Chromosomal aberrations and early mortality in a non-mammalian vertebrate: example from pressure-induced triploid Atlantic salmon
Data files
Oct 07, 2024 version files 1.54 MB
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README.md
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Supporting_data.zip
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Abstract
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.
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:
- 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.
- 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).
- 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.