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Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

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Integrative Zoology 2018年第5期13卷 553-568页

作者： Xian HOU Pengwei XU Zhenzhen LIN josephine d’urban-jackson AndrewdIXON Batbayar BOLd Jiliang XU Xiangjiang ZHAN Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijingChina School of Nature Conservation Beijing Forestry UniversityBeijingChina BGI-Tech BGI-ShenzhenShenzhenChina Milner Centre for Evolution Department of Biology and BiochemistryUniversity of BathBathUK Emirates Falconers’Club Abu DhabiUnited Arab Emirates Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research BeijingChina Wildlife Science and Conservation Center UlaanbaatarMongolia Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingChina

Accurate individual identification is required to estimate survival rates in avian *** endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a source of dNA for microsatellite markers,are preferred because of less disturbance,easy sample preparation and high *** the availability of many avian genomes,a few pipelines isolating genome-wide microsatellites have been published,but it is still a challenge to isolate microsatellites from the reference genome ***,we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference *** have identified over 95000 microsatellite loci and established a system comprising 10 highly polymorphic markers(PIC value:0.49–0.93,mean:0.79)for an endangered species,saker falcon(Falco cherrug).These markers(except 1)were successfully amplified in 126 molted feathers,exhibiting high amplification success rates(83.9–99.7%),high quality index(0.90–0.97)and low allelic dropout rates(1–9.5%).To further assess the efficiency of this marker system in a population study,we identified individual sakers using these molted feathers(adult)and 146 plucked feathers(offspring).The use of parent and offspring samples enabled us to infer the genotype of missing samples(N=28),and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in *** study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.

关键词： breeding turnover Falco cherrug feather microsatellite isolation parentage analysis reference genome saker falcon

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