nardò plants (≈18%), an increase was observed in Leccino plants under drought/Xf combined stresses (+11.2%). An opposite behavior among cvs was also observed for sucrose, as an accumulation of the disaccharide was recorded in stressed Leccino plants (≈37%). The different response to combined stress by Xf-resistant plants was confirmed considering genes coding for the sucrose or monosaccharide transporter (OeSUT1, OeMST2), the cell wall or vacuolar invertase (OeINV-CW, OeINV-V), the granule-bound starch synthase I (OeGBSSI) and sucrose synthase (OeSUSY), with a higher expression than at least one single stress (e.g., ≈1-fold higher or more than Xf for OeMST2, OeINV-CW, OeINV-V, OeGBSSI). It is probable that the pathways involved in drought stress response induce positive effects useful for pathogen resistance in cv Leccino, confirming the importance of investigating the mechanisms of cross-talk of biotic and abiotic responses.
Collapse
Affiliation(s)
- Mariarosaria De Pascali
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.D.P.); (C.N.); (D.G.); (E.S.); (L.D.B.); (A.L.)
| | - Marzia Vergine
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.D.P.); (C.N.); (D.G.); (E.S.); (L.D.B.); (A.L.)
- Correspondence:
| | - Carmine Negro
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.D.P.); (C.N.); (D.G.); (E.S.); (L.D.B.); (A.L.)
| | - Davide Greco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.D.P.); (C.N.); (D.G.); (E.S.); (L.D.B.); (A.L.)
| | - Federico Vita
- Department of Biology, University of Bari Aldo Moro, 70121 Bari, Italy;
| | - Erika Sabella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.D.P.); (C.N.); (D.G.); (E.S.); (L.D.B.); (A.L.)
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.D.P.); (C.N.); (D.G.); (E.S.); (L.D.B.); (A.L.)
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.D.P.); (C.N.); (D.G.); (E.S.); (L.D.B.); (A.L.)
| |
Collapse
|
7
|
Cai B, Wang T, Fu W, Harun A, Ge X, Li Z. Dosage-Dependent Gynoecium Development and Gene Expression in Brassica napus-Orychophragmus violaceus Addition Lines. PLANTS (BASEL, SWITZERLAND) 2021; 10:1766. [PMID: 34579298 PMCID: PMC8469106 DOI: 10.3390/plants10091766] [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: 07/21/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Distant hybridization usually leads to female sterility of the hybrid but the mechanism behind this is poorly understood. Complete pistil abortion but normal male fertility was shown by one Brassica napus-Orychophragmus violaceus monosomic alien addition line (MA, AACC + 1 IO, 2n = 39) produced previously. To study the effect of a single O. violaceus chromosome addition on pistil development in different genetic backgrounds, hybrids between the MA and B. carinata (BBCC), B. juncea (AABB), and two synthetic hexaploids (AABBCC) were firstly produced in this study which show complete female sterility. A microspore culture was further performed to produce the haploid monosomic alien addition line (HMA, AC + 1 IO, 2n = 20) and disomic addition line (DA, AACC + 2 IO, 2n = 40) together with haploid (H, AC, 2n = 19) and double haploid (DH, AACC, 2n = 38) plants of B. napus from MA to investigate the dosage effect of the alien O. violaceus chromosome on pistil development and gene expression. Compared to MA, the development of the pistils of DA and HMA was completely or partially recovered, in which the pistils could swell and elongate to a normal shape after open pollination, although no seeds were produced. Comparative RNA-seq analyses revealed that the numbers of the differentially expressed genes (DEGs) were significantly different, dosage-dependent, and consistent with the phenotypic difference in pairwise comparisons of HMA vs. H, DA vs. DH, MA vs. DH, MA vs. DA, and MA vs. HMA. The gene ontology (GO) enrichment analysis of DEGs showed that a number of genes involved in the development of the gynoecium, embryo sac, ovule, and integuments. Particularly, several common DEGs for pistil development shared in HMA vs. H and DA vs. DH showed functions in genotoxic stress response, auxin transport, and signaling and adaxial/abaxial axis specification. The results provided updated information for the molecular mechanisms behind the gynoecium development of B. napus responding to the dosage of alien O. violaceus chromosomes.
Collapse
Affiliation(s)
| | | | | | | | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (B.C.); (T.W.); (W.F.); (A.H.); (Z.L.)
| | | |
Collapse
|
8
|
Yadav S, Carvalho J, Trujillo I, Prado M. Microsatellite Markers in Olives ( Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies. Foods 2021; 10:foods10081907. [PMID: 34441688 PMCID: PMC8394707 DOI: 10.3390/foods10081907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
The olive fruit, a symbol of Mediterranean diets, is a rich source of antioxidants and oleic acid (55–83%). Olive genetic resources, including cultivated olives (cultivars), wild olives as well as related subspecies, are distributed widely across the Mediterranean region and other countries. Certain cultivars have a high commercial demand and economical value due to the differentiating organoleptic characteristics. This might result in economically motivated fraudulent practices and adulteration. Hence, tools to ensure the authenticity of constituent olive cultivars are crucial, and this can be achieved accurately through DNA-based methods. The present review outlines the applications of microsatellite markers, one of the most extensively used types of molecular markers in olive species, particularly referring to the use of these DNA-based markers in cataloging the vast olive germplasm, leading to identification and authentication of the cultivars. Emphasis has been given on the need to adopt a uniform platform where global molecular information pertaining to the details of available markers, cultivar-specific genotyping profiles (their synonyms or homonyms) and the comparative profiles of oil and reference leaf samples is accessible to researchers. The challenges of working with microsatellite markers and efforts underway, mainly advancements in genotyping methods which can be effectively incorporated in olive oil varietal testing, are also provided. Such efforts will pave the way for the development of more robust microsatellite marker-based olive agri-food authentication platforms.
