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Background  Formation of triploid organism is useful in genetics and breeding. In this study, autotriploid  Carassius auratus  (3nRR, 3n = 150) was generated from  Carassius auratus  red var. (RCC, 2n = 100) (♀) and autotetraploid  Carassius auratus  (4nRR, 4n = 200) (♂). The female 3nRR produced haploid, diploid and triploid eggs, whereas the male 3nRR was infertile. The aim of the present study was to explore fertility of potential candidate genes of 3nRR.    Results  Gonadal transcriptome profiling of four groups (3 females RCC (FRCC), 3 males 4nRR (M4nRR), 3 males 3nRR (M3nRR) and 3 females 3nRR (F3nRR)) was performed using RNA-SEq. A total of 78.90 Gb of clean short reads and 24,262 differentially expressed transcripts (DETs), including 20,155 in F3nRR vs. FRCC and 4,107 in M3nRR vs. M4nRR were identified. A total of 106 enriched pathways were identified through KEGG enrichment analysis. Out of the enriched pathways, 44 and 62 signalling pathways were identified in F3nRR vs. FRCC and M3nRR vs. M4nRR, respectively. A total of 80 and 25 potential candidate genes for fertility-related in F3nRR and M3nRR were identified, respectively, through GO, KEGG analyses and the published literature. Moreover, protein-protein interaction (PPI) network construction of these fertility-associated genes were performed. Analysis of the PPI networks showed that 6 hub genes ( MYC ,  SOX2 ,  BMP4 ,  GATA4 ,  PTEN  and  BMP2 ) were involved in female fertility of F3nRR, and 2 hub genes ( TP53  and  FGF2 ) were involved in male sterility of M3nRR.    Conclusions  Establishment of autotriploid fish offers an ideal model to study reproductive traits of triploid fish. RNA-Seq data revealed 6 genes, namely,  MYC ,  SOX2 ,  BMP4 ,  GATA4 ,  PTEN  and  BMP2 , involved in the female fertility of the F3nRR. Moreover, 2 genes, namely,  TP53  and  FGF2 , were related to the male sterility of the M3nRR. These findings provide information on reproduction and breeding in triploid fish.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07753-5.

Formation of autotriploid Carassius auratus and its fertility-related genes analysis