Cite this paper:
SONG Chenyu, FENG Ziyi, LI Chunhou, SUN Zhicheng, GAO Tianxiang, SONG Na, LIU Lu. Profile and development of microsatellite primers for Acanthogobius ommaturus based on high-throughput sequencing technology[J]. Journal of Oceanology and Limnology, 2020, 38(6): 1880-1890

Profile and development of microsatellite primers for Acanthogobius ommaturus based on high-throughput sequencing technology

SONG Chenyu1, FENG Ziyi1, LI Chunhou2, SUN Zhicheng1, GAO Tianxiang3, SONG Na1, LIU Lu1
1 Fisheries College, Ocean University of China, Qingdao 266003, China;
2 South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China;
3 National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
Acanthogobius ommaturus, a fish species of the Family Gobiidae, is a marine commercial fish perched on the bottom of seawater. In this study, Illumina high-throughput sequencing technology was applied to obtain the candidate microsatellite markers of A. ommaturus. A total of 4 746 microsatellite-rich fragments were found, of which 4 542 microsatellites are with primer fragments, containing 971 dinucleotide sequences, 2 643 trinucleotide sequences, 569 tetranucleotide sequences, 406 pentanucleotide sequences, and 212 hexanucleotide sequences. Based on the results of high-throughput sequencing, a total of 141 pairs of the microsatellite primers were designed and screened. And then 24 polymorphic primers were finally obtained by polyacrylamide gel electrophoresis. In total, 271 alleles were detected in the 24 pairs of primers. The number of alleles for different primers ranged from 5 to 19. The average number of effective alleles (Na) was 11.292; the average observed heterozygosity (Ho) of the 24 pairs of primers was 0.665, the average expected heterozygosity (He) was 0.880, and the average polymorphic information content was 0.846. All sites were highly polymorphic (PIC>0.50).
Key words:    microsatellite|Acanthogobius ommaturus|high-throughput sequencing|polymorphic sites   
Received: 2019-06-04   Revised: 2019-09-23
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