APIS: an updated parentage assignment software managing triploids induced from diploid parents

Area of Science:

• Aquaculture
• Genetics
• Bioinformatics

Background:

• Sterile triploids offer production advantages in aquaculture but cannot reproduce.
• Accurate DNA parentage assignment is essential for breeding value estimation in triploids.
• Existing software lacks the capability to assign parentage for triploid individuals.

Purpose of the Study:

• To update the R package APIS for triploid parentage assignment.
• To develop methods accounting for unique genetic contributions in triploid reproduction.
• To establish a reliable tool for genetic management in aquaculture.

Main Methods:

• Updated APIS package with new exclusion and likelihood tables for triploids.
• Accounted for double allelic contribution from the dam and meiotic recombination.
• Utilized single nucleotide polymorphism (SNP) markers and evaluated assignment power based on marker quality and quantity.

Main Results:

• 96-192 SNPs are sufficient for high parentage assignment rates in rainbow trout.
• Assignment power is influenced by marker quality (minor allele frequency, call rate).
• Likelihood approach is efficient for limited markers; exclusion excels with more markers, achieving high sensitivity and specificity.

Conclusions:

• The updated APIS package provides an efficient solution for assigning triploids to their diploid parents.
• This tool supports genetic improvement programs in aquaculture by enabling breeding value estimation.
• The findings offer practical guidelines for marker selection and data quality in parentage assignment studies.