DOI: 10.5281/zenodo.17353147
title: Sablefish (Anoplopoma fimbria) genotypes derived from a 300-locus SNP panel: Analyzes of these data are reported in in Gill et al. (Aquaculture; in revision) and Liu et al. (Aquaculture, in revision)

description: This dataset contains sablefish phenotype (weight in kg) and genotype data used for GWAS, Genome Prediction and PHATE analyses. These data are reported in two manuscripts:

“Phenomic and genomic analyses of spine shape in 800 cultured sablefish (Anoplopoma fimbria)”. This study used 300-locus genotypes, spine phenotypes, and PHATE analyses to test the hypothesis that spine curvatures are influenced by genetic variation. This paper reported sample collection details: Implant-1, 2019: 200 individuals collected at harvest in August 2021; Implant-2, 2019: 200 individuals collected at harvest in October 2021; Implant-5, 2019: 380 individuals collected at harvest in February and March 2022.

“Predicting growth rate in sablefish (Anoplopoma fimbria) using a 300-locus SNP panel”. This study used 300-locus genotypes and weight data at harvest to test the hypothesis that variation at one or more of the 300 SNPs was associated with variation in weight. This paper utilized the same data as above but pooled Implant-1 and Implant-2 samples into 'Group-1' (N=400). 'Group-2' (N=380) included individuals from Implant-5, 2019. 
description: Designing the 300 SNP Panel:

The 300-SNP panel was developed before a sablefish chromosome-level genome assembly was available. The reference genome (GCA_000499045.1) contained 208, 506 contigs. One SNP from each of the largest contigs was selected (500 SNPs). For the final panel, 300 of these were selected in an effort to maximize even spacing throughout the genome, while ensuring high minor allele frequencies across all the different aquaculture populations. These 300 loci have now been mapped to the latest genome assembly (see genome.png).

 

Creating shape score table:

Images of sablefish taken using an iPhone at harvest were compiled into TPS files with tpsUtil (Rohlf, 2015). Using tpsDIG2 (Rohlf, 2015), fifty evenly spaced, fixed landmarks were placed along the dorsal surface of each fish, and ten fixed landmarks were placed along a straight line connecting the base of the pectoral fin to the end of the caudal peduncle. After excluding images where fish were out of frame or where landmarks could not accurately be placed, 728 individuals were included in the study. Procrustes superimposition was performed in R Statistical Software (v4.3.1; R Core Team 2023) using the gpagen function with default settings from the geomorph package (Adams et al., 2024; Baken et al., 2021). The superimposed landmark (x,y) coordinates were utilized for subsequent PHATE (Potential of Heat-diffusion for Affinity-based Trajectory Embedding) analyses, which embeds these data (60 x,y coordinates for 728 fish) and generates a 3D visualization (x,y,z coordinates recorded in Shape_Scores Table).  Then we reduced fish positions in the 3D shape-PHATE representation to a single value using principal component analysis (PCA). Specifically, we applied PCA to the three (x, y, z) PHATE coordinates and used the first principal component (PC1, which explained 72% of the variance) as a 1D “shape score” (also recorded in Shape_Scores Table).  PC1 was then treated as a continuous variable in a linear mixed-model Genome-Wide Assosciation Study that included a kinship matrix to control for relatedness among individuals. Fish were largely sorted by collection date on the PC1 axis.  We speculate that photography inconsistencies among sample dates was a confounding factor, that influenced both shape and genetics.
description: Files included in this dataset:



“genotypes_implant1.csv” – Table of 300 SNP loci genotypes for sablefish from Implant-1, 2019 (Group-1) collected in August 2021. 

“genotypes_implant2.csv” – Table of 300 SNP loci genotypes for sablefish from Implant-2, 2019 (Group-1) collected in October 2021.

“genotypes_implant5.csv” – Table of 300 SNP loci genotypes for sablefish from Implant-5, 2019 (Group-2) collected in February and March 2022. 

“weights_implant1.csv” – Table of weight at harvest for sablefish from Implant-1, 2019 (Group-1) collected in August 2021. 

“weights_implant2.csv” – Table of weight at harvest for sablefish from Implant-2, 2019 (Group-1) collected in October 2021. 

“weights_implant5.csv” – Table of weight at harvest for sablefish from Implant-5, 2019 (Group-2) collected in February and March 2022. 

“implant1.png” – Relatedness heatmap for Implant-1, 2019 (Group-1).

“implant2.png” – Relatedness heatmap for Implant-2, 2019 (Group-1).

“implant5.png” – Relatedness heatmap for Implant-5, 2019 (Group-2).

"genome.png" – SNP positions on chromosomes.

“shape_scores.csv" – Table of sablefish PHATE (x, y, z) values, and the first principal component which describes 72% of the variance.
description: 'A' represents the minor allele at each locus and genotypes are coded as follows: 0 for missing data, 1 for AA, 2 for AB, and 3 for BB.