Transcriptomic analysis and screening of development-related genes of prickles for different Rubus corchorifolius cultivars

Objective This study aimed to identify the candidate genes and signaling pathways related to prickle development for raspberry based on transcriptome sequencing data，so as to provide theoretical references for elucidating the molecular mechanism of raspberry prickle development and cultivating prickleless raspberry cultivars.Method Using Qianmei 1 （non-prickle type， C） and Rubus niveus Thunb. （multi-prickle type， D） as experimental materials， the transcriptome sequencing analysis was performed on the stem epidermis tissues of the primary lateral branches （C1，D1）， secondary lateral branches （C2，D2）， and tertiary lateral branches （C3，D3）. After screening differentially expressed genes （DEGs） using DESeq2， GO functional annotation and KEGG signaling enrichment analysis were conducted， and sequencing results were validated through real-time fluorescence quantitative PCR.Result A total of 116.89 Gb of clean data was obtained from transcriptome sequencing， with a GC content of 45.29%-46.08% and Q30 values above 96.94%. In the comparison groups of C1 vs D1，C2 vs D2，C3 vs D3， and D1vs D3， the numbers of identifies DEGs were 3164， 2835， 2331， and 1740， respectively. Among these， the number of up-regulated DEGs was 1514， 1892， 1435， and 1368， while the number of down-regulated DEGs was 1650， 943， 896， and 327， respectively. A total of 279 DEGs were shared among all four comparison groups. The GO functional annotation analysis revealed that the DEGs were classified into three major categories—biological process， cellular component， and molecular function—which were primarily enriched incellular processes， signaling， cellular anatomical entity， intracellular， protein-containing complex， binding， and Molecular function regulator. The KEGG signaling pathway enrichment showed that DEGs were enriched in the signaling pathways such as plant hormone signal transduction， phenylpropanoid biosynthesis， and flavonoid biosynthesis. Finally， 13 DEGs related to raspberry prickle development were screened： genes involved in plant hormone signal transduction were bHLH93 and bHLH35 from bHLH transcription factor family， APL and MYBC1 from MYB transcription factor family， and ARF6， LAX2， IAA26， and AUR50 related to auxin components. Two genes related to lignin synthesis， CCR1 and CAD6， were involved in phenylpropanoid biosynthesis signaling pathway. Three genes related to flavone synthesis， F3H， OMT3， and UFGT7， were involved in flavonoid biosynthesis. All these genes exhibited obvious difference in expression pattern in different development stages. Results of real-time fluorescence quantitative PCR proved that the data of transcriptome sequences was reliable.Conclusion Prickle development of Qianmei 1 and Rubus niveus Thunb. is regulated by genes including up-regulated genes （bHLH35， IAA26 and F3H） and down-regulated genes （bHLH93， CCR1， and CAD6）. These genes synthetically regulate the process of prickle development through plant hormone signal transduction， phenylpropanoid biosynthesis， and flavonoid biosynthesis.