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Tassone MR, Bagnaresi P, Desiderio F, Bassolino L, Barchi L, Florio FE, Sunseri F, Sirangelo TM, Rotino GL, Toppino L. A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant. Cells 2022; 11:2548. [PMID: 36010625 PMCID: PMC9406753 DOI: 10.3390/cells11162548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a female parent the fully resistant line '305E40' and as a male parent the partially resistant line '67/3'. The fully resistant trait to Fom was introgressed from the allied species S. aethiopicum. In this work, the RIL population was assessed for the responses to Fom and by using a genomic mapping approach, two major QTLs on chromosomes CH02 and CH11 were identified, associated with the full and partial resistance trait to Fom, respectively. A targeted BSAseq procedure in which Illumina reads bulks of RILs grouped according to their resistance score was aligned to the appropriate reference genomes highlighted differentially enriched regions between resistant/susceptible progeny in the genomic regions underlying both QTLs. The characterization of such regions allowed us to identify the most reliable candidate genes for the two resistance traits. With the aim of revealing exclusive species-specific contigs and scaffolds inherited from the allied species and thus associated with the full resistance trait, a draft de-novo assembly of available Illumina sequences of the '305E40' parent was developed to better resolve the non-recombining genomic region on its CH02 carrying the introgressed Fom resistance locus from S. aethiopicum.
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Affiliation(s)
- Maria Rosaria Tassone
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
- Department of Agricultural Science, University Mediterranea of Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 29017 Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 29017 Fiorenzuola d’Arda, Italy
| | - Laura Bassolino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
- Council for Agricultural Research and Economics, Cereal and Industrial Crops Research Center, 40128 Bologna, Italy
| | - Lorenzo Barchi
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy
| | - Francesco Elia Florio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Francesco Sunseri
- Department of Agricultural Science, University Mediterranea of Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Tiziana Maria Sirangelo
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Giuseppe Leonardo Rotino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Laura Toppino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
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Florio FE, Gattolin S, Toppino L, Bassolino L, Fibiani M, Lo Scalzo R, Rotino GL. A SmelAAT Acyltransferase Variant Causes a Major Difference in Eggplant ( Solanum melongena L.) Peel Anthocyanin Composition. Int J Mol Sci 2021; 22:ijms22179174. [PMID: 34502081 PMCID: PMC8431300 DOI: 10.3390/ijms22179174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 12/15/2022] Open
Abstract
Eggplant berries are rich in anthocyanins like delphinidin-3-rutinoside (D3R) and nasunin (NAS), which are accumulated at high amounts in the peel. NAS is derived by D3R through acylation and glycosylation steps. The presence of D3R or NAS is usually associated with black-purple or lilac fruit coloration of the most cultivated varieties, respectively. Building on QTL mapping position, a candidate gene approach was used to investigate the involvement of a BAHD anthocyanin acyltransferase (SmelAAT) in determining anthocyanin type. The cDNA sequence comparison revealed the presence of a single-base deletion in D3R-type line ‘305E40’ (305E40_aat) with respect to the NAS-type reference line ‘67/3’. This is predicted to cause a frame shift mutation, leading to a loss of SmelAAT function and, thus, D3R retention. RT-qPCR analyses confirmed SmelAAT and 305E40_aat expression during berry maturation. In D3R-type lines, ‘305E40’ and ‘DR2’, overexpressing the functional SmelAAT allele from ‘67/3’, the transcript levels of the transgene correlated with the accumulation of NAS in fruit peel. Furthermore, it was also found a higher expression of the transcript for glucosyltransferase Smel5GT1, putatively involved with SmelAAT in the last steps of anthocyanin decoration. Finally, an indel marker matching with anthocyanin type in the ‘305E40’ × ’67/3’ segregating population was developed and validated in a wide number of accessions, proving its usefulness for breeding purposes.
