Identifying microRNAs and their downstream transcriptional regulatory network during prickle development in Rubus spp

Blackberry fruit is rich in bioactive substances and has antioxidant function, with broad market prospects. However, most blackberry cultivars have prickles all over their bodies, which is highly inconvenient for the management and harvesting. This study revealed that the content of lignin and PAL, an enzyme which related to lignin synthesis increases with the occurrence of prickles. The miRNA expression profiles and potential target gene regulation patterns of the cortex and stem tips of the thorny blackberry cultivar 'Boysenberry' and its bud-mutated thornless cultivar 'Zaohong' cortex were obtained through small RNA sequencing. This study identified a total of 50 differentially expressed miRNAs. The target genes of these differentially expressed miRNAs play important roles in the phenylalanine synthesis and plant hormone signal transduction pathway. Novel_151 - CAD , fve-miR396b-5p-CAD , fve-miR396b-5p-POD , fve-miR396a-5p-POD genes can increase lignin production, while novel_186-GUAT , fve-miR164a-5p-UXS genes can increase cell wall polysaccharides production, and thus promote the formation of cell wall. Novel_159-AUX/IAA , fve-miR159b-AUX/IAA and novel_128-AUX/IAA genes can affect lignin production by activating the auxin signaling pathway. Those genes may play important regulatory roles in the occurrence of blackberry prickle. The results will provide a reference for the research on blackberry prickle, and lay the foundation for breeding cultivars without prickle and the development of blackberry industry. • Detected the lignin and relevant enzyme content of two blackberry stems. • A total of 14 miRNAs involved in prickle formation were screened in blackberries. • Proposed three possible miRNA regulatory networks of blackberry prickle formation.