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Di Giacomo M, Vega TA, Cambiaso V, Picardi LA, Rodríguez GR, Pereira da Costa JH. An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life. Plants (Basel) 2023; 12:2812. [PMID: 37570966 PMCID: PMC10421356 DOI: 10.3390/plants12152812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.
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Affiliation(s)
- Melisa Di Giacomo
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
| | - Tatiana Alejandra Vega
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Liliana Amelia Picardi
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Javier Hernán Pereira da Costa
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
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Vazquez DV, Pereira da Costa JH, Godoy FNI, Cambiaso V, Rodríguez GR. Genetic basis of the lobedness degree in tomato fruit morphology. Plant Sci 2022; 319:111258. [PMID: 35487666 DOI: 10.1016/j.plantsci.2022.111258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Fruit shape is a key trait in tomato (Solanum lycopersicum L.). Since most studies focused on proximo-distal fruit morphology, we hypothesized that unknown QTLs for medio-lateral direction ones could be found analysing segregating populations where major shape genes are fixed. We examined the diversity of fruit morphology in medio-lateral direction; defined divergent traits in cultivars carrying identical genetic constitution at LC and FAS genes; and identified QTLs for lobedness degree (LD) by a QTL-seq approach. We found that LC and FAS genes were not enough to explain LD variability in a large tomato collection. Then, we derived F2 populations crossing cultivars divergent for LD where LC and FAS were fixed (Yellow Stuffer x Heinz 1439 [F2YSxH] and Voyage x Old Brooks [F2VxOB]). By QTL-seq we identified a QTL for LD on chromosome 8 in both F2, which was validated in F2YSxH by interval mapping accounting for ~ 17% of the variability. Other two QTLs located on chromosomes 6 and 11 with epistasis explained ~ 61% of the variability in the F2VxOB. In conclusion, three novel QTLs with major effect for LD (ld6, ld8, and ld11) were identified through the study of diversity and genetic segregation in intraspecific tomato crosses.
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Affiliation(s)
- Dana V Vazquez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina; Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina
| | - Javier H Pereira da Costa
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina; Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina
| | - Federico N I Godoy
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina; Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina
| | - Gustavo R Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina; Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA Zavalla, Santa Fe, Argentina.
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Gimenez MD, Vazquez DV, Trepat F, Cambiaso V, Rodríguez GR. Fruit quality and DNA methylation are affected by parental order in reciprocal crosses of tomato. Plant Cell Rep 2021; 40:171-186. [PMID: 33079280 DOI: 10.1007/s00299-020-02624-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Reciprocal effects were found for tomato fruit quality and DNA methylation. The epigenetic identity of reciprocal hybrids indicates that DNA methylation might be one of the mechanisms involved in POEs. Crosses between different genotypes and even between different species are commonly used in plant breeding programs. Reciprocal hybrids are obtained by changing the cross direction (or the sexual role) of parental genotypes in a cross. Phenotypic differences between these hybrids constitute reciprocal effects (REs). The aim of this study was to evaluate phenotypic differences in tomato fruit traits and DNA methylation profiles in three inter- and intraspecific reciprocal crosses. REs were detected for 13 of the 16 fruit traits analyzed. The number of traits with REs was the lowest in the interspecific cross, whereas the highest was found in the cross between recombinant inbred lines (RILs) derived from the same interspecific cross. An extension of gene action analysis was proposed to incorporate parent-of-origin effects (POEs). Maternal and paternal dominance were found in four fruit traits. REs and paternal inheritance were found for epiloci located at coding and non-coding regions. The epigenetic identity displayed by the reciprocal hybrids accounts for the phenotypic differences among them, indicating that DNA methylation might be one of the mechanisms involved in POEs.
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Affiliation(s)
- Magalí Diana Gimenez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- CIGEOBIO, (CONICET-UNSJ), Complejo Universitario "Islas Malvinas", FCEFN, Universidad de San Juan, Av. Ignacio de la Roza 590, J5402DCS, Rivadavia, San Juan, Argentina
| | - Dana Valeria Vazquez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Felipe Trepat
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
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Cambiaso V, Gimenez MD, da Costa JHP, Vazquez DV, Picardi LA, Pratta GR, Rodríguez GR. Selected genome regions for fruit weight and shelf life in tomato RILs discernible by markers based on genomic sequence information. Breed Sci 2019; 69:447-454. [PMID: 31598077 PMCID: PMC6776149 DOI: 10.1270/jsbbs.19015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/04/2019] [Indexed: 06/10/2023]
Abstract
Fruit weight (FW) and shelf life (SL) are important traits in commercial fresh market tomatoes. A tomato RIL population was developed by antagonistic and divergent selection for both traits from an interspecific cross between the Solanum lycopersicum L. cv. "Caimanta" and the S. pimpinellifolium L. accession "LA0722". The objective of this work was to evaluate phenotypic and genetic components for FW and SL. Phenotypic data from RILs were collected during 3-year trials. Sixteen SSR, 62 InDels developed based on the genome sequences of "Caimanta" and "LA0722", and four functional markers for fruit size genes were used. FW and SL had a significant genetic variability, and both traits showed a genotype by year interaction. Genome-wide molecular characterization of the population demonstrated that is genetically structured according to FW. Marker data was used to study changes on allelic frequencies at loci between the phenotypic extreme group of RILs for FW and SL. Twenty four markers were associated to FW, the LC gene in chromosome 2 and other six markers in chromosomes 1, 2, 6, and 11 presented the most significant associations. Finally, we reported three new genomic regions located on chromosomes 9, 10 and 12 that underlie SL in tomato.
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Affiliation(s)
- Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR). Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
| | - Magalí Diana Gimenez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR). Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
| | - Javier Hernán Pereira da Costa
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR). Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
| | - Dana Valeria Vazquez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR). Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
| | - Liliana Amelia Picardi
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR). Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
- Consejo de Investigaciones de la Universidad Nacional de Rosario. Universidad Nacional de Rosario,
Maipú 1065, S2000CGK Rosario, Santa Fe,
Argentina
| | - Guillermo Raúl Pratta
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR). Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR). Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino,
S2125ZAA Zavalla, Santa Fe,
Argentina
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