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Affiliation(s)
- Francesco Elia Florio
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133 Milan, Italy
| | - Stefano Gattolin
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
- CNR—National Research Council of Italy, Institute of Agricultural Biology and Biotechnology (IBBA), 20133 Milan, Italy
- Correspondence: (S.G.); (G.L.R.); Tel.: +39-037-1466-2507 (S.G.); +39-33-9548-4825 (G.L.R.)
| | - Laura Toppino
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
| | - Laura Bassolino
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
- CREA, Research Centre for Cereal and Industrial Crops, 40128 Bologna, Italy
| | - Marta Fibiani
- CREA, Research Centre for Engineering and Agro-Food Processing, 20133 Milan, Italy; (M.F.); (R.L.S.)
| | - Roberto Lo Scalzo
- CREA, Research Centre for Engineering and Agro-Food Processing, 20133 Milan, Italy; (M.F.); (R.L.S.)
| | - Giuseppe Leonardo Rotino
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
- Correspondence: (S.G.); (G.L.R.); Tel.: +39-037-1466-2507 (S.G.); +39-33-9548-4825 (G.L.R.)
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Mauceri A, Abenavoli MR, Toppino L, Panda S, Mercati F, Aci MM, Aharoni A, Sunseri F, Rotino GL, Lupini A. Transcriptomics reveal new insights into molecular regulation of nitrogen use efficiency in Solanum melongena. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4237-4253. [PMID: 33711100 DOI: 10.1093/jxb/erab121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen-use efficiency (NUE) is a complex trait of great interest in breeding programs because through its improvement, high crop yields can be maintained whilst N supply is reduced. In this study, we report a transcriptomic analysis of four NUE-contrasting eggplant (Solanum melongena) genotypes following short- and long-term exposure to low N, to identify key genes related to NUE in the roots and shoots. The differentially expressed genes in the high-NUE genotypes are involved in the light-harvesting complex and receptor, a ferredoxin-NADP reductase, a catalase and WRKY33. These genes were then used as bait for a co-expression gene network analysis in order to identify genes with the same trends in expression. This showed that up-regulation of WRKY33 triggered higher expression of a cluster of 21 genes and also of other genes, many of which were related to N-metabolism, that were able to improve both nitrogen uptake efficiency and nitrogen utilization efficiency, the two components of NUE. We also conducted an independent de novo experiment to validate the significantly higher expression of WRKY33 and its gene cluster in the high-NUE genotypes. Finally, examination of an Arabidopsis transgenic 35S::AtWRKY33 overexpression line showed that it had a bigger root system and was more efficient at taking up N from the soil, confirming the pivotal role of WRKY33 for NUE improvement.
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Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Laura Toppino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Mercati
- Istituto di Bioscienze e Biorisorse CNR - Consiglio Nazionale Ricerche, Corso Calatafimi 414, Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Giuseppe Leonardo Rotino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
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Phenotypic Characterization and Differential Gene Expression Analysis Reveal That Dwarf Mutant dwf Dwarfism Is Associated with Gibberellin in Eggplant. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7050114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dwarfism is a desirable trait in eggplant breeding, as it confers higher lodging resistance and allows simplified management and harvest. However, a few dwarf mutants have been reported, and the molecular mechanism underlying dwarfism in eggplant is completely unknown. Here, we report a dwarf mutant (dwf) isolated from an ethyl methyl sulfonate (EMS)-induced mutant library. The hypocotyl length, plant height, and length of internode cells of dwf were significantly decreased compared to those of the wild-type parent ‘14-345’ (WT). Differential gene expression analysis revealed that GA-related genes, including GA2ox and DELLA, were up-regulated whereas the gibberellin (GA3) content decreased in dwf. Moreover, exogenous GA3 treatment significantly increased the relative growth rate of dwf compared to WT, further indicating the important roles of GA in regulating the dwarf phenotype of dwf. Collectively, our findings shed light on GA-mediated dwarfism in dwf plants and offer a good germplasm that could be used for eggplant dwarfism breeding in the future.
