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A method for single nucleotide polymorphism selection for parentage assessment in goats.

A Talenti1, E L Nicolazzi2, S Chessa3

  • 1Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, via Celoria 10, Milano, 20133, Italy.

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Accurate goat parentage assessment is crucial for genetic improvement. This study developed a novel method to create small, highly accurate single nucleotide polymorphism (SNP) panels for reliable parentage testing.

Keywords:
goatparentage analysissingle nucleotide polymorphism

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Area of Science:

  • Animal Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Accurate pedigrees are vital for optimizing genetic improvement and conservation of animal genetic resources.
  • In goats, traditional parentage identification methods are hindered by mating practices and kidding management.
  • Single nucleotide polymorphisms (SNP) offer a potential alternative to microsatellites for parentage assessment in various species.

Purpose of the Study:

  • To develop a robust, three-step procedure for selecting a low-density single nucleotide polymorphism (SNP) panel for accurate parentage assessment in goats.
  • To address challenges in SNP selection for goats due to uncertainties in genome assembly.
  • To establish highly accurate SNP panels for parentage verification in goat populations.

Main Methods:

  • A novel three-step procedure was developed using parent-offspring identification, Mendelian error estimation, canonical discriminant analysis, and stepwise regression reduction.
  • The GoatSNP50 chip data was utilized to identify and refine SNP panels.
  • A reference sample of 109 Alpine goats with known pedigree relationships was used for panel development and validation.

Main Results:

  • Two final SNP panels, comprising 130 and 114 SNPs, were identified with extremely low probabilities of random coincidental match (1.51×10(-57) and 2.94×10(-34), respectively).
  • All developed SNP panels accurately identified parent-offspring combinations in the reference dataset, revealing a 40% error rate in breeder-provided pedigrees.
  • The identified parent-offspring relationships were confirmed by official microsatellite-based tests.

Conclusions:

  • The developed procedure effectively identifies highly accurate, low-density SNP panels for parentage assessment in goats, overcoming challenges related to genome assembly.
  • The findings indicate a significant rate of pedigree errors in goat breeding information, highlighting the need for molecular verification.
  • This methodology shows promise for application in other species, particularly those with unreliable marker positioning, for efficient and accurate parentage determination.