Browse > Article
http://dx.doi.org/10.5352/JLS.2020.30.3.291

Development and Genetic Diversity Analysis of Microsatellite Markers Using Next-generation Sequencing in Seriola quinqueradiata  

Dong, Chun Mae (Biotechnology Research Division, National Institute of Fisheries Science)
Lee, Mi-Nan (Biotechnology Research Division, National Institute of Fisheries Science)
Kim, Eun-Mi (Biotechnology Research Division, National Institute of Fisheries Science)
Park, Jung Youn (Biotechnology Research Division, National Institute of Fisheries Science)
Kim, Gun-Do (Department of Microbiology, College of Natural Sciences, Pukyong National University)
Noh, Jae Koo (Biotechnology Research Division, National Institute of Fisheries Science)
Publication Information
Journal of Life Science / v.30, no.3, 2020 , pp. 291-297 More about this Journal
Abstract
This study was conducted to develop microsatellite markers in Seriola quinqueradiata using next-generation sequencing. A total of 28,873,374 reads were generated on an Illumina Hiseq2500 system, yielding 7,247,216,874 bp sequences. The de novo assembly resulted in 466,359 contigs. A total of 132 contigs (0.43%), including 60 microsatellite loci, were derived from 30,729 contigs longer than 518 bp. A total of 60 primer sets were designed from the 132 microsatellite loci. A total of 15 polymorphic nuclear microsatellite loci were chosen to evaluate population genetic parameters in the parents and offspring. The mean number of effective alleles was 18.5, ranging from 11 to 30. The observed heterozygosity (HO) and expected heterozygosity (HE) ranged between 0.431 and 0.972 with an average of 0.812 and from 0.782 to 0.949 with an average of 0.896, respectively. No significant linkage disequilibrium was observed after Bonferroni revision in any loci. The results show that the 15 polymorphic nuclear microsatellite markers can be used to study the population and conservation genetics of S. quinqueradiata in Korea. To ensure the success of artificial seedling production technology, genetic variations between the parent and offspring populations should be monitored, and inbreeding should be controlled.
Keywords
Artificial reproduction; genetic variability; microsatellite loci; next generation sequencing; Seriola quinqueradiata;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Li, Q., Park, C., Endo, T. and Kijima, A. 2004. Loss of genetic variation at microsatellite loci in hatchery strains of the Pacific abalone (Haliotis discus hannai). Aquaculture 235, 207-222.   DOI
2 Nakada, M. 1999. Yellowtail and related species culture. Encyclopedia of Aquaculture.
3 Norris, A. T., Bradley, D. G. and Cunningham, E. P. 2000. Parentage and relatedness determination in farmed Atlantic salmon (Salmo salar) using microsatellite markers. Aquaculture 182, 73-83.   DOI
4 Ohara, E., Nishimura, T., Sakamoto, T., Nagakura, Y., Mushiake, K. and Okamoto, N. 2003. Isolation and characterization of microsatellite loci from yellowtail Seriola quinqueradiata and cross-species amplification within the genus Seriola. Mol. Ecol. 3, 390-391.   DOI
5 Peakall, R. and Smouse, P. E. 2006. GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Mol. Ecol. 6, 288-295.   DOI
6 Perez-Enriquez, R., Takagi, M. and Taniguchi, N. 1999. Genetic change and pedigrees tracing of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement, based on microsatellite DNA markers. Aquaculture 173, 413-423.   DOI
7 Roche, S. and Skaletsky, H. 1998. Primer 3. Code available at http://www.genome.wi.mit.edu/genome-software/other/primer3.html.
8 Rousset, F. 2008. GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol. Ecol. Resour. 8, 103-106.   DOI
9 Rudnick, J. A. and Lacy, R. C. 2008. The impact of assumptions about founder relationships on the effectiveness of captive breeding strategies. Conserv. Gen. 9, 1439-1450.   DOI
10 Allendorf, F. W. and Ryman, N. 1987. Genetic management of hatchery stocks. In: Ryman, N. Utter, F.W. (Eds.), Population genetics and fishery management. University of Washington Press, Seattle, pp. 141-159.
11 Allendort, F. W., Luikart, G. and Aitken, S. N. 2013. Conservation and the Genetics of Populations. Wiley-Blackwell, Oxford, U.K.
12 Baek, S. H., Lee, J. W., Hong, K. N., Lee, S. W., Ahn, J. Y. and Lee, M. W. 2016. Identification and characterization of polymorphic microsatellite loci using next generation sequencing in Quercus variabilis. J. Kor. For. Soc. 105, 186-192.   DOI
13 Botstein, D., White, R. L., Skolnick, M. and Davis, R. W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314.
14 Sugaya, T., Ikeda, M. and Fujio, Y. 1999. Comparison for the genetic variabilities of natural and seed populations of Japanese flounder based on PCR-RFLP analysis of mtDNA D-loop. Fish Gen. Breed. Sci. 28, 65-73.
