Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value

Abstract Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information...

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Autores principales:	Francesco Mercati, Ignazio Fontana, Alessandro Silvestre Gristina, Adriana Martorana, Mahran El Nagar, Roberto De Michele, Silvio Fici, Francesco Carimi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/be89bda4abde46bb841e00777fd0a7d9
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spelling	oai:doaj.org-article:be89bda4abde46bb841e00777fd0a7d92021-12-02T15:09:28ZTranscriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value10.1038/s41598-019-46613-x2045-2322https://doaj.org/article/be89bda4abde46bb841e00777fd0a7d92019-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-46613-xhttps://doaj.org/toc/2045-2322Abstract Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the first genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing effort produced nearly 80 million clean reads assembled into 124,723 unitranscripts. Careful annotation and comparison with public databases revealed homologs to genes with a key role in important metabolic pathways linked to abiotic stress tolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis, α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identified. We also used the transcriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 proved polymorphic and represent the first set of SSR markers for the genus Capparis. This transcriptome will be an important contribution to future studies and breeding programs for this orphan crop, aiding to the development of improved varieties to sustain agriculture in arid conditions.Francesco MercatiIgnazio FontanaAlessandro Silvestre GristinaAdriana MartoranaMahran El NagarRoberto De MicheleSilvio FiciFrancesco CarimiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-16 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Francesco Mercati Ignazio Fontana Alessandro Silvestre Gristina Adriana Martorana Mahran El Nagar Roberto De Michele Silvio Fici Francesco Carimi Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value
description	Abstract Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the first genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing effort produced nearly 80 million clean reads assembled into 124,723 unitranscripts. Careful annotation and comparison with public databases revealed homologs to genes with a key role in important metabolic pathways linked to abiotic stress tolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis, α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identified. We also used the transcriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 proved polymorphic and represent the first set of SSR markers for the genus Capparis. This transcriptome will be an important contribution to future studies and breeding programs for this orphan crop, aiding to the development of improved varieties to sustain agriculture in arid conditions.
format	article
author	Francesco Mercati Ignazio Fontana Alessandro Silvestre Gristina Adriana Martorana Mahran El Nagar Roberto De Michele Silvio Fici Francesco Carimi
author_facet	Francesco Mercati Ignazio Fontana Alessandro Silvestre Gristina Adriana Martorana Mahran El Nagar Roberto De Michele Silvio Fici Francesco Carimi
author_sort	Francesco Mercati
title	Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value
title_short	Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value
title_full	Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value
title_fullStr	Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value
title_full_unstemmed	Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value
title_sort	transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/be89bda4abde46bb841e00777fd0a7d9
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Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value

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