Collapse
Affiliation(s)
- Shambhavi Yadav
- Genetics and Tree Improvement Division, Forest Research Institute, P.O. New Forest, Dehradun 248001, India
- Correspondence: (S.Y.); (I.T.)
| | - Joana Carvalho
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal; (J.C.); (M.P.)
- Department of Analytical Chemistry, Nutrition and Food Science, Campus Vida, College of Pharmacy/School of Veterinary Sciences, University of Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Isabel Trujillo
- Excellence Unit of Maria de Maeztu, Department of Agronomy, Rabanales Campus, International Campus of Excellence on Agrofood (ceiA3), University of Córdoba, 14014 Córdoba, Spain
- Correspondence: (S.Y.); (I.T.)
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal; (J.C.); (M.P.)
| |
Collapse
|
9
|
Li Q, Zhao T, Liang L, Hou S, Wang G, Ma Q. Molecular cloning and expression analysis of hybrid hazelnut (Corylus heterophylla × Corylus avellana) ChaSRK1/2 genes and their homologs from other cultivars and species. Gene 2020; 756:144917. [PMID: 32590104 DOI: 10.1016/j.gene.2020.144917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 05/22/2020] [Accepted: 06/17/2020] [Indexed: 12/01/2022]
Abstract
The self-incompatibility system of Corylus is a sporophytic type that is phenotypically similar to that of Brassica. While the molecular mechanism of sporophytic self-incompatibility (SSI) has been investigated extensively in Brassica (Brassicaceae), little is known about the corresponding mechanism in Corylus (Betulaceae). Here, we discuss the SSI mechanism with respect to S-locus receptor kinase (SRK) gene homologs. To obtain two SRK candidate unigenes, we compared all of the unigenes in a transcriptional protein database from our previous study with BnSRK-1 (AB270767) using BLASTX with a cutoff e-value of 10-5. We then cloned the full-length cDNA of ChaSRK1 and ChaSRK2 genes from Ping'ou hybrid hazelnut (Corylus heterophylla × Corylus avellana) using RACE techniques. Bioinformatics approaches were used to analyze the cDNA sequences, protein sequences, and domains of the encoded proteins. The full-length ChaSRK1 cDNA was 2883 base pairs (bp) with a coding sequence (CDS) of 2,547 bp encoding 849 amino acid residues. The full-length ChaSRK2 cDNA was 2,693 bp, with a CDS of 2,433 bp encoding 811 amino acids. The ChaSRK1/2 proteins contained an S-domain (extracellular domain), a transmembrane domain, a Ser/Thr protein kinase active site (kinase domain), and DUF3660 and/or DUF3403 domains. The lengths of 18 partial SRK homologs ranged from 1347 to 1451 bp, and they contained the same structural domains as ChaSRK1 and ChaSRK2. Phylogenetic analysis revealed that all SRK homologs could be divided into two categories that were similar to the classification of SRKs in Brassica. The expression patterns of ChaSRK1 and ChaSRK2 differed: ChaSRK2 was predominantly expressed in mature stigmatic styles, while ChaSRK1 was expressed in other tissues with the highest in the root tips of Corylus. Using dual-color fluorescence in situ hybridization, ChaSRK1/2 expression was found to be localized in papillar cells. Collectively, these results revealed that SRKs from Corylus had similar characteristics to SRKs from Brassica. We therefore speculated that the SSI mechanism in Corylus might be more similar to the Brassica mechanism than to other SSI types.
Collapse
Affiliation(s)
- Qing Li
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Tiantian Zhao
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Lisong Liang
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Sihao Hou
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Guixi Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China
| | - Qinghua Ma
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Beijing 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China; National Hazelnut Industry Innovation Alliance, Beijing 100091, China.
| |
Collapse
|
10
|
Analyzing Differentially Expressed Genes and Pathways Associated with Pistil Abortion in Japanese Apricot via RNA-Seq. Genes (Basel) 2020; 11:genes11091079. [PMID: 32942711 PMCID: PMC7565994 DOI: 10.3390/genes11091079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Reproduction is a critical stage in the flower development process, and its failure causes serious problems affecting fruit quality and yield. Pistil abortion is one of the main factors in unsuccessful reproduction and occurs in many fruit plants. In Japanese apricot, the problem of pistil abortion is very common and affects fruit quality and plant yield; however, its molecular mechanism is not clearly understood. Therefore, in the current study, we used RNA-Seq to identify the differentially expressed genes (DEGs) and pathways actively involved in pistil abortion. A total of 3882 differentially expressed genes were found after cutoff and pairwise comparison analysis. According to KEGG pathway analysis, plant hormone signaling transduction and metabolic pathways were found most significantly enriched in this study. A total of 60 transcription factor families such as MADS-box, NAC and TCP showed their role in this process. RT-qPCR assays confirmed that the expression levels were consistent with RNA-Seq results. This study provides an alternative to be considered for further studies and understanding of pistil abortion processes in Japanese apricot, and it provides a reference related to this issue for other deciduous fruit crops.