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Fulvio F, Martinelli T, Paris R. Selection and validation of reference genes for RT-qPCR normalization in different tissues of milk thistle (Silybum marianum, Gaert.). Gene 2021; 768:145272. [PMID: 33122080 DOI: 10.1016/j.gene.2020.145272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/06/2020] [Accepted: 10/21/2020] [Indexed: 12/31/2022]
Abstract
Quantitative reverse transcription PCR is a sensitive technique for evaluating transcriptional profiles in different experimental datasets. To obtain a reliable quantification of the transcripts level, data normalization with stable reference genes is required. Stable reference genes are identified after analysis of their transcripts profile in every new experiment and species of interest. In Silybum marianum, a widely cultivated officinal plant, only few gene expression studies exist, and reference genes for RT-qPCR studies in the diverse plant tissues have never been investigated before. In this work, the expression stability of 10 candidate reference genes was evaluated in leaves, roots, stems and fruits of S. marianum grown under physiological environmental condition. The stability values for each candidate reference gene were calculated by four canonical statistical algorithms GeNorm, NormFinder, Bestkeeper and ΔCt method in different subsets of samples, then they were ranked with RefFinder from the most to the least suitable for normalization. Best combinations of reference genes are finally proposed for different experimental data sets, including all tissues, vegetative, and reproductive tissues separately. Three target genes putatively involved in important biosynthetic pathway leading to key metabolites in the fruits of milk thistle, such as silymarin and fatty acids, were analyzed with the chosen panels of reference genes, in comparison to the ones used in previous papers. To the best of our knowledge, this is the first report on a reliable and systematic identification and validation of the reference genes for RT-qPCR normalization to study gene expression in S. marianum.
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Affiliation(s)
- Flavia Fulvio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy
| | - Tommaso Martinelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy; Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Difesa e Certificazione, Via di Lanciola 12/A, Loc. Cascine del Riccio, 50125 Firenze, Italy
| | - Roberta Paris
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy.
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Andrea M, Francesco EF, Sergio I, Alessandra G, Maria AM, Cinzia C, Lorenzo B, Arianna M, Cecilia C, Patrizia R, Laura T, Giuseppe LR, Sergio L, Laura B. Identification of a new R3 MYB type repressor and functional characterization of the members of the MBW transcriptional complex involved in anthocyanin biosynthesis in eggplant (S. melongena L.). PLoS One 2020; 15:e0232986. [PMID: 32407419 PMCID: PMC7224497 DOI: 10.1371/journal.pone.0232986] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Here we focus on the highly conserved MYB-bHLH-WD repeat (MBW) transcriptional complex model in eggplant, which is pivotal in the transcriptional regulation of the anthocyanin biosynthetic pathway. Through a genome-wide approach performed on the recently released Eggplant Genome (cv. 67/3) previously identified, and reconfirmed by us, members belonging to the MBW complex (SmelANT1, SmelAN2, SmelJAF13, SmelAN1) were functionally characterized. Furthermore, a regulatory R3 MYB type repressor (SmelMYBL1), never reported before, was identified and characterized as well. Through a qPCR approach, we revealed specific transcriptional patterns of candidate genes in different plant tissue/organs at two stages of fruit development. Two strategies were adopted for investigating the interactions of bHLH partners (SmelAN1, SmelJAF13) with MYB counterparts (SmelANT1, SmelAN2 and SmelMYBL1): Yeast Two Hybrid (Y2H) and Bimolecular Fluorescent Complementation (BiFC) in A. thaliana mesophylls protoplast. Agro-infiltration experiments highlighted that N. benthamiana leaves transiently expressing SmelANT1 and SmelAN2 showed an anthocyanin-pigmented phenotype, while their co-expression with SmelMYBL1 prevented anthocyanin accumulation. Our results suggest that SmelMYBL1 may inhibits the MBW complex via the competition with MYB activators for bHLH binding site, although this hypothesis requires further elucidation.
