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Cork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oak.

Abstract Background Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy. Results Results provide direct evidence that QsMY1B targets genes encoding for enzymes involved in the lignin and suberin pathways as well as gene encoding for ABCG transporters and LTPs implicated in the transport of monomeric suberin units across the cellular membrane. These results highlight the role of QsMYB1 as a regulator of lignin and suberin biosynthesis, transport and assembly. Conclusion To our knowledge, this work constitutes the first ChIP-Seq experiment performed in cork oak, a non-model plant species with a long-life cycle, and these results will contribute to deepen the knowledge about the molecular mechanisms of cork formation and differentiation.

Cork oaks show a high capacity of bud sprouting as a response to injury, which is important for species survival when dealing with external factors, such as drought or fires. The characterization of the cork oak transcriptome involved in the different stages of bud sprouting is essential to understanding the mechanisms involved in these processes. In this study, the transcriptional profile of different stages of bud sprouting, namely (1) dormant bud and (2) bud swollen, vs. (3) red bud and (4) open bud, was analyzed in trees growing under natural conditions. The transcriptome analysis indicated the involvement of genes related with energy production (linking the TCA (tricarboxylic acid) cycle and the electron transport system), hormonal regulation, water status, and synthesis of polysaccharides. These results pinpoint the different mechanisms involved in the early and later stages of bud sprouting. Furthermore, some genes, which are involved in bud development and conserved between species, were also identified at the transcriptional level. This study provides the first set of results that will be useful for the discovery of genes related with the mechanisms regulating bud sprouting in cork oak.