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. 2023 Feb 15;13(2):220235. doi: 10.1098/rsob.220235

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© 2023 The Authors.

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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Figure 3. — Genomic analysis process of identification of the genomic loci associated with the pigmentation phenotype of YM snakehead. (a) GWAS analysis using logistic regression modelling revealed that only one genomic region (13.98 Mb) at Chr19 was responsible for the pigmentation phenotype of YM snakehead. (b) Identification of allele frequency differences by WGS method among three DNA bulks, generated from homozygous WW pool, YY pool and F₁ heterozygotes pool, respectively. (c) A total of 1 247 605 SNPs were detected among the three WGS bulks. SNP variants were further screened, resulting in 7068 qualified SNPs passing all filtering criteria. (d) Two hundred and ninety fell into the 13.98 Mb genomic interval of GWAS, containing 68 SNPs overlapped with the significantly associated SNPs of GWAS in 13.98 Mb candidate genomic interval. (e) A total of 23 filtered SNPs that were perfectly associated with pigmentation phenotype of the 40 fish samples used in GWAS analysis, which contained 1 non-sense (stop-gain) variant, 9 intergenic variants and 13 intronic variants.