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Affiliation(s)
- Moglia Andrea
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco (TO), Italy
| | - Elia Florio Francesco
- CREA, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo (LO), Italy
| | - Iacopino Sergio
- PlantLab, Scuola Superiore Sant'Anna, Institute of Life Sciences, Ghezzano (PI), Italy
- Department of Biology, University of Pisa, Pisa (PI), Italy
| | - Guerrieri Alessandra
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
| | - Anna Milani Maria
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco (TO), Italy
| | - Comino Cinzia
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco (TO), Italy
| | - Barchi Lorenzo
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco (TO), Italy
| | - Marengo Arianna
- Department of Drug Science and Technology, University of Torino, Torino (TO), Italy
| | - Cagliero Cecilia
- Department of Drug Science and Technology, University of Torino, Torino (TO), Italy
| | - Rubiolo Patrizia
- Department of Drug Science and Technology, University of Torino, Torino (TO), Italy
| | - Toppino Laura
- CREA, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo (LO), Italy
| | | | - Lanteri Sergio
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco (TO), Italy
| | - Bassolino Laura
- CREA, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo (LO), Italy
- CREA, Research Centre for Cereal and Industrial Crops, Bologna, Italy
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Mauceri A, Bassolino L, Lupini A, Badeck F, Rizza F, Schiavi M, Toppino L, Abenavoli MR, Rotino GL, Sunseri F. Genetic variation in eggplant for Nitrogen Use Efficiency under contrasting NO 3 - supply. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:487-508. [PMID: 31087763 DOI: 10.1111/jipb.12823] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/08/2019] [Indexed: 05/03/2023]
Abstract
Eggplant (Solanum melongena L.) yield is highly sensitive to N fertilization, the excessive use of which is responsible for environmental and human health damage. Lowering N input together with the selection of improved Nitrogen-Use-Efficiency (NUE) genotypes, more able to uptake, utilize, and remobilize N available in soils, can be challenging to maintain high crop yields in a sustainable agriculture. The aim of this study was to explore the natural variation among eggplant accessions from different origins, in response to Low (LN) and High (HN) Nitrate (NO3 - ) supply, to identify NUE-contrasting genotypes and their NUE-related traits, in hydroponic and greenhouse pot experiments. Two eggplants, AM222 and AM22, were identified as N-use efficient and inefficient, respectively, in hydroponic, and these results were confirmed in a pot experiment, when crop yield was also evaluated. Overall, our results indicated the key role of N-utilization component (NUtE) to confer high NUE. The remobilization of N from leaves to fruits may be a strategy to enhance NUtE, suggesting glutamate synthase as a key enzyme. Further, omics technologies will be used for focusing on C-N metabolism interacting networks. The availability of RILs from two other selected NUE-contrasting genotypes will allow us to detect major genes/quantitative trait loci related to NUE.
