刺参疣足数目性状“转录因子-miRNA-lncRNA-基因”调控网络研究

刺参是我国水产养殖重要种类之一。疣足数目既是影响刺参品相和价格的主要指标也是刺参良种选育的重要目标性状。目前，关于刺参疣足数目性状的分子生物学研究比较薄弱，尚无系统全面的理论研究。本研究拟结合前期工作，从转录和转录后水平进一步挖掘和筛选影响刺参疣足数目且具有靶向关系的关键转录因子基因、miRNAs、lncRNAs和非转录因子基因，在此基础上，以获得的具有靶向关系的刺参疣足数目性状关键转录因子基因、miRNAs、lncRNAs和非转录因子基因为内部“节点”（Node），以各节点间的靶向关系为“边”（Edge）构建刺参疣足数目性状“转录因子-miRNA-lncRNA-基因”调控网络并进行网络整体关联性评价以及生物学验证，以期系统地了解和揭示刺参疣足数目性状的分子调控网络和规律，为进一步阐明刺参疣足数目性状的分子调控机制以及开展“多疣足”刺参的分子辅助育种提供理论参考。

The sea cucumber Apostichopus japonicus (Selenka 1867) is one of the most dominant and economically important species of sea cucumber in China. It has considerable edible and medicinal value. The aquaculture yield of A. japonicus in China increased from 93 kilotons in 2008 to 174 kilotons in 2018. The papillae are the fleshy, conical ambulacral appendages of A. japonicus. The number of A. japonicus papillae is critically important to the pricing and grading of living A. japonicus individuals and A. japonicus products, as this metric serves as a proxy for A. japonicus quality. For this reason, the genes, regulatory elements (or factors), and molecular mechanisms involved in the regulation of papilla numbers in A. japonicus might be useful targets for selective breeding of A. japonicus, but these genes, regulatory elements (or factors), and molecular mechanisms remain unidentified. To develop a systematic understanding of the transcriptome-level regulatory mechanism that underlies the regulation of the number of papillae in A. japonicus, we here aim (1) to identify major transcriptional factors (TFs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and their common target genes that may be associated with the number of papillae in A. japonicus during different stages of the organism’s development; (2) to establish the interactions of these key TFs, miRNAs, lncRNAs, and their common target genes; (3) to define and predict a global TF-miRNA-lncRNA-gene (TML-gene) network associated with the number of papillae in A. japonicus and then characterize the topology and features of this TML-gene network; and (4) to evaluate and verify the TML-gene network using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR), yeast two-hybrid technique, dual-luciferase reporter assay, RNA electrophoretic mobility shift assay (RNA-EMSA), RNA interference (RNAi), and microarray in A. japonicus aquaculture. All data observed in this project will enrich our knowledge of molecular regulatory mechanisms underlying the regulation of the number of papillae in sea cucumbers. The use of these data will provide more theoretical support that could be used to increase the efficiency of selective sea cucumber breeding and promote the development of sea cucumber aquaculture and industry.