Collapse
|
11
|
Somatic Embryogenesis from Mature Embryos of Olea europaea L. cv. 'Galega Vulgar' and Long-Term Management of Calli Morphogenic Capacity. PLANTS 2020; 9:plants9060758. [PMID: 32560502 PMCID: PMC7355655 DOI: 10.3390/plants9060758] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/12/2020] [Accepted: 06/13/2020] [Indexed: 02/07/2023]
Abstract
Several olive cultivars, characterized by high-quality olive oil show agronomical issues such as excessive vigor, high susceptibility to biotic and abiotic stresses, and low propagation ability. They are strong candidates for breeding based on new technologies to improve their performance in a short period of time. For this reason, the first step is developing efficient somatic embryogenesis (SE) protocols. Somatic embryogenesis in olive is highly genotype-dependent for both adult tissues and mature embryos as initial explants, requiring the development of specific protocols for each genotype. Trials using cotyledons and radicles as initial explants, isolated from ripe seeds from the Portuguese olive cv. ‘Galega vulgar’, gave more than 95% calli development. Radicles proved to be the most responsive tissue for SE induction, with an average of 2 embryos per callus after callus transfer to expression medium, and 14 embryos per callus after subculture on the olive cyclic embryogenesis medium (ECO). Embryogenic competence could be recovered after several subcultures on ECO medium that maintained cyclic embryogenesis for an indeterminate period of time. Embryo conversion and plant acclimatization were also attained with high success rates. Media management for cyclic embryogenesis maintenance is of general importance for SE protocols in any olive genotype. Somatic embryogenesis was thus attained for the first time in embryo-derived explants of cv. ‘Galega vulgar’.
Collapse
|
12
|
Salimonti A, Carbone F, Romano E, Pellegrino M, Benincasa C, Micali S, Tondelli A, Conforti FL, Perri E, Ienco A, Zelasco S. Association Study of the 5'UTR Intron of the FAD2-2 Gene With Oleic and Linoleic Acid Content in Olea europaea L. FRONTIERS IN PLANT SCIENCE 2020; 11:66. [PMID: 32117401 PMCID: PMC7031445 DOI: 10.3389/fpls.2020.00066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/16/2020] [Indexed: 05/21/2023]
Abstract
Cultivated olive (Olea europaea L. subsp. europaea var. europaea) is the most ancient and spread tree crop in the Mediterranean basin. An important quality trait for the extra virgin olive oil is the fatty acid composition. In particular, a high content of oleic acid and low of linoleic, linolenic, and palmitic acid is considered very relevant in the health properties of the olive oil. The oleate desaturase enzyme encoding-gene (FAD2-2) is the main responsible for the linoleic acid content in the olive fruit mesocarp and, therefore, in the olive oil revealing to be the most important candidate gene for the linoleic acid biosynthesis. In this study, an in silico and structural analysis of the 5'UTR intron of the FAD2-2 gene was conducted with the aim to explore the natural sequence variability and its role in the gene expression regulation. In order to identify functional allele variants, the 5'UTR intron was isolated and partially sequenced in 97 olive cultivars. The sequence analysis allowed to find a 117-bp insertion including two long duplications never found before in FAD2-2 genes in olive and the existence of many intron-mediated enhancement (IME) elements. The sequence polymorphism analysis led to detect 39 SNPs. The candidate gene association study conducted for oleic and linoleic acids content revealed seven SNPs and one indel significantly associated able to explain a phenotypic variation ranging from 7% to 16% among the years. Our study highlighted new structural variants within the FAD2-2 gene in olive, putatively involved in the regulation mechanisms of gene expression associated with the variation of the content of oleic and linoleic acid.
Collapse
Affiliation(s)
- Amelia Salimonti
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Fabrizio Carbone
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Elvira Romano
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | | | - Cinzia Benincasa
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Sabrina Micali
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Roma, Italy
| | - Alessandro Tondelli
- Research Centre for Genomics and Bioinformatics, CREA, Fiorenzuola D’Arda, Italy
| | - Francesca L. Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Enzo Perri
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | | | - Samanta Zelasco
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
- *Correspondence: Samanta Zelasco,
| |
Collapse
|
13
|
Inês C, Corbacho J, Paredes MA, Labrador J, Cordeiro AM, Gomez-Jimenez MC. Regulation of sterol content and biosynthetic gene expression during flower opening and early fruit development in olive. PHYSIOLOGIA PLANTARUM 2019; 167:526-539. [PMID: 30912149 DOI: 10.1111/ppl.12969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Phytosterols are lipophilic membrane components essential not only for diverse cellular functions but also are biosynthetic precursors of the plant hormone, brassinosteroid (BR). However, the interaction between phytosterol and BR during early fleshy-fruit growth remains largely uncharacterized. In olive, phytosterols are important lipids because they affect oil quality, but phytosterol composition during flowering and early fruit development has not been explored. Here, we first investigated the temporal changes in phytosterol composition, and biosynthetic gene expression that occurred during olive flower opening and early fruit growth. Next, we analyzed the interrelationship between phytosterol and BR, whose levels we manipulated through the application of exogenous BRs (24-epibrassinolide, EBR) or a BR biosynthesis inhibitor (brassinazole, Brz). In this report, the profiling of phytosterol measurement revealed that β-sitosterol is the most abundant in olive reproductive organs. Our data demonstrate that both OeCYP51 and OeSMT2 genes are upregulated during floral anthesis in good agreement with the rise in cholesterol and β-sitosterol contents in olive flower. By contrast, the OeCYP51 and OeSMT2 genes displayed different expression patterns during early olive-fruit development. Furthermore, our data show that exogenous EBR enhanced the early olive-fruit growth, as well as the OeSMT2 transcript and β-sitosterol levels, but decreased the OeCYP51 transcript, squalene, campesterol and cholesterol levels, whereas the Brz treatment exerted the opposite effect. Overall, our findings indicate an up-regulation of β-sitosterol biosynthesis by BR at the transcriptional level during early olive-fruit growth, providing a valuable tool to unravel the physiological function of SMT2 in future studies.
