†Locus used for PCR-RFLP sexing assay
‡Two females had low read count for these SNPs, but reference allele was
present
§One male had low read count for these SNPs but alternative allele was
present
Figure 1. Visual summary of individual genotypes for sex-linked
loci for 50 individual male Macquarie perch (numbered columns) for
scaffold 633 region 90152-94017 (data in Supplementary Material S4).
Loci with male-specific alleles: homozygote for the reference allele
light blue, heterozygote- intermediate blue, homozygotes for alternative
allele- dark blue. XY-gametologs: homozygotes for the reference allele-
light yellow, heterozygotes- light orange, homozygotes for alternative
allele- dark orange. Loci numbered in red text are XY-gametologous
indels, black text-SNPs. All females were homozygous for the reference
alleles at these loci (as per colour-coded genotype in the last column).
Y-linked alleles for loci 1-13 appear in four distinct linkage patterns:
(i) two loci: 1 and 9 (26 males); (ii) ten loci: 2, 3, 5-8, 10-13 (8
males); (iii) 10 loci: 1, 4-8, 10-13 (7 males); and (iv) 4 loci: 1, 7-9
(1 male).