Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing

Yujing Liu1, 3, Yu Guo2, Deke Xing1, and Chunlin Long3*
The petiole of Colocasia gigantea (Blume) Schott is an important agricultural and biological organ, which contains high dietary fiber, pyridoxine, and nicotinamide. However, available genomic resources of C. gigantea are scarce, and this restricts further genetic diversity research, linkage map construction, and marker-assisted selection in C. gigantea. A large-scale genomic DNA study of C. gigantea was conducted using the 454 sequencing technology to develop simple sequence repeats (SSRs). We identified 31 069 putative genomic C. gigantea SSRs, and 100 primers were randomly selected to validate their usefulness in 10 C. gigantea samples. The specificity of six primers yielded amplification products with expected sizes and exhibited polymorphism. The number of alleles per locus ranged from 3 to 7 alleles and the polymorphic information content (PIC) ranged from 0.561 to 0.756. The newly developed SSRs in this study should be useful tools for assessing genetic diversity, understanding population structure, and conserving and using C. gigantea effectively.
Keywords: Microsatellite markers, 454 sequencing.
1Jiangsu University, College of Agricultural Equipment and Engineering, Zhenjiang 212013, PR China.
2BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
3Minzu University of China, College of Life and Environmental Sciences, Beijing 100081, China.
*Corresponding author (long@mail.kib.ac.cn).