Collapse
Affiliation(s)
- Carla Inês
- Plant Physiology, Faculty of Science, University of Extremadura, Badajoz, 06006, Spain
| | - Jorge Corbacho
- Plant Physiology, Faculty of Science, University of Extremadura, Badajoz, 06006, Spain
| | - Miguel A Paredes
- Plant Physiology, Faculty of Science, University of Extremadura, Badajoz, 06006, Spain
| | - Juana Labrador
- Plant Physiology, Faculty of Science, University of Extremadura, Badajoz, 06006, Spain
| | - António M Cordeiro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., UEIS Biotecnologia e Recursos Genéticos, Elvas, 7351-901, Portugal
| | - Maria C Gomez-Jimenez
- Plant Physiology, Faculty of Science, University of Extremadura, Badajoz, 06006, Spain
| |
Collapse
|
14
|
Sabella E, Aprile A, Genga A, Siciliano T, Nutricati E, Nicolì F, Vergine M, Negro C, De Bellis L, Luvisi A. Xylem cavitation susceptibility and refilling mechanisms in olive trees infected by Xylella fastidiosa. Sci Rep 2019; 9:9602. [PMID: 31270378 PMCID: PMC6610111 DOI: 10.1038/s41598-019-46092-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/19/2019] [Indexed: 01/09/2023] Open
Abstract
In olive trees, Xylella fastidiosa colonizes xylem vessels and compromises water transport causing the olive quick decline syndrome (OQDS). The loss of hydraulic conductivity could be attributed to vessel occlusions induced both by the bacteria biofilm and by plant responses (tyloses, gums, etc.) that could trigger embolism. The ability of the infected plants to detect embolism and to respond, by activating mechanisms to restore the hydraulic conductivity, can influence the severity of the disease symptomatology. In order to investigate these mechanisms in the X. fastidiosa-resistant olive cultivar Leccino and in the susceptible Cellina di Nardò, sections of healthy olive stems were analysed by laser scanning microscope to calculate the cavitation vulnerability index. Findings indicated that the cultivar Leccino seems to be constitutively less susceptible to cavitation than the susceptible one. Among the vascular refilling mechanisms, starch hydrolysis is a well-known strategy to refill xylem vessels that suffered cavitation and it is characterized by a dense accumulation of starch grains in the xylem parenchima; SEM-EDX analysis of stem cross-sections of infected plants revealed an aggregation of starch grains in the Leccino xylem vessels. These observations could indicate that this cultivar, as well as being anatomically less susceptible to cavitation, it also could be able to activate more efficient refilling mechanisms, restoring vessel's hydraulic conductivity. In order to verify this hypothesis, we analysed the expression levels of some genes belonging to families involved in embolism sensing and refilling mechanisms: aquaporins, sucrose transporters, carbohydrate metabolism and enzymes related to starch breakdown, alpha and beta-amylase. The obtained genes expression patterns suggested that the infected plants of the cultivar Leccino strongly modulates the genes involved in embolism sensing and refilling.
Collapse
Affiliation(s)
- Erika Sabella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| | - Alessio Aprile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy.
| | - Alessandra Genga
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| | - Tiziana Siciliano
- Department of Physic and Math, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| | - Eliana Nutricati
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| | - Francesca Nicolì
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| | - Marzia Vergine
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| | - Carmine Negro
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Monteroni 165, 73100, Lecce, Italy
| |
Collapse
|
15
|
Montemurro C, Dambruoso G, Bottalico G, Sabetta W. Self-Incompatibility Assessment of Some Italian Olive Genotypes ( Olea europaea L.) and Cross-Derived Seedling Selection by SSR Markers on Seed Endosperms. FRONTIERS IN PLANT SCIENCE 2019; 10:451. [PMID: 31031787 PMCID: PMC6473062 DOI: 10.3389/fpls.2019.00451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/26/2019] [Indexed: 05/29/2023]
Abstract
The morphology of olive flowers allows either self- or cross-pollination that could partially explain the existence of both reproductive features in this species. However, a high degree of self-incompatibility is reported for many olive genotypes, that could be an important reproductive barrier influencing olive yield. Due to the strong environmental influence, results of compatibility tests are often contradictory, making cultivar classification quite imprecise. In this study, the self-incompatibility value has been determined for four olive genotypes (Bella di Spagna, Coratina, Leccino, and Ogliarola barese) widespread in the Mediterranean basin. Moreover, the incompatibility relationships of cultivar Coratina with some suitable pollinizers (Leccino, Oliastro, and Picholine) have been studied in controlled crosses: the in vitro germination potential of progenies has been evaluated and the selection of cross-derived embryos has been indirectly performed by the molecular characterization of the corresponding endosperm. The results increase knowledge on factors affecting self-compatibility in olive. Moreover, they provide useful information to farmers about the most effective cultivars for the set-up of new olive grove or for graft planning. Finally, they provide a new strategy and procedure based on endosperm analysis by SSRs for an accurate, fast, and relatively cheap screening of embryos/seedlings.
Collapse
Affiliation(s)
- Cinzia Montemurro
- Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro,”, Bari, Italy
- SINAGRI S.r.l. – Spin off University of Bari, Bari, Italy
| | - Giovanni Dambruoso
- Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro,”, Bari, Italy
| | - Giovanna Bottalico
- Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro,”, Bari, Italy
- SINAGRI S.r.l. – Spin off University of Bari, Bari, Italy
| | - Wilma Sabetta
- Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro,”, Bari, Italy
- SINAGRI S.r.l. – Spin off University of Bari, Bari, Italy
| |
Collapse
|
16
|
Alagna F, Caceres ME, Pandolfi S, Collani S, Mousavi S, Mariotti R, Cultrera NGM, Baldoni L, Barcaccia G. The Paradox of Self-Fertile Varieties in the Context of Self-Incompatible Genotypes in Olive. FRONTIERS IN PLANT SCIENCE 2019; 10:725. [PMID: 31293602 PMCID: PMC6606695 DOI: 10.3389/fpls.2019.00725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/16/2019] [Indexed: 05/09/2023]
Abstract
Olive, representing one of the most important fruit crops of the Mediterranean area, is characterized by a general low fruit yield, due to numerous constraints, including alternate bearing, low flower viability, male-sterility, inter-incompatibility, and self-incompatibility (SI). Early efforts to clarify the genetic control of SI in olive gave conflicting results, and only recently, the genetic control of SI has been disclosed, revealing that olive possesses an unconventional homomorphic sporophytic diallelic system of SI, dissimilar from other described plants. This system, characterized by the presence of two SI groups, prevents self-fertilization and regulates inter-compatibility between cultivars, such that cultivars bearing the same incompatibility group are incompatible. Despite the presence of a functional SI, some varieties, in particular conditions, are able to set seeds following self-fertilization, a mechanism known as pseudo-self-compatibility (PSC), as widely reported in previous literature. Here, we summarize the results of previous works on SI in olive, particularly focusing on the occurrence of self-fertility, and offer a new perspective in view of the recent elucidation of the genetic architecture of the SI system in olive. Recent advances in research aimed at unraveling the molecular bases of SI and its breakdown in olive are also presented. The clarification of these mechanisms may have a huge impact on orchard management and will provide fundamental information for the future of olive breeding programs.
