Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla

To investigate the molecular mechanism underlying fruit development and color change,comparative transcriptome analysis was employed to generate transcriptome profiles of two typical wild varieties of Fragaria pentaphylla at three fruit developmental stages(green fruit stage,turning stage,and ripe fruit stage).We identified 25,699 long noncoding RNAs(lncRNAs)derived from 25,107 loci in the F.pentaphylla fruit transcriptome,which showed distinct stage-and genotype-specific expression patterns.Time course analysis detected a large number of differentially expressed protein-coding genes and lncRNAs associated with fruit development and ripening in both of the F.pentaphylla varieties.The target genes downregulated in the late stages were enriched in terms of photosynthesis and cell wall organization or biogenesis,suggesting that lncRNAs may act as negative regulators to suppress photosynthesis and cell wall organization or biogenesis during fruit development and ripening of F.pentaphylla.Pairwise comparisons of two varieties at three developmental stages identified 365 differentially expressed lncRNAs in total.Functional annotation of target genes suggested that lncRNAs in F.pentaphylla may play roles in fruit color formation by regulating the expression of structural genes or regulatory factors.Construction of the regulatory network further revealed that the low expression of Fra a and CHS may be the main cause of colorless fruit in F.pentaphylla.

Genome-wide Dissection of Co-selected UV-B Responsive Pathways in the UV-B Adaptation of Qingke

Qingke (Tibetan hulless barley) has long been cultivated and exposed to long-term and strong UV-B radiation on the Tibetan Plateau, which renders it an ideal species for elucidating novel UV-B responsive mechanisms in plants. Here we report a comprehensive metabolite profiling and metabolite-based genome-wide association study (mGWAS) using 196 diverse qingke and barley accessions. Our results demonstrated both constitutive and induced accumulation, and common genetic regulation, of metabolites from different branches of the phenylpropanoid pathway that are involved in UV-B protection. A total of 90 significant mGWAS loci for these metabolites were identified in barley-qingke differentiation regions, and a number of high-level metabolite trait alleles were found to be significantly enriched in qingke, suggesting co-selection of various phenylpropanoids. Upon dissecting the entire phenylpropanoid pathway, we identified some key determinants controlling natural variation of phenylpropanoid content, including three novel proteins, a flavone C-pentosyltransferase, a tyramine hydroxycinnamoyl acyltransferase, and a MYB transcription factor. Our study, furthermore, demonstrated co-selection of both constitutive and induced phenylpropanoids for UV-B protection in qingke.