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Updated: Nov 6, 2025

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Measuring genetic connectedness between herds based on high density SNP markers.

Zi Wen Zhou1, Xue Wang1, Xiang Dong Ding1

  • 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University,Beijing 100193, China.

Yi Chuan = Hereditas
|May 11, 2021
PubMed
Summary

High-density SNP markers improve the assessment of genetic connectedness between herds compared to traditional pedigree data. The connectedness rating (CR) method is recommended as a robust and reliable approach for evaluating genetic connections.

Keywords:
genetic connectednessgenomepedigreerelationship matrixswine

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Area of Science:

  • Animal Breeding and Genetics
  • Genomic Evaluation
  • Quantitative Genetics

Background:

  • Genetic evaluations' accuracy depends on genetic connectedness among herds.
  • Pedigree data is traditionally used to assess genetic connectedness.
  • High-density SNP markers offer a potential improvement for this assessment.

Purpose of the Study:

  • To evaluate the application of high-density SNP markers in assessing genetic connectedness.
  • To compare genetic connectedness derived from genomic data versus pedigree data.
  • To assess the performance of six different methods using various relationship matrices.

Main Methods:

  • Utilized simulated and SNP chip data from pig breeding farms.
  • Implemented six methods: PEVD, PEVD(x), VED, CD, r, and CR.
  • Employed five relationship matrices: A (pedigree), G, Gs, G0.5 (genomic), and H (combined).

Main Results:

  • Genomic data (G, Gs, G0.5 matrices) generally provided superior genetic connectedness estimates over pedigree data (A matrix).
  • The H matrix (combined data) yielded results between A and G matrices.
  • CR demonstrated robustness and reliability, being less affected by heritability than other methods; PEVD is a useful supplement for quantifying prediction errors.

Conclusions:

  • High-density SNP markers offer advantages over pedigree analysis for measuring genetic connectedness.
  • The connectedness rating (CR) is a robust, reliable, and easily calculated method for assessing genetic connectedness, suitable for various heritabilities.
  • The G matrix better reflects genetic connectedness than its extensions (Gs, G0.5).