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First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.).
BMC Plant Biol. 2019 Feb 06; 19(1):61.BP

Abstract

BACKGROUND

Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species. The development of next-generation sequencing technologies (NGS) as RNA-sequencing (RNA-seq) opens a new horizon for mapping and quantifying transcriptome to understand the molecular basis of pathways that could regulate parthenocarpy in this species. The aim of the current study was to analyze fruit transcriptome of two cultivars of zucchini, a non-parthenocarpic cultivar and a parthenocarpic cultivar, in an attempt to identify key genes involved in parthenocarpy.

RESULTS

RNA-seq analysis of six libraries (unpollinated, pollinated and auxin treated fruit in a non-parthenocarpic and parthenocarpic cultivar) was performed mapping to a new version of C. pepo transcriptome, with a mean of 92% success rate of mapping. In the non-parthenocarpic cultivar, 6479 and 2186 genes were differentially expressed (DEGs) in pollinated fruit and auxin treated fruit, respectively. In the parthenocarpic cultivar, 10,497 in pollinated fruit and 5718 in auxin treated fruit. A comparison between transcriptome of the unpollinated fruit for each cultivar has been performed determining that 6120 genes were differentially expressed. Annotation analysis of these DEGs revealed that cell cycle, regulation of transcription, carbohydrate metabolism and coordination between auxin, ethylene and gibberellin were enriched biological processes during pollinated and parthenocarpic fruit set.

CONCLUSION

This analysis revealed the important role of hormones during fruit set, establishing the activating role of auxins and gibberellins against the inhibitory role of ethylene and different candidate genes that could be useful as markers for parthenocarpic selection in the current breeding programs of zucchini.

Authors+Show Affiliations

Genomics and Biotechnology Department, IFAPA Research Centre La Mojonera, Camino de San Nicolás, 1, 04745 La Mojonera, Almería, Spain.Genomics and Biotechnology Department, IFAPA Research Centre La Mojonera, Camino de San Nicolás, 1, 04745 La Mojonera, Almería, Spain.Genomics and Biotechnology Department, IFAPA Research Centre Alameda del Obispo, Avd. Menéndez Pidal s/n, 14004, Córdoba, Spain.Genetics Department, University of Cordoba, Av. de Medina Azahara, 5, 14071, Córdoba, Spain.Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.Genomics and Biotechnology Department, IFAPA Research Centre La Mojonera, Camino de San Nicolás, 1, 04745 La Mojonera, Almería, Spain. pedro.gomez.j@juntadeandalucia.es.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30727959

Citation

Pomares-Viciana, Teresa, et al. "First RNA-seq Approach to Study Fruit Set and Parthenocarpy in Zucchini (Cucurbita Pepo L.)." BMC Plant Biology, vol. 19, no. 1, 2019, p. 61.
Pomares-Viciana T, Del Río-Celestino M, Román B, et al. First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). BMC Plant Biol. 2019;19(1):61.
Pomares-Viciana, T., Del Río-Celestino, M., Román, B., Die, J., Pico, B., & Gómez, P. (2019). First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). BMC Plant Biology, 19(1), 61. https://doi.org/10.1186/s12870-019-1632-2
Pomares-Viciana T, et al. First RNA-seq Approach to Study Fruit Set and Parthenocarpy in Zucchini (Cucurbita Pepo L.). BMC Plant Biol. 2019 Feb 6;19(1):61. PubMed PMID: 30727959.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). AU - Pomares-Viciana,Teresa, AU - Del Río-Celestino,Mercedes, AU - Román,Belén, AU - Die,Jose, AU - Pico,Belén, AU - Gómez,Pedro, Y1 - 2019/02/06/ PY - 2018/05/10/received PY - 2019/01/04/accepted PY - 2019/2/8/entrez PY - 2019/2/8/pubmed PY - 2019/3/8/medline KW - Cucurbita pepo KW - Differential gene expression KW - Fruit set KW - Parthenocarpy KW - RNA-seq KW - Zucchini SP - 61 EP - 61 JF - BMC plant biology JO - BMC Plant Biol VL - 19 IS - 1 N2 - BACKGROUND: Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species. The development of next-generation sequencing technologies (NGS) as RNA-sequencing (RNA-seq) opens a new horizon for mapping and quantifying transcriptome to understand the molecular basis of pathways that could regulate parthenocarpy in this species. The aim of the current study was to analyze fruit transcriptome of two cultivars of zucchini, a non-parthenocarpic cultivar and a parthenocarpic cultivar, in an attempt to identify key genes involved in parthenocarpy. RESULTS: RNA-seq analysis of six libraries (unpollinated, pollinated and auxin treated fruit in a non-parthenocarpic and parthenocarpic cultivar) was performed mapping to a new version of C. pepo transcriptome, with a mean of 92% success rate of mapping. In the non-parthenocarpic cultivar, 6479 and 2186 genes were differentially expressed (DEGs) in pollinated fruit and auxin treated fruit, respectively. In the parthenocarpic cultivar, 10,497 in pollinated fruit and 5718 in auxin treated fruit. A comparison between transcriptome of the unpollinated fruit for each cultivar has been performed determining that 6120 genes were differentially expressed. Annotation analysis of these DEGs revealed that cell cycle, regulation of transcription, carbohydrate metabolism and coordination between auxin, ethylene and gibberellin were enriched biological processes during pollinated and parthenocarpic fruit set. CONCLUSION: This analysis revealed the important role of hormones during fruit set, establishing the activating role of auxins and gibberellins against the inhibitory role of ethylene and different candidate genes that could be useful as markers for parthenocarpic selection in the current breeding programs of zucchini. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/30727959/First_RNA_seq_approach_to_study_fruit_set_and_parthenocarpy_in_zucchini__Cucurbita_pepo_L___ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-1632-2 DB - PRIME DP - Unbound Medicine ER -