Collapse
Affiliation(s)
- F. Alagna
- Dipartimento Tecnologie Energetiche (DTE), Centro Ricerche Trisaia, ENEA Agenzia nazionale per le nuove tecnologie, l’energia e lo sviluppo economico sostenibile, Rotondella, Italy
| | - M. E. Caceres
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - S. Pandolfi
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - S. Collani
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - S. Mousavi
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - R. Mariotti
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - N. G. M. Cultrera
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - L. Baldoni
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
- *Correspondence: L. Baldoni,
| | - G. Barcaccia
- Laboratorio di Genomica, Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente (DAFNAE), Università di Padova, Legnaro, Italy
| |
Collapse
|
17
|
Farinelli D, Breton C, Koubouris G, Famiani F, Villemur P, Bervillé A. Reply to Saumitou-Laprade et al. (2017) "Controlling for genetic identity of varieties, pollen contamination and stigma receptivity is essential to characterize the self-incompatibility system of Olea europaea L.". Eva:https://doi.org/10.1111/eva.12498. Evol Appl 2018; 11:1465-1470. [PMID: 30151053 PMCID: PMC6099824 DOI: 10.1111/eva.12633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 02/26/2018] [Indexed: 01/10/2023] Open
Abstract
This study was carried out to examine the validity of previous studies on the intercompatibility of olive and to compare the approach and techniques used for proposing the diallelic self-incompatibility system and the sporophytic self-incompatibility system. Analysis of the literature indicates that the mating system of the olive tree is a controversial issue and requires further studies to clearly and fully comprehend it. All possible approaches should be used to maximize reliability of the final conclusions on the olive mating system.
Collapse
Affiliation(s)
- Daniela Farinelli
- Dipartimento di Scienze AgrarieAlimentari e Ambientali (DSA3)Università degli Studi di PerugiaPerugiaItaly
| | - Catherine Breton
- Institut des Sciences de l’Évolution de Montpellier (ISE‐M)UMR CNRS 5554MontpellierFrance
| | - Georgios Koubouris
- Institute for Olive Tree, Subtropical Crops & ViticultureHellenic Agricultural Organization “Demeter” (ex. NAGREF)ChaniaGreece
| | - Franco Famiani
- Dipartimento di Scienze AgrarieAlimentari e Ambientali (DSA3)Università degli Studi di PerugiaPerugiaItaly
| | | | | |
Collapse
|
18
|
Exploration of miRNAs and target genes of cytoplasmic male sterility line in cotton during flower bud development. Funct Integr Genomics 2018; 18:457-476. [PMID: 29626311 DOI: 10.1007/s10142-018-0606-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/30/2018] [Accepted: 03/20/2018] [Indexed: 12/13/2022]
Abstract
Cytoplasmic male sterility (CMS) lines provide crucial material to harness heterosis for crop plants, which serves as an important strategy for hybrid seed production. However, the molecular mechanism remains obscure. Although microRNAs (miRNAs) play important roles in vegetative growth and reproductive growth, there are few reports on miRNAs regulating the development of male sterility in Upland cotton. In present study, 12 small RNA libraries were constructed and sequenced for two development stages of flower buds from a CMS line and its maintainer line. Based on the results, 256 novel miRNAs were allocated to 141 new miRNA families, and 77 known miRNAs belonging to 54 conserved miRNA families were identified as well. Comparative analysis revealed that 61 novel and 10 conserved miRNAs were differentially expressed. Further transcriptome analysis identified 232 target genes for these miRNAs, which participated in cellular developmental process, cell death, pollen germination, and sexual reproduction. In addition, expression patterns of typical miRNA and the negatively regulated target genes, such as PPR, ARF, AP2, and AFB, were verified by qRT-PCR in cotton flower buds. These targets were previously reported to be related to reproduction development and male sterility, suggesting that miRNAs might act as regulators of CMS occurrence. Some miRNAs displayed specific expression profiles in special developmental stages of CMS line and its fertile hybrid (F1). Present study offers new information on miRNAs and their related target genes in exploiting CMS mechanism, and revealing the miRNA regulatory networks in Upland cotton.
