Fig. 2
Screening and identification of sex-determining gene through multi-omics in Spotted knifejaw. A Localization of candidate sex-determining genes (amhr2, aldh1l2, wnt4, gdf11) in Fst value distribution maps for selective sweep analysis. B Overall analysis of gene resequencing information. Starting from the outermost layer, the lengths of each chromosome (in Mb) are represented. Gene density within various window regions of chromosomes is depicted using frequency histograms, while a scatter plot illustrates SNP density across different chromosome regions. Key structural variations are marked with colored lines: orange for DUP (tandem repeat), purple for DEL (large fragment deletion), green for INS (insertion), and blue for INV (inverted structural variation). Additionally, pairwise chromosomes show BND (structural variation of chromosomal translocation type) along the inner line. C Localization of candidate sex-determining genes (amhr2, aldh1l2, wnt4, gdf11) in Q model for GWAS of male Spotted knifejaw. D Tissue-specific and early developmental expression profiles of candidate genes (amhr2, aldh1l2, wnt4, gdf11). Different letters indicate that the expression levels in different tissues were significantly different. T: testis; O: ovary; B: brain; L: liver; K: kidney; I: intestine; M: muscle; St: stomach; G: gill; Sk: skin; H: heart; S: spleen; E: eye. e–h. Relative expression of amhr2 mRNA transcript variants from 5 to 360 dph. *, P < 0.05. E Combined multi-omics screening of target genes Wayne diagrams. F Analysis of screened genes linkage disequilibrium in male Spotted knifejaw (amhr2, aldh1l2, wnt4, gdf11). Red lines indicate significance thresholds within scaffolds (p = 0.05 for bonferroni correction). The color of each SNP reflects the value of r2, with red indicating high values and yellow indicating low values. G Analysis of differences in FPKM values of sex-related genes between male and female gonads of Spotted knifejaw. F-1, F-2, F-3, F-4 represent FPKM values in the ovaries and M-1, M-2,—M-3, M-4 represent FPKM values in the testes of Spotted knifejaw