Triploid crucian carp (TCC) is obtained by hybridization of female diploid red crucian carp (Carassius auratus red var., RCC) and male allotetraploid hybrids. In this study, high-throughput sequencing was used to conduct the transcriptome analysis of the female hypothalamus of diploid RCC, diploid common carp (Cyprinus carpio L., CC) and TCC. The key functional expression genes of the hypothalamus were obtained through functional gene annotation and differential gene expression screening. A total of 71.56 G data and 47,572 genes were obtained through sequencing and genome mapping, respectively. The Fuzzy Analysis Clustering assigned the differentially expressed genes (DEGs) into eight groups, two of which, overdominance expression (6005, 12.62%) and underdominance expression (3849, 8.09%) in TCC were further studied. KEGG enrichment analysis showed that the DEGs in overdominance were mainly enriched in four pathways. The expression of several fertility-related genes was lower levels in TCC, whereas the expression of several growth-related genes and immune-related genes was higher levels in TCC. Besides, 15 DEGs were verified by quantitative real-time PCR (qPCR). The present study can provide a reference for breeding sterility, fast-growth, and disease-resistant varieties by distant hybridization.

三倍体鲫鱼（TCC）是由雌性二倍体红鲫（Carassius auratus red var.，RCC）和雄性异源四倍体杂种杂交获得的。本研究采用高通量测序技术对二倍体肾细胞癌雌性下丘脑、二倍体鲤鱼（Cyprinus carpioL., CC) 和 TCC。通过功能基因注释和差异基因表达筛选获得下丘脑的关键功能表达基因。通过测序和基因组作图，分别获得了 71.56 个 G 数据和 47,572 个基因。模糊分析聚类将差异表达基因（DEGs）分为八组，其中两组进一步研究了TCC中的过度表达（6005，12.62％）和不足表达（3849，8.09％）。KEGG富集分析表明，优势度的DEGs主要富集在四个途径。TCC中几种生育相关基因的表达水平较低，而TCC中几种生长相关基因和免疫相关基因的表达水平较高。此外，通过定量实时PCR（qPCR）验证了15个DEG。