Collapse
|
19
|
Chen Z, Rao P, Yang X, Su X, Zhao T, Gao K, Yang X, An X. A Global View of Transcriptome Dynamics During Male Floral Bud Development in Populus tomentosa. Sci Rep 2018; 8:722. [PMID: 29335419 PMCID: PMC5768756 DOI: 10.1038/s41598-017-18084-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 12/05/2017] [Indexed: 02/01/2023] Open
Abstract
To obtain a comprehensive overview of the dynamic transcriptome during male floral bud development in Populus tomentosa, high-throughput RNA-seq was conducted during eight flowering-related stages. Among the 109,212 de novo assembled unigenes, 6,959 were differentially expressed during the eight stages. The overrepresented classed of genes identified by Gene Ontology (GO) enrichment included 'response to environmental stimuli' and 'plant-type spore development'. One-third of the differentially expressed genes were transcription factors (TFs). Several genes and gene families were analyzed in depth, including MADS-box TFs, Squamosa promoter binding protein-like family, receptor-like kinases, FLOWERING LOCUS T/TERMINAL-FLOWER-LIKE 1 family, key genes involved in anther and tapetum development, as well as LEAFY, WUSCHEL and CONSTANS. The results provided new insights into the roles of these and other well known gene families during the annual flowering cycle. To explore the mechanisms regulating poplar flowering, a weighted gene co-expression network was constructed using 98 floral-related genes involved in flower meristem identity and flower development. Many modules of co-expressed genes and hub genes were identified, such as APETALA1 and HUA1. This work provides many new insights on the annual flowering cycle in a perennial plant, and a major new resource for plant biology and biotechnology.
Collapse
Affiliation(s)
- Zhong Chen
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China.
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Pian Rao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoyu Yang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoxing Su
- Berry Genomics Co., Ltd, Beijing, 100015, China
| | - Tianyun Zhao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Kai Gao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiong Yang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xinmin An
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331, USA.
| |
Collapse
|
20
|
Belaj A, de la Rosa R, Lorite IJ, Mariotti R, Cultrera NGM, Beuzón CR, González-Plaza JJ, Muñoz-Mérida A, Trelles O, Baldoni L. Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management. FRONTIERS IN PLANT SCIENCE 2018; 9:1320. [PMID: 30298075 PMCID: PMC6160578 DOI: 10.3389/fpls.2018.01320] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/22/2018] [Indexed: 05/08/2023]
Abstract
Germplasm collections are basic tools for conservation, characterization, and efficient use of olive genetic resources. The identification of the olive cultivars maintained in the collections is an important ongoing task which has been performed by both, morphological and molecular markers. In the present study, based on the sequencing results of previous genomic projects, a new set of 1,043 EST-SNP markers has been identified. In order to evaluate its discrimination capacity and utility in diversity studies, this set of markers was used in a representative number of accessions from 20 different olive growing countries and maintained at the World Olive Germplasm Collection of IFAPA Centre 'Alameda del Obispo' (Córdoba, Spain), one of the world's largest olive germplasm bank. Thus, the cultivated material included: cultivars belonging to previously defined core collections by means of SSR markers and agronomical traits, well known homonymy cases, possible redundancies previously identified in the collection, and recently introduced accessions. Marker stability was tested in repeated analyses of a selected number of accessions, as well as in different trees and accessions belonging to the same cultivar. In addition, 15 genotypes from a cross 'Picual' × 'Arbequina' cultivars from the IFAPA olive breeding program and a set of 89 wild genotypes were also included in the study. Our results indicate that, despite their relatively wide variability, the new set of EST-SNPs displayed lower levels of genetic diversity than SSRs in the set of olive core collections tested. However, the EST-SNP markers displayed consistent and reliable results from different plant material sources and plant propagation events. The EST-SNPs revealed a clear cut off between inter- and intra-cultivar variation in olive. Besides, they were able to reliably discriminate among different accessions, to detect possible homonymy cases as well as efficiently ascertain the presence of redundant germplasm in the collection. Additionally, these markers were highly transferable to the wild genotypes. These results, together with the low genotyping error rates and the easy and fully automated procedure used to get the genotyping data, validate the new set of EST-SNPs as possible markers of choice for olive cultivar identification.
Collapse
Affiliation(s)
- Angjelina Belaj
- IFAPA Centro Alameda del Obispo, Córdoba, Spain
- *Correspondence: Angjelina Belaj,
| | | | | | | | | | - Carmen R. Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - J. J. González-Plaza
- Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
- Present address: J. J. González-Plaza, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czechia
| | - A. Muñoz-Mérida
- CIBIO, InBIO – Research Network in Biodiversity and Evolutionary Biology, University of Porto, Porto, Portugal
| | - O. Trelles
- Department of Integrated Bioinformatics, National Institute for Bioinformatics, Universidad de Málaga, Málaga, Spain
| | - Luciana Baldoni
- CNR – Institute of Biosciences and Bioresources, Perugia, Italy
| |
Collapse
|
21
|
|
22
|
Saumitou-Laprade P, Vernet P, Vekemans X, Billiard S, Gallina S, Essalouh L, Mhaïs A, Moukhli A, El Bakkali A, Barcaccia G, Alagna F, Mariotti R, Cultrera NGM, Pandolfi S, Rossi M, Khadari B, Baldoni L. Elucidation of the genetic architecture of self-incompatibility in olive: Evolutionary consequences and perspectives for orchard management. Evol Appl 2017; 10:867-880. [PMID: 29151878 PMCID: PMC5680433 DOI: 10.1111/eva.12457] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/05/2017] [Indexed: 12/15/2022] Open
Abstract
The olive (Olea europaea L.) is a typical important perennial crop species for which the genetic determination and even functionality of self‐incompatibility (SI) are still largely unresolved. It is still not known whether SI is under gametophytic or sporophytic genetic control, yet fruit production in orchards depends critically on successful ovule fertilization. We studied the genetic determination of SI in olive in light of recent discoveries in other genera of the Oleaceae family. Using intra‐ and interspecific stigma tests on 89 genotypes representative of species‐wide olive diversity and the compatibility/incompatibility reactions of progeny plants from controlled crosses, we confirmed that O. europaea shares the same homomorphic diallelic self‐incompatibility (DSI) system as the one recently identified in Phillyrea angustifolia and Fraxinus ornus. SI is sporophytic in olive. The incompatibility response differs between the two SI groups in terms of how far pollen tubes grow before growth is arrested within stigma tissues. As a consequence of this DSI system, the chance of cross‐incompatibility between pairs of varieties in an orchard is high (50%) and fruit production may be limited by the availability of compatible pollen. The discovery of the DSI system in O. europaea will undoubtedly offer opportunities to optimize fruit production.