15 Chang, D. S., Yoo, J. T., Kim, B. Y., Lee, S. J., Kwon, D. H., Koo, J. H., Ahn, G. M. and Oh, I. Y. 2010. A characteristics on the forming of fishing ground and population ecological study of Yellow tail, Seriola-quinqueradiata, in the coastal waters off Gim-nyeong of Jeju Island, Korea. J. Kor. Soc. Fish. Tech. 46, 406-415.   DOI
16 DeWoody, J. A. and Avise, J. C. 2000. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J. Fish. Biol. 56, 461-473.   DOI
17 Evans, B., Bartlett, J., Sweijd, N., Cook, P. and Elliott, N. G. 2004. Loss of genetic variation at microsatellite loci in hatchery produced abalone in Australia (Haliotis rubra) and South Africa (Haliotis midae). Aquaculture 233, 109-127.   DOI
18 Sekino, M., Hara, M. and Taniguchi, N. 2002. Loss of microsatellite and mitochondrial DNA variation in hatchery strains of Japanese flounder Paralichthy olivaceus. Aquaculture 213, 101-122.   DOI
19 Spencer, C. C., Neigel, J. E. and Leberg, P. L. 2000. Experimental evaluation of the usefulness of microsatellite DNA fordetecting demographic bottlenecks. Mol. Ecol. 9, 1517-1528.   DOI
20 Weir, B. S. and Cockerham, C. C. 1984. Estimating F-sta tistics for the analysis of population structure. Evolution 38, 1358-1370.   DOI
21 Fujio, Y., Sasaki, N., Sasaki, M. and Koganezawa, A. 1985. Genetic aspect of natural and released population of plaice. Bull. Tohoku Reg. Fish. Res. Lab. 47, 51-57.
22 Yang, S. G., Kim, J. H., Kim, H. W., An, C. M., Ji, S. C., Jeong, M. H., Myeong, J. I., Lee, Y. D. and Kim, D. J. 2018. Biological characterization for the seeding production of Yellowtail Kingfish. Seriola lalandi. JFM. SE. 30, 1866-1875.
23 Yoshida, K., Takagi, M., Tanaka, M. and Taniguchil, N. 2000. Genetic variability and divergence of wild and artificially raised Japanese flounder Paralichthys olivaceus inferred from microsatellite DNA analysis. Fish Gen. Breed. Sci. 29, 93-102.
24 Zalapa, J. E., Cuevas, H., Zhu, H., Steffan, S., Senalik, D., Zeldin, E., McCown, B., Harbut, R. and Simon, P. 2012. Using nextgeneration sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am. J. Bot. 99, 193-208.   DOI
25 Excoffier, L., Laval, G. and Schneider, S. 2005. Arlequin (ver. 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47-50.
26 Frankham, R., Ballow, J. D. and Briscoe, D. A. 2004. A primer of conservation genetics. Cambridge University Press, Cambridge, U.K.
27 Hara, M. and Sekino, M. 2003. Efficient detection of parentage in a cultured Japanese flounder Paralichthy olivaceus using microsatellite DNA marker. Aquaculture 217, 107-114.   DOI
28 Gardner, M. G., Fitch, A. J., Bertozzi, T. and Lowe, A. J. 2011. Rise of the machines-recommendations for ecologists when using next generation sequencing for microsatellite development. Mol. Ecol. Resour. 11, 1093-1101.   DOI
29 Goudet, J. 1995. FSTAT (version 1.2): a computer program to calculate F-statistics. J. Hered. 86, 485-486.   DOI
30 Hara, N. 1990. An abundance index of yellow tail immigrating into the sea of Japan and its yearly variation. Nip. Sui. Gak. 56, 25-30.   DOI
31 Jeong, D. S., Kim, K. S. and Kim, K. K. 2006. Evaluation of effective breeders number (Ne) for stock enhancement in olive flounder Paralichthys olivaceus using microsatellite DNA markers. Aquaculture 19, 205-209.
32 Jeong, D. S., Gonzalez, E. B., Morishima, K. Arai, K. and Umino, T. 2007. Parentage assignment of stocked black sea bream, Acanthopagrus schlegeli in Hiroshima Bay using microsatellite DNA markers. Fish. Sci. 73, 823-830.   DOI
33 Kim, K. S., Noh, C. H., Sade, A. and Bang, I. C. 2015. Effectiveness of microsatellite markers for parentage analysis of giant grouper (Epinephelus lanceolatus). Kor. J. Ich. 27, 10-15.
34 Kang, J. H., Kim, Y. K., Park, J. Y., Noh, E. S., Jeong, J. E., Lee, Y. S. and Choi, T. J. 2013. Development of microsatellite markers for a hard-shelled mussel, Mytilus coruscus, and cross-species transfer. Gen. Mole. Res. 12, 4009-4017.   DOI
35 Kang, J. H., Kang, H. S., Noh, E. S., Park, J. Y. and An, C. M. 2014. Isolation and characterization of novel microsatellite markers for the northern mauxia shrimp, Acetes chinensis, using pyrosequencing. Mar. Genomics 18, 67-69.   DOI
36 Kalinowski, S. T., Taper, M. L. and Marshall, T. C. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16, 1099-1106.   DOI
37 Kim, E. M., Kang, H. S., Kang, J. H., Kim, D. G., An, C. M., Lee, H. W. and Park, J. Y. 2015. Genetic Relationships of Sandfish (Arctoscopus japonicas) from five different areas of Korea and Japan based on mitochondrial DNA and microsatellite analyses. J. Life Sci. 25, 1204-1213.   DOI
38 Kim, J. T., Rho, H. K. and Kim, S. H. 2002. Studies on the forming mechanism of the fishing ground of yellowtail, Seriola quinqueradiata, in the adjacent sea of Jeju Island, Bull. Kor. Soc. Fish. Tech. 38, 20-35.   DOI
39 Koh, H. W., Rani, S., Hwang, H. B. and Park, S. J. 2016. Microbial community structure analysis from Jeju marine sediment. Kor. J. Micro. 52, 375-379.   DOI
40 Lee, S. J. and Go, Y. B. 2006. Winter warming and long-term variation in catch of Yellowtail (Seriola quinqueradiata) in the South Sea, Korea. Kor. J. Ich. 18, 319-328.
41 Lee, S. K., Kim, Y. U., Myoung, J. G. and Kim, J. M. 2000. Dictionary of Korean fish names, pp. 222. Junginsa Pub. Co. Seoul.