Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey ( Rhinopith
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METHODS AND RESOURCES ARTICLE
Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey (Rhinopithecus roxellana) Chen Ling1 · Wu Lixia1 · Hou Rong1 · Shen Fujun1 · Zhang Wenping1 · Tang Yao2 · Yuan Yaohua3 · Zhao Bo4 · Zhang Liang1 Received: 13 November 2019 / Accepted: 30 March 2020 © The Author(s) 2020
Abstract Microsatellite markers are popular for assigning parentage, but single-nucleotide polymorphisms (SNPs) have only been applied in this area recently. To evaluate these two markers which have been previously studied in golden snub-nosed monkeys, we genotyped 12 individuals using 37 microsatellite loci and 37 SNP markers. The data showed that 32 of 37 microsatellite loci were polymorphic, and most microsatellite loci were high informative (mean PIC = 0.599). Meanwhile, 24 of 37 SNP markers were polymorphic and most were low informative (mean PIC = 0.244). For microsatellites, the combined exclusion probability with one-parent-unknown/known (CE-1P/CE-2P) nearly reached 1, while for the SNP markers, CE-2P only reached 0.9582. Under the condition of one parent known/unknown, the CE-2P and CE-1P could meet the international human parental standard (0.9973) by using five or nine microsatellite loci respectively. For SNP markers, we doubled the loci (n = 48) and simulated parentage testing, and the data showed that the CE-2P was 0.998 while the CE-1P was still low. This result indicated that the SNP loci which we used here had low polymorphism and that more loci need to be developed in the future. In addition, we corrected one case of failed identification by excluding siblings and reducing the range of candidate paternities. Keywords Rhinopithecus roxellana · microsatellite · SNP · parentage testing
Introduction The golden snub-nosed monkey is an endemic endangered species in China with a current wild population of ~ 22,000 individuals. According to data from the 2017 International Studbook of Golden Monkey (Chinese Association of Zoological Gardens), at the end of 2017, there were 488 individuals in captivity in 46 institutes around the world. Genetic management is essential for the conservation of both the exsitu and in-situ populations of endangered wildlife. Although
* Zhang Liang [email protected] 1
Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu 610057, Sichuan, China
2
Fuzhou Zoo, Fuzhou 350000, Fujian, China
3
Shanghai Zoo, Shanghai 200336, China
4
Chengdu Zoo, Sichuan 610081, China
much research has been done on the population structure and population dynamics of this species, parentage testing has not developed well. In captivity, revising the pedigree by parentage testing can help to reduce problems caused by inbreeding such as low viability, low fertility, and high mortality. Microsatellite markers have been used in the animal husbandry industry, initially for horses, since the 1990s because of their high rate of pol
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