Abstract
Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and ‘Spinoso sardo’ is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant plants in open-field production. These off-type phenotypes showed highly pinnate-parted leaves and late inflorescence budding, and emerged from some branches of the true-to-type ‘Spinoso sardo’ plants. This phenomenon cannot be foreseen and is reversible through generations, suggesting the occurrence of epigenetic alterations. Here, we report an exploratory study on DNA methylation patterns in off-type/true-to-type globe artichoke plants, using a modified EpiRADseq technology, which allowed the identification of 2897 differentially methylated loci (DML): 1998 in CG, 458 in CHH, and 441 in CHG methylation contexts of which 720, 88, and 152, respectively, were in coding regions. Most of them appeared involved in primary metabolic processes, mostly linked to photosynthesis, regulation of flower development, and regulation of reproductive processes, coherently with the observed phenotype. Differences in the methylation status of some candidate genes were integrated with transcriptional analysis to test whether these two regulation levels might interplay in the emergence and spread of the ‘Spinoso sardo’ non-conventional phenotype.
Highlights
Globe artichoke (Cynara cardunculus L. var. scolymus) is a diploid (2n = 2× = 34), mostly cross-pollinated species native of the Mediterranean basin, with a genome size of ~1.07 Gbp [1].It is a perennial crop belonging to the Asteraceae family, mostly cultivated for its edible immature inflorescence, and exploited as a source for the production of nutraceutically and pharmaceutically active compounds [2,3,4,5,6] as well as of biofuels and oil crop [7,8,9,10]
3.5% of reads were identified as low quality after the process of trimming and cleaning and were removed (Table S1)
We focused on 14 genes, which showed a perfect restriction site in the locus sequence and are involved in epigenetic and transcriptional regulation of organ and developmental maturation and plant reproduction (e.g., Gene ontology (GO):0021700, GO:0048646, and GO:0000003), processes likely fitting to our contrasting phenotypes [54,55,56,57,58,59,60,61,62,63,64,65,66,67,68] (Table 1)
Summary
Scolymus) is a diploid (2n = 2× = 34), mostly cross-pollinated species native of the Mediterranean basin, with a genome size of ~1.07 Gbp [1]. Traditional propagation method, based onuse theofuse of underground the the traditional propagation method, based on the underground dormant dormant and vegetative (‘carducci’), rise toagricultural some agricultural such buds (‘ovoli’)buds and(‘ovoli’). Vegetative offshoots offshoots (‘carducci’), gives risegives to some issues issues such as plant as plant heterogeneity, multiplication low rate, and disease transmission [11,12]. Multiplication low rate, and disease transmission [11,12]. Globe artichoke virus-free virus-free propagation via in vitro culture of meristematic apices has been well-established propagation via in vitro culture of meristematic apices [13,14,15,16]
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