title: Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system.
abstract: BACKGROUND
  The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda.
  
  
  RESULTS
  By screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What's more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system.
  
  
  CONCLUSIONS
  The microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual identification method and the genetic diversity analysis method in this study provided adequate material for the future study of giant panda.
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P R China. huangjie66666@163.com.
authors.forename: Jie
authors.initials: J
authors.lastname: Huang
authors.affiliation: Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China. yuzhi5654@gmail.com.
authors.forename: Yu-Zhi
authors.initials: YZ
authors.lastname: Li
authors.affiliation: Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, P R China. adu220@126.com.
authors.forename: Lian-Ming
authors.initials: LM
authors.lastname: Du
authors.affiliation: China Research and Conservation Centre for the Giant Panda, Wenchuan, 623006, China. 353770595@qq.com.
authors.forename: Bo
authors.initials: B
authors.lastname: Yang
authors.affiliation: Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China. shenfj001@sina.com.
authors.forename: Fu-Jun
authors.initials: FJ
authors.lastname: Shen
authors.affiliation: China Research and Conservation Centre for the Giant Panda, Wenchuan, 623006, China. wolong_zhm@126.com.
authors.forename: He-Min
authors.initials: HM
authors.lastname: Zhang
authors.affiliation: Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China. zhangzhh@mail.sc.cninfo.net.
authors.forename: Zhi-He
authors.initials: ZH
authors.lastname: Zhang
authors.affiliation: Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, P R China. zhangxy317@126.com.
authors.forename: Xiu-Yue
authors.initials: XY
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P R China. bsyue@scu.edu.cn.
authors.forename: Bi-Song
authors.initials: BS
authors.lastname: Yue
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D014644:Genetic Variation; D016678:Genome; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D001503:Ursidae / Q000235:genetics*