This is the first report assessing epigenetic variation in garlic. High genetic and epigenetic polymorphism during in vitro culture was detected.Sequencing of MSAP fragments revealed homology with ESTs. Garlic (Allium sativum) is a worldwide crop of economic importance susceptible to viral infections that can cause significant yield losses. Meristem tissue culture is the most employed method to sanitize elite cultivars.Often the virus-free garlic plants obtained are multiplied in vitro (micro propagation). However, it was reported that micro-propagation frequently produces somaclonal variation at the phenotypic level, which is an undesirable trait when breeders are seeking to maintain varietal stability. We employed amplification fragment length polymorphism and methylation sensitive amplified polymorphism (MSAP) methodologies to assess genetic and epigenetic modifications in two culture systems: virus-free plants obtained by meristem culture followed by in vitro multiplication and field culture. Our results suggest that garlic exhibits genetic and epigenetic polymorphism under field growing conditions. However, during in vitro culture system both kinds of polymorphisms intensify indicating that this system induces somaclonal variation. Furthermore, while genetic changes accumulated along the time of in vitro culture, epigenetic polymorphism reached the major variation at 6 months and then stabilize, being demethylation and CG methylation the principal conversions.Cloning and sequencing differentially methylated MSAP fragments allowed us to identify coding and unknown sequences of A. sativum, including sequences belonging to LTR Gypsy retrotransposons. Together, our results highlight that main changes occur in the initial 6 months of micro propagation. For the best of our knowledge, this is the first report on epigenetic assessment in garlic.
Capsicum annuum is a species that has undergone an expansion of the size of its genome caused mainly by the amplification of repetitive DNA sequences, including mobile genetic elements. Based on information obtained from sequencing the genome of pepper, the estimated fraction of retroelements is approximately 81%, and previous results revealed an important contribution of lineages derived from Gypsy superfamily. However, the dynamics of the retroelements in the C. annuum genome is poorly understood. In this way, the present work seeks to investigate the phylogenetic diversity and genomic abundance of the families of autonomous (complete and intact) LTR retroelements from C. annuum and inspect their distribution along its chromosomes. In total, we identified 1151 structurally full-length retroelements (340 Copia; 811 Gypsy) grouped in 124 phylogenetic families in the base of their retrotranscriptase. All the evolutive lineages of LTR retroelements identified in plants were present in pepper; however, three of them comprise 83% of the entire LTR retroelements population, the lineages Athila, Del/Tekay, and Ale/Retrofit. From them, only three families represent 70.8% of the total number of the identified retroelements. A massive family-specific wave of amplification of two of them occurred in the last 0.5 Mya (GypsyCa_16; CopiaCa_01), whereas the third is more ancient and occurred 3.0 Mya (GypsyCa_13). Fluorescent in situ hybridization performed with family and lineagespecific probes revealed contrasting patterns of chromosomal affinity. Our results provide a database of the populations LTR retroelements specific to C. annuum genome. The most abundant families were analyzed according to chromosome insertional preferences, suppling useful tools to the design of retroelement-based markers specific to the species.
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