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

Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its fower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classifcation of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the frst genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing efort produced nearly 80million 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 identifed. We also used the transcriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 proved polymorphic and represent the frst 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.