apparent

apparent performs SNP-based parentage inference from genome-wide SNP datasets as an R package, enabling identification of parent-progeny relationships without prior pedigree, generational, or sex information.

Key Features:

• Novel Methodology: Compares theoretically expected progeny EP_ij, inferred at all homozygous loci for a putative parental pair, to potential offspring PO_k using the Gower Dissimilarity metric (GD) to assess genetic identity.
• Significance Testing: Evaluates the significance of each parental-pair–offspring triad by comparing GD_ij|k to the distribution of all GD_ij|k values within the population.
• Empirical Performance: Correctly identified parental pairs for 15 lines with known pedigrees within a test population of 77 Actinidia arguta accessions and outperformed five other commonly used parentage analysis tools in empirical tests.
• Inconclusive Triad Analysis (Dyad): Performs dyad analysis when one parent is absent, with an average accuracy of 73.3% without pedigree information and 100% accuracy when minimal generational data are provided.

Scientific Applications:

• Plant Breeding: Determines parentage within germplasm collections to inform breeding decisions and pedigree reconstruction.
• Conservation Strategies: Identifies progeny from natural populations without prior family-structure knowledge to support conservation of plant genetic resources.
• Genetic Resource Management: Assists management and utilization of ex situ collections where traditional pedigree information is lacking or incomplete.

Methodology:

Infer EP_ij at homozygous loci for each putative parental pair, compute Gower Dissimilarity (GD) between EP_ij and PO_k, assess triad significance by comparing GD_ij|k to the population distribution, and perform dyad analysis when one parent is absent.