Genome-wide screening of microsatellites in golden snub-nosed monkey (Rhinopithecus roxellana), for the development of a standardized genetic marker system

Golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered primate endemic to China. The lack of standardized genetic markers limits its conservation works. In the present study, a total of 1,400,552 perfect STRs was identified in the reference genome of R. roxellana. By comparing it with the 12 resequencing genomes of four geographical populations, a total of 1,927 loci were identified as perfect tetranucleotides and shared among populations. We randomly selected 74 loci to design primer pairs. By using a total of 64 samples from the Chengdu Zoo captive population and the Pingwu wild population, a set of 14 novel STR loci were identified with good polymorphism, strong stability, high repeatability, low genotyping error rate that were suitable for non-invasive samples. These were used to establish a standardized marker system for golden snub-nosed monkeys. The genetic diversity analysis showed the average H(O), H(E,) and PIC was 0.477, 0.549, and 0.485, respectively, in the Chengdu Zoo population; and 0.516, 0.473, and 0.406, respectively, in Pingwu wild population. Moreover, an individual identification method was established, which could effectively distinguish individuals with seven markers. The paternity tests were conducted on seven offspring with known mothers from two populations, and their fathers were determined with high confidence. A genotyping database for the captive population in the Chengdu Zoo (n = 25) and wild population in Pingwu country (n = 8) was acquired by using this marker system.