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Using genomic selection to correct pedigree errors in kiwiberry breeding.

Daniel Mertten1,2, Catherine M McKenzie3, Susan Thomson4

  • 1The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, 1142 New Zealand.

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Summary
This summary is machine-generated.

Pedigree errors reduce breeding value accuracy in kiwiberry selection. Genomic selection offers a more robust approach, improving predictions by accurately capturing genetic relationships, especially for traits in male genotypes.

Keywords:
Best linear unbiased predictionBreeding valueDioeciousPedigree errorPrediction accuracy

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Area of Science:

  • Plant breeding
  • Genetics
  • Horticulture

Background:

  • Accurate breeding value estimation is vital for selecting superior genotypes in plant breeding programs.
  • Traditional methods using pedigree information are susceptible to errors, impacting accuracy, particularly in long-lived perennial vines like kiwiberries.
  • Pedigree errors can lead to misidentified relationships, compromising the reliability of genetic merit predictions.

Purpose of the Study:

  • To evaluate the impact of pedigree errors on breeding value predictions in kiwiberry (Actinidia spp.) breeding.
  • To explore the advantages of genomic selection over traditional pedigree-based methods in the presence of pedigree inaccuracies.
  • To assess the effectiveness of genomic selection for predicting genetic merit in both female and male kiwiberry genotypes.

Main Methods:

  • Applied Best Linear Unbiased Prediction (BLUP) for estimating breeding values using pedigree information.
  • Simulated four scenarios with varying degrees of alteration in pedigree-based relationship matrices to represent inaccurate genotype relationships.
  • Compared pedigree-based breeding values with genomic estimated breeding values (GEBV) for vine- and fruit-related quantitative traits.

Main Results:

  • Prediction accuracy of pedigree-based breeding values decreased significantly with increasing levels of altered population structure.
  • Genomic selection demonstrated robustness by maintaining realized relationships between genotypes, unaffected by pedigree errors.
  • Marker-based predictions outperformed pedigree-based predictions, particularly for genotypes lacking phenotypic data, such as male siblings.

Conclusions:

  • Genomic selection provides more accurate breeding value predictions in kiwiberry breeding programs compared to traditional pedigree-based methods.
  • Genomic selection effectively mitigates the negative impact of pedigree errors by utilizing marker inheritance to capture true genetic relationships.
  • The implementation of genomic selection is recommended for kiwiberry breeding to enhance selection efficiency and accuracy, especially for traits in male genotypes.