Genetic characterization of a captive marmoset (Callithrix jacchus) colony using genotype-by-sequencing

Abstract

The marmoset is a fundamental nonhuman primate model for the study of aging, neurobiology, and many other topics. Genetic management of captive marmoset colonies is complicated by frequent chimerism in the blood and other tissues, a lack of tools to enable cost-effective, genome-wide interrogation of variation, and historic mergers and migrations of animals between colonies. We implemented genotype-by-sequencing (GBS) of hair follicle derived DNA (a minimally chimeric DNA source) of 82 marmosets housed at the Southwest National Primate Research Center (SNPRC). Our primary goals were the genetic characterization of our marmoset population for pedigree verification and colony management and to inform the scientific community of the functional genetic makeup of this valuable resource. We used the GBS data to reconstruct the genetic legacy of recent mergers between colonies, to identify genetically related animals whose relationships were previously unknown due to incomplete pedigree information, and to show that animals in the SNPRC colony appear to exhibit low levels of inbreeding. Of the >99,000 single-nucleotide variants (SNVs) that we characterized, >9800 are located within gene regions known to harbor pathogenic variants of clinical significance in humans. Overall, we show the combination of low-resolution (sparse) genotyping using hair follicle DNA is a powerful strategy for the genetic management of captive marmoset colonies and for identifying potential SNVs for the development of biomedical research models.

Keywords: Callithrix jacchus; biomedical research; captive nonhuman primates; genetic ancestry; hair follicle DNA; pedigree.

Figure 1.. Admixture in the SNPRC colony.

(A-D) High quality SNVs from GBS of 82 marmosets were integrated with whole genome sequencing from WNPRC (columns 1–2, n=2), SNPRC (columns 3–7, n=5) and NEPRC (columns 8–9, n=2) to infer recent ancestry of pedigreed animals in the USA. Each bar shows the inferred ancestry proportions of each animal specifying 2–5 ancestral populations (K=2–5, with K=3 the best cross-validation score). In Fig 1E, ancestry was independently inferred in a supervised analysis using the population labels shown below the first 9 bars and corresponding to each NPRC. Each analysis showed a subdivided population, where most animals have a major ancestry component from a single population. Fig 1F shows the known pedigree with each animal included in the ADMIXTURE analysis shaded to represent the proportion of NEPRC, SNPRC, and WNPRC ancestry. Dashed lines show where an individual is placed multiple times in the figure. Given the complex nature of large pedigrees this is an artifact of plotting data.

Figure 2.. Inference of relatedness from GBS data.

(A) A comparison of expected (x axis) and inferred kinship from GBS (π̂, y axis). The grey dashed line shows the expectation from a perfect correlation between approaches, the black dashed line shows the observed relationship between approaches. Highlighted in the red dots are comparisons between 12 individuals which are discordant between approaches. (B) Pedigree of 11 of the 12 individuals uncovered using GBS. (C) A heatmap showing the pedigree (upper triangle) and GBS (lower triangle) based estimates of relatedness. Darker colors denote a higher degree of relatedness between individuals. Highlighted by a box in the top right corner are the individuals shown in red in Fig 2A. The large difference in estimates of relatedness between the GBS and pedigree based estimates is driven by incomplete pedigree information from a single individual subject to migration between colonies. (D) Inferred ancestry components for each individual, darker colors represent the proportion of ancestry from Fig 1E.