Data from: Applying SNP-derived molecular coancestry estimates to captive breeding programs

Captive breeding programs for wildlife species typically rely on pedigrees
to inform genetic management. Although pedigree-based breeding strategies
are quite effective at retaining long-term genetic variation, management
of zoo-based breeding programs continues to be hampered when pedigrees are
poorly known. The objective of this study was to evaluate two options for
generating single nucleotide polymorphism (SNP) data to resolve unknown
relationships within captive breeding programs. We generated SNP data for
a zoo-based population of addax (Addax nasomasculatus) using both the
Illumina BovineHD BeadChip and double digest restriction site-associated
DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele
sharing (AS) between pairs of individuals exhibited low variances. Average
AS variances were highest when using 50 loci (SNPchipall = 0.00159;
ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when
sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling
≥500 loci. Furthermore, the correlation between the SNPchipall and
ddRADall AS datasets was 0.88 (95%CI = 0.84 – 0.91) when subsampling 500
loci. Collectively, our results indicated that both SNP genotyping methods
produced sufficient data for accurately estimating relationships, even
within an extremely bottlenecked population. Our results also suggested
that analytic assumptions historically integrated into the addax pedigree
are not adversely impacting long-term pedigree-based management; kinships
calculated from the analytic pedigree were significantly correlated (p
>>0.001) with AS estimates. Overall, our conclusions are
intended to serve as both a proof of concept and a model for applying
molecular data to the genetic management of captive breeding programs.