Study on difference of expression profile of long and short fruits of pepper

<bold>Objective</bold> Fruit length is an important part of pepper yield.Revealing the mechanism of pepper fruit elongation and mining the important genes regulating pepper fruit elongation can enrich the genetic and molecular basis of Solanaceae fruit morphogenesis theory. <bold>Method</bold> The inbred lines of long-fruited pepper “chicken intestine” and short-fruited pepper “Chaotian pepper” were used as experimental materials.The ovary on the day of flowering and the fruits at the red ripening stage were analyzed by paraffin sectioning technology，and the fruits at the highest elongation rate were analyzed by transcriptome sequencing and real-time fluorescence quantitative PCR. <bold>Result</bold> The morphological length of the red-ripened fruits of the two materials differed by 6 times，and the difference was mainly dominated by the number of cells.The statistical analysis of differentially expressed genes during the period with the highest elongation growth rate showed that 2 179 genes were differentially expressed during this period，including 1 098 up-regulated genes and 1 081 down-regulated genes，respectively.The results of GO functional enrichment analysis showed that the differentially expressed genes were significantly enriched in the following three functional modules：biological processes，which were mainly involved in protein complex assembly，cytokinin biosynthesis regulation and plant secondary metabolic processes；Cell group classification，focusing on cell wall structure，plasma membrane system and membrane-related components；molecular function，which is associated with ADP-binding activity and trans-zeatin O-β-D-glucosyltransferase activity.The results of KEGG enrichment analysis showed that DEGs were mainly distributed in zeatin biosynthesis，plant hormone signal transduction and plant mitogen-activated protein kinase（MAPK）pathway，and 44 DEGs in response to zeain biosynthesis and plant hormone signal transduction were screened，and it was speculated that these genes were related to the elongation process of pepper fruit.Eleven transcription factor family genes，including MYB，bHLH，AP2/ERF and WRKY，were screened from the differential genes，MYB and bHLH family genes were the most numerous.The mRNA expression trend of 10 DEGs was consistent with that in transcriptome analysis. <bold>Conclusion</bold> The morphological and cytological differences between long-fruited and short-fruited peppers were statistically analyzed，and the results of transcriptomic analysis showed that the differential expression of cell division-related genes such as <italic>CKX5</italic> and <italic>ZOG</italic> was the key factor leading to the difference in the number of cell divisions between the two materials.The synergistic expression patterns of plant hormone signal transduction-related genes <italic>ARF1</italic>，<italic>ARF9</italic>，<italic>IAA17</italic> and <italic>IAA20</italic> suggested that hormone homeostasis plays an important role in fruit morphological development.In addition，the differential expression of some members of the bHLH and MYB transcription factor families suggests that these regulators may be involved in regulating fruit elongation through the construction of gene expression networks.