Phenological studies are important to understand the influence of climate dynamics on vegetative and reproductive growth of pineapple. In this study, 10 principal stages (0-9) and 48 secondary stages in the entire growth cycle of pineapple were accurately detailed using the extended Biologische Bundesantalt, Bundessortenamt and Chemische Industrie scale. This study focused on the entire flower and fruit development stages of pineapple and presented the correlation between phenophase and temperature. Normative descriptions can facilitate the implementation of production management measures and guidance for scientific experimental design.

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DNA methylation changes can occur in some loci during callus culture, resulting in somaclonal variations (SVs). In the present study, we applied whole genome bisulfite sequencing to analyze context-specific DNA methylation changes in the pineapple genome between the cutting seedings and 5 SV plants. In general, SV plants exhibited methylation patterns analogous to those of cutting seedlings (CK). A total of 27.98% of the genomic cytosines of CK were methylcytosines, which was higher than that of 5 SV plants. Moreover, mCG and mCHG was hypermethylated, whereas mCHH was hypomethylated among the 5 SV plants genomic when compared with the CK. Most of the variation of DNA methylation was distributed in gene bodies, thus suggesting that phenotypic differences are probably perturbed by genes methylated from callus culture. In addition, the methylated genes were highly enriched for the Gene Ontology (GO) categories of binding and catalytic activity, cell part and organelle, cellular process, abiotic stimulus, and DNA modification. These results suggest that methylation mediates these pathways in the callus culture of pineapple. The results also suggested that the callus culture induced DNA methylation may result in the SV.