Fig. 2

Detailed diagram of the putative XX/XY sex-determining region in LG23 in GIFT. a Position of the five sex-linked SNPs along the assembled Nile tilapia LG23. Each dot (red and black) represents the magnitude of association between the particular SNP and phenotypic sex for each family. SNPs with red dots were designed from BSA-ddRAD analysis for individual analysis of GIFT samples. Candidate sex-determining gene - Amh (green dot) including two sex-linked microsatellite markers (UNH898 – yellow dot, ARO172 – blue dot) are also located within this region (previous study, −log₁₀P values were random). b Gene content information in the region of higher association (position 9,560,000 to 10,370,000). This includes 32 genes, of which 14 are annotated, with 26 gaps (19 to 29,961 nt; white regions). Green: genes on the plus strand, red: genes on the minus strand, black: normal nts with no identified gene. c Similarities and dissimilarities in the analysed Y-linked AmhΔy and Amhy between GIFT and the previous study of Amh gene [12]; AmhΔy in GIFT had exon 0 deletion (161 bp), 5 bp insertion in exon VI (ATGTC) and 233 bp deletion in exon VII compared to Amh (i.e. no differences were detected between the two studies); Amhy in GIFT had the 5608 bp promoter deletion previously observed in Amhy [12], but had a 3 bp insertion (AAG) in exon 0 and lacked the C → T substitution observed in exon II