Zhang, Feifei, Wang, Yulan, Xu, Min, Wei, Lili, Zhong, Qiwang
Published: February 12, 2018
Genet. Mol. Res. 17(1): gmr16039880
DOI: https://doi.org/10.4238/gmr16039880
Cite this Article:
F. Zhang, Y. Wang, M. Xu, L. Wei, Q. Zhong (2018). Development and characterization of twenty-eight polymorphic microsatellite for rice field eel (Monopterus albus) using RAD tag sequencing. Genet. Mol. Res. 17(1): gmr16039880. https://doi.org/10.4238/gmr16039880
About the Authors
Zhang, Feifei, Wang, Yulan, Xu, Min, Wei, Lili, Zhong, Qiwang
Corresponding Author
Qiwang Zhong and Lili Wei
Email: zhongqw2000@163.com; hbliliwei@163.com
ABSTRACT
Monopterus albus is a special economic aquatic animal in China. Most of cultured M. albus are wild species captured from different areas, and this makes the wild resources of M. albus are under great threat. Microsatellite markers can help us understand the genetic resources of M. albus in different areas. In this study, using RAD-seq (restriction site associated DNA sequencing) protocol, a total of 9,897 microsatellites were identified in the genome with average frequency of 195 microsatellites per megabase of genomic sequences. Among these SSRs, the dinucleotide repeat motif was the most abundant type representing 61.77 % of the total microsatellite loci, followed by pentanucleotides (13.91 %), trinucleotides (12.08 %), tetranucleotides (9.30 %) and hexanucleotides (2.94 %). A total of 100 SSR primers were designed for PCR ampliï¬cation. The polymorphism analysis showed that 28 primer pairs could successfully amplify the polymorphic fragments and the number of alleles per polymorphic locus ranged from 2 to 13, with an average of 5.70 alleles/locus. The values of observed and expected heterozygosity’s ranged from 0.0333 to 0.8000 and 0.0333 to 0.8887, respectively. This microsatellite locus will be useful to understand the structure, genetic diversity, and genetic difference of this species.
Key words: RAD-seq, Monopterus albus, Microsatellite, Polymorphic marker.