Collapse
Affiliation(s)
- Pierre Saumitou-Laprade
- CNRSUMR 8198 Evo-Eco-Paleo Université de Lille - Sciences et Technologies Villeneuve d'Ascq France
| | - Philippe Vernet
- CNRSUMR 8198 Evo-Eco-Paleo Université de Lille - Sciences et Technologies Villeneuve d'Ascq France
| | - Xavier Vekemans
- CNRSUMR 8198 Evo-Eco-Paleo Université de Lille - Sciences et Technologies Villeneuve d'Ascq France
| | - Sylvain Billiard
- CNRSUMR 8198 Evo-Eco-Paleo Université de Lille - Sciences et Technologies Villeneuve d'Ascq France
| | - Sophie Gallina
- CNRSUMR 8198 Evo-Eco-Paleo Université de Lille - Sciences et Technologies Villeneuve d'Ascq France
| | | | - Ali Mhaïs
- Montpellier SupAgro UMR 1334 AGAP Montpellier France.,INRAUR Amélioration des Plantes Marrakech Morocco.,Laboratoire AgroBiotech L02B005 Faculté des Sciences et Techniques Guéliz University Cadi Ayyad Marrakech Morocco
| | | | - Ahmed El Bakkali
- INRAUR Amélioration des Plantes et Conservation des Ressources Phytogénétiques Meknès Morocco
| | - Gianni Barcaccia
- Laboratory of Genomics and Plant Breeding DAFNAE - University of Padova Legnaro PD Italy
| | - Fiammetta Alagna
- Research Unit for Table Grapes and Wine Growing in Mediterranean Environment CREATuriBA Italy.,CNRInstitute of Biosciences and BioresourcesPerugiaItaly
| | | | | | | | - Martina Rossi
- CNRInstitute of Biosciences and BioresourcesPerugiaItaly
| | - Bouchaïb Khadari
- Montpellier SupAgro UMR 1334 AGAP Montpellier France.,INRA/CBNMed UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP) Montpellier France
| | | |
Collapse
|
23
|
Li W, Zhang L, Ding Z, Wang G, Zhang Y, Gong H, Chang T, Zhang Y. De novo sequencing and comparative transcriptome analysis of the male and hermaphroditic flowers provide insights into the regulation of flower formation in andromonoecious taihangia rupestris. BMC PLANT BIOLOGY 2017; 17:54. [PMID: 28241786 PMCID: PMC5329940 DOI: 10.1186/s12870-017-0990-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/31/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Taihangia rupestris, an andromonoecious plant species, bears both male and hermaphroditic flowers within the same individual. However, the establishment and development of male and hermaphroditic flowers in andromonoecious Taihangia remain poorly understood, due to the limited genetic and sequence information. To investigate the potential molecular mechanism in the regulation of Taihangia flower formation, we used de novo RNA sequencing to compare the transcriptome profiles of male and hermaphroditic flowers at early and late developmental stages. RESULTS Four cDNA libraries, including male floral bud, hermaphroditic floral bud, male flower, and hermaphroditic flower, were constructed and sequenced by using the Illumina RNA-Seq method. Totally, 84,596,426 qualified Illumina reads were obtained and then assembled into 59,064 unigenes, of which 24,753 unigenes were annotated in the NCBI non-redundant protein database. In addition, 12,214, 7,153, and 8,115 unigenes were assigned into 53 Gene Ontology (GO) functional groups, 25 Clusters of Orthologous Group (COG) categories, and 126 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. By pairwise comparison of unigene abundance between the samples, we identified 1,668 differential expressed genes (DEGs), including 176 transcription factors (TFs) between the male and hermaphroditic flowers. At the early developmental stage, we found 263 up-regulated genes and 436 down-regulated genes expressed in hermaphroditic floral buds, while 844 up-regulated genes and 314 down-regulated genes were detected in hermaphroditic flowers at the late developmental stage. GO and KEGG enrichment analyses showed that a large number of DEGs were associated with a wide range of functions, including cell cycle, epigenetic processes, flower development, and biosynthesis of unsaturated fatty acid pathway. Finally, real-time quantitative PCR was conducted to validate the DEGs identified in the present study. CONCLUSION In this study, transcriptome data of this rare andromonoecious Taihangia were reported for the first time. Comparative transcriptome analysis revealed the significant differences in gene expression profiles between male and hermaphroditic flowers at early and late developmental stages. The transcriptome data of Taihangia would be helpful to improve the understanding of the underlying molecular mechanisms in regulation of flower formation and unisexual flower establishment in andromonoecious plants.
