Aquaculture

Accounting for Different Ploidy Levels in Trout Genetic Evaluations in a Commercial Breeding Program

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Abstract

Triploidy induced by high‑pressure shock prevents extrusion of the second maternal polar body, producing offspring with three chromosome sets: one paternal and two maternal. This mechanism is used to generate sterile fish for aquaculture. Genetic evaluations rely on additive genetic relationship matrices (A) from pedigrees, but diploid‑based matrices misrepresent relationships when ploidy differs. We analyzed two Troutldoge's rainbow trout groups phenotyped for growth: diploids reared in raceways and triploids under river conditions. Using MiXBLUP, we constructed alternative inverse relationship matrices (A⁻¹) that account for individual ploidy and the probability that two alleles within a gamete are identical by descent (λ). This probability reflects cytological mechanisms: unreduced gametes arise via first or second division restitution (FDR/SDR), equivalent to retention of the first or second polar body. Under SDR, sister chromatids are retained, and with limited centromere‑proximal recombination, λ approaches 1; models suggest λ ≈ 0.9 for salmonid females, consistent with sex‑specific recombination patterns. Construction of A⁻¹ followed rules for mixed‑ploidy pedigrees: using the extended pedigree with gametic ploidy and λ for each parent, we first built the coancestry matrix (K). Diagonals were determined by inbreeding coefficients that depend on gametic contributions and λ, and off‑diagonals were built recursively via parental contribution vectors. A⁻¹ was recursively computed using elements of K and the scaling factor (2√(vX vY))⁻¹, where v is half the ploidy level. Four scenarios were tested: (1) equal ploidy for all animals (incorrect baseline, λ = 0); (2a) triploidy modeled with sire and dam λ = 0 (no intragametic IBD); (2b) dam λ = 0.918 (partial double haploid with crossover); and (2c) dam λ = 1, treating the maternal contribution as double haploid without crossover. Scenario 2b was biologically most plausible and used as reference for variance components and EBV comparisons. Correlations of off-diagonals elements of the adapted A⁻¹ matrices with scenario 1 ranged from 0.9 to 0.99, while diagonal elements were less correlated to the baseline (0.77-0.9); triploid heritability (estimated with DMU) dropped from 0.30 ± 0.05 (scenario 1) to 0.22 ± 0.04 in scenarios 2a-2c, while diploid heritability (0.48 ± 0.04) and genetic correlation (≈0.67 ± 0.11) remained stable. EBVs for the triploid trait in diploid selection candidates were first centered on a genetic reference to reduce level bias. After scaling by additive genetic SDs, biases were corrected: scenario 1 dropped from 21% to 1.35%, while the ploidy‑aware scenarios yielded slopes near unity after the same step, reducing level and dispersion bias. The large bias in the diploid model was primarily due to variance component differences inflating EBV spread. These results show that incorporating ploidy and realistic λ in A⁻¹ enables unbiased EBV estimation across ploidy levels, supporting selection for triploid performance in diploid breeding programs.

Keywords: 2026

How to Cite:

Bink, M., Calus, M., Correa, K., Janssen, K., Martin, K., ten Napel, J., Vandenplas, J. & Vereijken, A., (2026) “Accounting for Different Ploidy Levels in Trout Genetic Evaluations in a Commercial Breeding Program”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285430. doi: https://doi.org/10.31274/wcgalp.23702

Rights: 1