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 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.

The genetic legacy of fragmentation and overexploitation in the threatened medicinal African pepper-bark tree, Warburgia salutaris

“…Although these markers are species specific, the increasing accessibility to next-generation sequencing 41 has enabled the development of SSRs for the so-called orphan, neglected or wild crop relative species (e.g. [42][43][44][45] ), although sequencing large plant genomes still remains a challenge 46 .…”

Transcriptomics and Metabolomics Reveal Purine and Phenylpropanoid Metabolism Response to Drought Stress in Dendrobium sinense, an Endemic Orchid Species in Hainan Island

“…Recent work indicated that the nucleotide metabolism pathway was an important pathway for D. wangliangii to adapt to drought stress (Zhao et al, 2019). The IMPHD gene was reported as the rate-limiting enzyme of guanine nucleoside biosynthesis, directly affecting the biosynthesis of guanine, xanthine, and hypoxanthine (Mercati et al, 2019). In DSA vs. DSB, the IMPHD gene was upregulated, and the content of guanine, xanthine, and hypoxanthine increased.…”

An Updated Checklist of the Sicilian Native Edible Plants: Preserving the Traditional Ecological Knowledge of Century-Old Agro-Pastoral Landscapes

“…This list includes 39 plant species having good performances under harsh environmental conditions, being able to overcome at least one out of four severe stress factors, i.e., two edaphic (low soil nutrient content and high soil salinity) ad two climatic (lack of water and extreme thermic events). In particular, Capparis species can be considered well adapted to harsh climatic and edaphic conditions (Mercati et al, 2019), with Capparis sicula showing a high ecological plasticity, as it can survive both in poorly aerated, salty and clayey soils as well as in secondary habitats such as roadsides (Gristina et al, 2014), while C. spinosa mainly colonizes coastal rocky cliffs. Wild cabbages (Brassica spp.)…”