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An R package for SNP marker-based parent-offspring tests.

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This study introduces an R package for parent-offspring testing using SNP markers to ensure genetic integrity in crop research. The tool helps identify potential errors in sample handling and genotyping processes for accurate genetic studies.

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Area of Science:

  • Plant genetics
  • Bioinformatics
  • Genomic analysis

Background:

  • Advancements in genotyping technologies enable whole genome and high-density SNP marker usage in crops.
  • Ensuring the integrity of genotyped individuals is crucial before downstream SNP data analysis.

Purpose of the Study:

  • To develop an R package for parent-offspring testing using SNP markers.
  • To facilitate the verification of individual genotypes for genetic studies.

Main Methods:

  • Developed an R package named 'ParentOffspring'.
  • Utilizes monomorphic SNP loci to calculate similarity between offspring and parents.
  • Applies a threshold based on similarity to include individuals in further analysis.

Main Results:

  • The 'ParentOffspring' R package was developed and tested.
  • Demonstrated application using an F5-derived soybean population genotyped with 1,536 SNPs.
  • The package effectively calculates parent-offspring similarity.

Conclusions:

  • The 'ParentOffspring' R package aids in detecting variants and potential errors in sample handling and genotyping.
  • Applicable to any crop genotyped with a fixed set of SNP markers.
  • Enhances the reliability of genetic studies using SNP data.