DOI: 10.5061/dryad.4xgxd25jx
title: Chromosomal aberrations and early mortality in a non-mammalian vertebrate: example from pressure-induced triploid Atlantic salmon

description: In commercial aquaculture, the production of triploid fish is currently
 the most practical approach to prevent maturation and farm-to-wild
 introgression following escapes. However, triploids often exhibit poor
 welfare, and the underlying mechanisms remain unclear. Inheritance issues
 associated with sub-optimal hydrostatic pressure treatments used to induce
 triploidy, or the genetic background of parental fish, have been
 speculated to contribute. We tested this by quantifying the frequency and
 type of chromosomal aberrations in Atlantic salmon subjected to a gradient
 of sub-optimal pressure treatments (Experiment 1) and from multiple
 mothers (Experiment 2). From these experiments, we genotyped a subsample
 of ~900 eyed eggs and all ~3,300 surviving parr across ~20
 microsatellites. In contrast to the low frequency of chromosomal
 aberrations in the diploid (no hydrostatic pressure) and triploid (full
 9,500 PSI treatment) controls, eyed eggs subjected to sub-optimal pressure
 treatments (6,500 – 8,500 PSI) had a higher incidence of chromosomal
 aberrations such as aneuploidy and uniparental disomy, corresponding to
 lower triploidization success and higher egg mortality rates. We also
 observed maternal effects on triploidization success and incidence of
 chromosomal aberrations, with certain half-sibling families exhibiting
 more aberrations than others.  Chromosomal aberrations were rare
 among surviving parr, suggesting a purge of maladapted individuals during
 early development. This study demonstrates that sub-optimal hydrostatic
 pressure treatments and maternal effects not only influence the success of
 triploidization treatments but may also affect the incidence of
 chromosomal aberrations and early mortality. The results have important
 implications for aquaculture breeding programs and their efforts to
 prevent farm-to-wild introgression.
description: # Chromosomal aberrations and early mortality in a non-mammalian
 vertebrate: example from pressure-induced triploid Atlantic salmon Three
 datasets are provided as a supplement to the associated article. Each
 dataset contains data from two experiments. In the first experiment,
 Atlantic salmon offspring from three half-sibling families (3 dams, 1
 common sire) were subjected to five hydrostatic pressure treatments
 shortly after fertilization. This was to explore the effects of
 sub-optimal pressure treatments (6500 PSI, 7500 PSI, and 8500 PSI) on
 ploidy and inheritance, compared to standard diploid (0 PSI) and triploid
 (9500 PSI) controls. In the second experiment, Atlantic salmon offspring
 from twelve half-sibling families (12 dams, 1 common sire) were subjected
 to two hydrostatic pressure treatments representing standard diploid and
 triploid procedures (0 PSI and 9500 PSI). This was to further explore
 family effects on ploidy and inheritance following standard diploid (0
 PSI) and triploid (9500 PSI) treatments. Each dataset contains data from
 two sampling points for both experiments. A subsample of eyed-eggs was
 genotyped, and later all surviving offspring were genotyped at the parr
 (juveniles, pre-smolt) stage. Description of each dataset: 1.
 **Genotypes.xlsx**: Microsatellite genotypes of offspring inferred using
 MAC-PR, provided across four spreadsheets: Experiment 1 eggs, Experiment 1
 parr, Experiment 2 eggs, Experiment 2 parr. Parent genotypes are also
 provided in the fifth spreadsheet. Headers are as follows: * Sample_Name:
 Unique sample identifier * treatment: Hydrostatic pressure treatment. For
 experiment 1: 0 PSI, 6500 PSI, 7500 PSI, 8500 PSI, or 9500 PSI. For
 Experiment 2: 0 PSI or 9500 PSI. * Remaining columns: Microsatellite
 genotypes across 20 loci (Experiment 1) and 19 loci (Experiment 2) in
 triploid configuration (3 alleles per locus). NA refers to missing data or
 lack of a third allele at disomic loci. * Parent genotypes are provided in
 the fifth spreadsheet. Headers indicate sample ID, Parent type (Dam or
 Sire), Family number, and diploid genotypes across 20 microsatellite loci.
 2. **Genotypes_summary statistics.xlsx**: Microsatellite genotype summary
 statistics for all offspring. The data are provided across four
 spreadsheets: Experiment 1 eggs, Experiment 1 parr, Experiment 2 eggs,
 Experiment 2 parr. Headers are as follows: * Sample_Name: Unique sample
 identifier * family: Offspring assignment to one of three half-sibling
 families (Experiment 1) and 12 half-sibling families (Experiment 2).
 Family was known for eggs as they were separated by the family group at
 the hatchery when sampled. Family assignment of parr was inferred from
 genotypes using the Family Assignment Program. * treatment: Hydrostatic
 pressure treatment. For experiment 1: 0 PSI, 6500 PSI, 7500 PSI, 8500 PSI,
 or 9500 PSI. For Experiment 2: 0 PSI or 9500 PSI. * Next 20 columns
 (Experiment 1) and 19 columns (Experiment 2): microsatellite genotypes in
 'short-format' (i.e. homozygous A, disomic AB, trisomic AAB,
 ABB, or ABC). NA refers to missing data. * Aberration: Inheritance
 aberration type, if present. Aberration types are the inheritance of 2
 paternal alleles (2 paternal), base-pair shifts (bp shift), and missing
 maternal alleles (Missing maternal, with the number of loci involved). *
 replicate (only for Experiment 1): Offspring were grouped into two
 replicates (R1 and R2) for each of the five pressure treatments. *
 count_NA: Counts of missing genotypes per individual. * count_A to
 count_ABC: counts of occurrence of each locus configuration for each
 individual. * count_trisomic: counts of trisomic loci (count_AAB +
 count_ABB + count_ABC) for each individual. * sum: number of loci in the
 dataset * prop.trisomic: Proportion of (informative) heterozygous loci
 that are trisomic. * ploidy: Ploidy inferred by prop.trisomic. Can be
 Diploid (prop.trisomic = 0), Triploid (prop.trisomic = 1), or Aneuploid
 (prop.trisomic between 0 and 1). 3. **Genotype_mismatches.xlsx**:
 Individuals flagged as having a genotype inconsistent with that of their
 parents. The genotype of the offspring is shown against that of its mother
 (dam) and father (sire). Possible causes of the mismatch are shown above
 the locus involved. The data are provided across four spreadsheets:
 Experiment 1 eggs, Experiment 1 parr, Experiment 2 eggs, Experiment 2
 parr. Headers are as follows: * Offspring/parent: for each triad
 comparison, one row for each of Offspring, Sire, and Dam. *
 Offspring/parent ID: unique sample identifier * family: Family assignment
 of the offspring. Family 1 indicates the mother is Dam M1. * Remaining
 columns: 20 microsatellite loci (Experiment 1) and 19 microsatellite loci
 (Experiment 2), showing genotypes of offspring and parents at those loci,
 and a header describing the inheritance aberration type, if present.