Collapse
Affiliation(s)
- Weiguo Li
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Lihui Zhang
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
| | - Zhan Ding
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Guodong Wang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Yandi Zhang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Hongmei Gong
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Tianjun Chang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Yanwen Zhang
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
| |
Collapse
|
24
|
Cirilli M, Caruso G, Gennai C, Urbani S, Frioni E, Ruzzi M, Servili M, Gucci R, Poerio E, Muleo R. The Role of Polyphenoloxidase, Peroxidase, and β-Glucosidase in Phenolics Accumulation in Olea europaea L. Fruits under Different Water Regimes. FRONTIERS IN PLANT SCIENCE 2017; 8:717. [PMID: 28536589 PMCID: PMC5422556 DOI: 10.3389/fpls.2017.00717] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/19/2017] [Indexed: 05/14/2023]
Abstract
Olive fruits and oils contain an array of compounds that contribute to their sensory and nutritional properties. Phenolic compounds in virgin oil and olive-derived products have been proven to be highly beneficial for human health, eliciting increasing attention from the food industry and consumers. Although phenolic compounds in olive fruit and oil have been extensively investigated, allowing the identification of the main classes of metabolites and their accumulation patterns, knowledge of the molecular and biochemical mechanisms regulating phenolic metabolism remains scarce. We focused on the role of polyphenoloxidase (PPO), peroxidase (PRX) and β-glucosidase (β-GLU) gene families and their enzyme activities in the accumulation of phenolic compounds during olive fruit development (35-146 days after full bloom), under either full irrigation (FI) or rain-fed (RF) conditions. The irrigation regime affected yield, maturation index, mesocarp oil content, fruit size, and pulp-to-pit ratio. Accumulation of fruit phenolics was higher in RF drupes than in FI ones. Members of each gene family were developmentally regulated, affected by water regime, and their transcript levels were correlated with the respective enzyme activities. During the early phase of drupe growth (35-43 days after full bloom), phenolic composition appeared to be linked to β-GLU and PRX activities, probably through their effects on oleuropein catabolism. Interestingly, a higher β-GLU activity was measured in immature RF drupes, as well as a higher content of the oleuropein derivate 3,4-DHPEA-EDA and verbascoside. Activity of PPO enzymes was slightly affected by the water status of trees during ripening (from 120 days after full bloom), but was not correlated with phenolics content. Overall, the main changes in phenolics content appeared soon after the supply of irrigation water and remained thereafter almost unchanged until maturity, despite fruit growth and the progressive decrease in pre-dawn leaf water potential. We suggest that enzymes involved in phenolic catabolism in the olive fruit have a differential sensitivity to soil water availability depending on fruit developmental stage.
Collapse
Affiliation(s)
- Marco Cirilli
- Laboratorio di Ecofisiologia Molecolare delle Piante Arboree, Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della TusciaViterbo, Italy
| | - Giovanni Caruso
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di PisaPisa, Italy
| | - Clizia Gennai
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di PisaPisa, Italy
| | - Stefania Urbani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli studi di PerugiaPerugia, Italy
| | - Eleonora Frioni
- Laboratorio di Ecofisiologia Molecolare delle Piante Arboree, Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della TusciaViterbo, Italy
| | - Maurizio Ruzzi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agro-alimentari e Forestali, Università degli Studi della TusciaViterbo, Italy
| | - Maurizio Servili
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli studi di PerugiaPerugia, Italy
| | - Riccardo Gucci
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di PisaPisa, Italy
| | - Elia Poerio
- Dipartimento per la Innovazione nei Sistemi Biologici, Agro-alimentari e Forestali, Università degli Studi della TusciaViterbo, Italy
| | - Rosario Muleo
- Laboratorio di Ecofisiologia Molecolare delle Piante Arboree, Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della TusciaViterbo, Italy
- Tree and Timber Institute, National Research Council of ItalySesto Fiorentino, Italy
- *Correspondence: Rosario Muleo,
| |
Collapse
|
25
|
Zafra A, Carmona R, Traverso JA, Hancock JT, Goldman MHS, Claros MG, Hiscock SJ, Alche JD. Identification and Functional Annotation of Genes Differentially Expressed in the Reproductive Tissues of the Olive Tree ( Olea europaea L.) through the Generation of Subtractive Libraries. FRONTIERS IN PLANT SCIENCE 2017; 8:1576. [PMID: 28955364 PMCID: PMC5601413 DOI: 10.3389/fpls.2017.01576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/28/2017] [Indexed: 05/07/2023]
Abstract
The olive tree is a crop of high socio-economical importance in the Mediterranean area. Sexual reproduction in this plant is an essential process, which determines the yield. Successful fertilization is mainly favored and sometimes needed of the presence of pollen grains from a different cultivar as the olive seizes a self-incompatibility system allegedly determined of the sporophytic type. The purpose of the present study was to identify key gene products involved in the function of olive pollen and pistil, in order to help elucidate the events and signaling processes, which happen during the courtship, pollen grain germination, and fertilization in olive. The use of subtractive SSH libraries constructed using, on the one hand one specific stage of the pistil development with germinating pollen grains, and on the other hand mature pollen grains may help to reveal the specific transcripts involved in the cited events. Such libraries have also been created by subtracting vegetative mRNAs (from leaves), in order to identify reproductive sequences only. A variety of transcripts have been identified in the mature pollen grains and in the pistil at the receptive stage. Among them, those related to defense, transport and oxidative metabolism are highlighted mainly in the pistil libraries where transcripts related to stress, and response to biotic and abiotic stimulus have a prominent position. Extensive lists containing information as regard to the specific transcripts determined for each stage and tissue are provided, as well as functional classifications of these gene products. Such lists were faced up to two recent datasets obtained in olive after transcriptomic and genomic approaches. The sequences and the differential expression level of the SSH-transcripts identified here, highly matched the transcriptomic information. Moreover, the unique presence of a representative number of these transcripts has been validated by means of qPCR approaches. The construction of SSH libraries using pistil and pollen, considering the high interaction between male-female counterparts, allowed the identification of transcripts with important roles in stigma physiology. The functions of many of the transcripts obtained are intimately related, and most of them are of pivotal importance in defense, pollen-stigma interaction and signaling.
Collapse
Affiliation(s)
- Adoración Zafra
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Rosario Carmona
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - José A. Traverso
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - John T. Hancock
- Faculty of Health and Life Sciences, University of the West of EnglandBristol, United Kingdom
| | - Maria H. S. Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São PauloSão Paulo, Brazil
| | - M. Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Universidad de MálagaMálaga, Spain
| | - Simon J. Hiscock
- School of Biological Sciences, University of BristolBristol, United Kingdom
| | - Juan D. Alche
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
- *Correspondence: Juan D. Alche
| |
Collapse
|