Dataset Information

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

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.

SUBMITTER: Cai Y

PROVIDER: S-EPMC7326997 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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

Cai YanSen Y Yu HaoYang H Liu Hua H Jiang Cong C Sun Ling L Niu LiLi L Liu XuanZhen X Li DaYong D Li Jing J

Scientific reports 20200630 1

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 prim ...[more]

PMID: 32606319

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Project description:BACKGROUND:Small, isolated populations often experience loss of genetic variation due to random genetic drift. Unlike neutral or nearly neutral markers (such as mitochondrial genes or microsatellites), major histocompatibility complex (MHC) genes in these populations may retain high levels of polymorphism due to balancing selection. The relative roles of balancing selection and genetic drift in either small isolated or bottlenecked populations remain controversial. In this study, we examined the mechanisms maintaining polymorphisms of MHC genes in small isolated populations of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) by comparing genetic variation found in MHC and microsatellite loci. There are few studies of this kind conducted on highly endangered primate species. RESULTS:Two MHC genes were sequenced and sixteen microsatellite loci were genotyped from samples representing three isolated populations. We isolated nine DQA1 alleles and sixteen DQB1 alleles and validated expression of the alleles. Lowest genetic variation for both MHC and microsatellites was found in the Shennongjia (SNJ) population. Historical balancing selection was revealed at both the DQA1 and DQB1 loci, as revealed by excess non-synonymous substitutions at antigen binding sites (ABS) and maximum-likelihood-based random-site models. Patterns of microsatellite variation revealed population structure. FST outlier analysis showed that population differentiation at the two MHC loci was similar to the microsatellite loci. CONCLUSIONS:MHC genes and microsatellite loci showed the same allelic richness pattern with the lowest genetic variation occurring in SNJ, suggesting that genetic drift played a prominent role in these isolated populations. As MHC genes are subject to selective pressures, the maintenance of genetic variation is of particular interest in small, long-isolated populations. The results of this study may contribute to captive breeding and translocation programs for endangered species.

Dataset Information

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

Publications

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

Similar Datasets

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