Abstract
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 HO, HE, 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.
Highlights
Golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered primate endemic to China
By genome-wide screening short tandem repeats (STRs) in golden snub-nosed monkey and comparing it with 12 resequencing genomes, we developed a standardized STR marker system based on 14 novel loci
By genome-wide screening for STRs in reference genomic data and comparing it with the 12 resequencing genomes in golden snub-nosed monkey, a total of 14 novel polymorphic tetranucleotide marker were proved to be reliable and valid for non-invasion samples to establish a standardized marker system
Summary
Golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered primate endemic to China. 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 conservation strategies of golden snub-nosed monkeys mainly include the protection of the wild population and the protection of the captive population They are both limited by the lack of a standardized genetic marker. The lack of standardized genetic markers makes it impossible to compare the genetic diversity within the same population of different periods In this case, the two studies on the Shennongjia population seem to indicate that the genetic diversity of this population was the lowest among all golden snub-nosed monkey populations, but it was hard to say whether the diversity had increased or decreased after decades of conservation work. There is still a lack of STR markers that can be widely applied to non-invasive samples
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