Development and characterization of 33 SNP markers for the red-crowned crane (Grus japonensis) using a genotyping-by-sequencing approach

  • Nan Xu
  • Yining Chen
  • Jiaming Zhang
  • Qingzheng Zhang
  • Jing Yang
  • Jingjing Li
  • Hongyi LiuEmail author
Technical Note


The red-crowned crane (Grus japonensis) is an endangered wading bird distributed in northeast Asia. The population of G. japonensis is continuing to decline owing to the loss and degradation of habitats. In order to protect G. japonensis, we developed 33 single nucleotide polymorphism (SNP) markers for this species using a genotyping-by-sequencing approach. The minor allele frequency ranged from 0.033 to 0.483, the observed heterozygosity ranged from 0.067 to 0.833, the expected heterozygosity ranged from 0.066 to 0.508, and the polymorphism information content ranged from 0.062 to 0.375. Among these SNPs, two loci showed deviations from the Hardy–Weinberg equilibrium (P < 0.05). The novel polymorphic SNPs can lay the foundation for future studies on evolution and conservation genetics of G. japonensis.


Grus japonensis SNP marker Genotyping-by-sequencing Conservation genetics 



This study was supported by the National Natural Science Foundation of China (31800453), the Natural Science Foundation of Jiangsu Province (BK20160927), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).


  1. Cao MC, Xu HG, Le ZF, Zhu MC, Cao Y (2015) A multi-scale approach to investigating the red-crowned crane-habitat relationship in the Yellow River Delta Nature Reserve, China: implications for conservation. PLoS ONE 10:e0129833CrossRefGoogle Scholar
  2. IUCN (2019) The IUCN red list of threatened species. Version 2019-2. Accessed 02 Nov 2019
  3. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106CrossRefGoogle Scholar
  4. Li N, Wang Z, Xia L, Yan F, Xu LQ, Qiao YJ, Li XH, An SQ, Fang SB (2019) Effects of long-term coastal reclamation on suitable habitat and wintering population size of the endangered Red-crowned Crane, Grus japonensis. Hydrobiologia 827:21–29CrossRefGoogle Scholar
  5. Luo JM, Ye YJ, Gao ZY, Wang WF (2014) Essential and nonessential elements in the red-crowned crane Grus japonensis of Zhalong Wetland, northeastern China. Toxicol Environ Chem 96:1096–1105CrossRefGoogle Scholar
  6. Na XD, Zhou HT, Zang SY, Wu CS, Li WL, Li M (2018) Maximum Entropy modeling for habitat suitability assessment of red-crowned crane. Ecol Indic 91:439–446CrossRefGoogle Scholar
  7. Rousset F (2008) Genepop’007: a complete re-implementation of the genepop software for windows and linux. Mol Ecol Resour 8:103–106CrossRefGoogle Scholar
  8. Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34:275–305CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina

Personalised recommendations