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Identity-by-descent genomic selection using selective and sparse genotyping.

Jørgen Odegård1, Theo H E Meuwissen

  • 1AquaGen AS, P,O, Box 1240, Sluppen, NO-7462 Trondheim, Norway. jorgen.odegard@nmbu.no.

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Low-cost genomic selection using identity-by-descent (IBD-GS) significantly boosts genetic gain in aquaculture breeding programs. This method effectively uses sparse genotyping and selective phenotyping of relatives for improved selection efficiency.

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Area of Science:

  • Animal Breeding and Genetics
  • Quantitative Genetics
  • Aquaculture

Background:

  • Genomic selection (GS) typically requires dense genotyping, which is costly and challenging for species with intense selection in both sexes.
  • Alternative low-cost GS methods, such as identity-by-descent genomic selection (IBD-GS), utilize selective genotyping and sparse marker panels to estimate relationships via linkage analysis.
  • IBD-GS offers a potential solution for improving selection programs in aquaculture by leveraging relationships among relatives.

Purpose of the Study:

  • To evaluate the efficacy of low-cost IBD-GS methods in breeding programs for continuous traits.
  • To assess the potential of IBD-GS in a typical aquaculture population where selection candidates' sibs are measured.
  • To compare the realized genetic gain of IBD-GS against classical selection methods.

Main Methods:

  • Stochastic simulation generated phenotypic and genomic data for a Gaussian trait in an aquaculture population (100 families).
  • Low-density marker data (~40 markers/Morgan) were used to trace identity-by-descent relationships.
  • Selective genotyping focused on top-ranking families' candidates and extreme-ranking training sibs, with all phenotypes included in analyses.

Main Results:

  • IBD-GS increased genetic gain by 13-32% compared to classical selection, with greater gains at higher heritabilities.
  • Maximum additional gain was achieved by genotyping the top 5% of phenotypically extreme sibs within selected families.
  • Further genotyping yielded diminishing returns, indicating efficiency in selective sampling.

Conclusions:

  • IBD-GS proved substantially more effective than classical selection, even with sparse markers and selective genotyping.
  • Low-cost genomic selection programs can succeed by integrating sparse/selective genotyping with pedigree and linkage information.
  • IBD-GS presents a viable, cost-effective strategy for enhancing genetic improvement in aquaculture.