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

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.