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Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Laura Bassolino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Franz Badeck
- CREA Centro di ricerca Genomica e Bioinformatica, I-29017, Fiorenzuola d'Arda, Italy
| | - Fulvia Rizza
- CREA Centro di ricerca Genomica e Bioinformatica, I-29017, Fiorenzuola d'Arda, Italy
| | - Massimo Schiavi
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Laura Toppino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Giuseppe L Rotino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
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Sarwar MB, Ahmad Z, Anicet BA, Sajid M, Rashid B, Hassan S, Ahmed M, Husnain T. Identification and validation of superior housekeeping gene(s) for qRT-PCR data normalization in Agave sisalana (a CAM-plant) under abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:567-584. [PMID: 32205931 PMCID: PMC7078421 DOI: 10.1007/s12298-020-00760-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 05/24/2023]
Abstract
The adaptive mechanisms in Agave species enable them to survive and exhibit remarkable tolerance to abiotic stresses. Quantitative real-time PCR is a highly reliable approach for validation of targeted differential gene expression. However, stable housekeeping gene(s) is prerequisite for accurate normalization of expression data by qRT-PCR. Till date, no systematic validation study for candidate housekeeping gene identification or evaluation has been carried-out in Agave species. A total of 17 candidate housekeeping genes were identified from the de novo assembled transcriptomic data of A. sisalana and rigorously analyzed for expression stability assessment under drought, heat, cold and NaCl stress. Different statistical algorithms like geNorm, BestKeeper, NormFinder, and RefFinder on expression data determined the superior housekeeping gene(s) for accurate normalization of the gene of interest (GOI). The comprehensive evaluation revealed the β-Tub 4, WIN-1 and CYC-A as the most stable, while EEF1α, GAPDH, and UBE2 were ranked as the least stable genes in pooled samples. Pairwise combination by geNorm showed that up to two housekeeping genes would be adequate to normalize the GOI expression data precisely. Validation of identified most and least stable housekeeping genes was carried-out by normalizing the expression data of AsHSP20 under abiotic stress conditions. Copy number of AsHSP20 gene supports the reliability of the genes used for normalization. This is the first report on the screening and validation of the housekeeping genes under abiotic stress condition in A. sisalana that would assist to understand the stress tolerance mechanisms by novel gene identification and accurate validation.
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Affiliation(s)
- Muhammad Bilal Sarwar
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Zarnab Ahmad
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Batcho Agossa Anicet
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Moon Sajid
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Bushra Rashid
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Sameera Hassan
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Mukhtar Ahmed
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
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9
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Forti C, Ottobrino V, Bassolino L, Toppino L, Rotino GL, Pagano A, Macovei A, Balestrazzi A. Molecular dynamics of pre-germinative metabolism in primed eggplant ( Solanum melongena L.) seeds. HORTICULTURE RESEARCH 2020; 7:87. [PMID: 32528699 PMCID: PMC7261768 DOI: 10.1038/s41438-020-0310-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 03/24/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Seed priming, a pre-sowing technique that enhances the antioxidant/DNA repair activities during the pre-germinative metabolism, still retains empirical features. We explore for the first time the molecular dynamics of pre-germinative metabolism in primed eggplant (Solanum melongena L.) seeds in order to identify hallmarks (expression patterns of antioxidant/DNA repair genes combined with free radical profiles) useful to discriminate between high- and low-quality lots. The hydropriming protocol hereby developed anticipated (or even rescued) germination, when applied to lots with variable quality. ROS (reactive oxygen species) raised during hydropriming and dropped after dry-back. Upregulation of antioxidant/DNA repair genes was observed during hydropriming and the subsequent imbibition. Upregulation of SmOGG1 (8-oxoguanine glycosylase/lyase) gene detected in primed seeds at 2 h of imbibition appeared as a promising hallmark. On the basis of these results, the investigation was restricted within the first 2 h of imbibition, to verify whether the molecular landscape was reproducible in different lots. A complex pattern of antioxidant/DNA repair gene expression emerged, reflecting the preponderance of seed lot-specific profiles. Only the low-quality eggplant seeds subjected to hydropriming showed enhanced ROS levels, both in the dry and imbibed state, and this might be a useful signature to discriminate among lots. The plasticity of eggplant pre-germinative metabolism stimulated by priming imposes a plethora of heterogeneous molecular responses that might delay the search for quality hallmarks. However, the information hereby gained could be translated to eggplant wild relatives to speed-up their use in breeding programs or other agronomical applications.
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Affiliation(s)
- Chiara Forti
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Valentino Ottobrino
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Laura Bassolino
- CREA-Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, LO Italy
- CREA-Research Centre for Cereal and Industrial Crops, Bologna, Italy
| | - Laura Toppino
- CREA-Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, LO Italy
| | | | - Andrea Pagano
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
- Present Address: Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Anca Macovei
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
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