Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai)

Qi Li; Jing Shu; Cui Zhao; Shikai Liu; Lingfeng Kong; Xiaodong Zheng

doi:10.1007/s00343-010-9233-9

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Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai)

Updated：2023-05-16

- Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai)
- Journal of Oceanology and Limnology Vol. 28, Issue 1, Pages: 46-54(2010)
- Affiliations：
  
  Fisheries College Ocean University of China
- Author bio：
- Funds：
- DOI：10.1007/s00343-010-9233-9
  CLC：
- Online First：27 January 2010，
  
  Published：2010
- Accepted：
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Li, Q., Shu, J., Zhao, C. et al. Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai)., Chin. J. Ocean. Limnol. 28, 46–54 (2010). https://doi.org/10.1007/s00343-010-9233-9
DOI：

Li, Q., Shu, J., Zhao, C. et al. Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai)., Chin. J. Ocean. Limnol. 28, 46–54 (2010). https://doi.org/10.1007/s00343-010-9233-9 DOI：

摘要

Abstract

Simple sequence repeat (SSR) markers were developed from the expressed sequence tags (ESTs) of Pacific abalone (Haliotis discus hannai). Repeat motifs were found in 4.95% of the ESTs at a frequency of one repeat every 10.04 kb of EST sequences

after redundancy elimination. Seventeen polymorphic EST-SSRs were developed. The number of alleles per locus varied from 2–17

with an average of 6.8 alleles per locus. The expected and observed heterozygosities ranged from 0.159 to 0.928 and from 0.132 to 0.922

respectively. Twelve of the 17 loci (70.6%) were successfully amplified in H. diversicolor. Seventeen loci segregated in three families

with three showing the presence of null alleles (17.6%). The adequate level of variability and low frequency of null alleles observed in H. discus hannai

together with the high rate of transportability across Haliotis species

make this set of EST-SSR markers an important tool for comparative mapping

marker-assisted selection

and evolutionary studies

not only in the Pacific abalone

but also in related species.

关键词

Keywords

references

An H S, Han S J. 2006. Isolation and characterization of microsatellite DNA markers in the Pacific abalone, Haliotis discus hannai. Mol. Ecol. Notes, 6: 11–13.

Ardren W R, Borer S, Thrower F, Joyce J E, Kapuscinski A R. 1999. Inheritance of 12 microsatellite loci in Oncorhynchus mykiss. J. Hered., 90: 529–536.

Arnold C, Rossetto M, McNally J, Henry R J. 2002. The application of SSRs characterized for grape (Vitis vinifera) to conservation studies in Vitaceae. Am. J. Bot., 89: 22–28.

Callen D F, Thompson A D, Shen Y, Phillips H A, Richards R I, Mulley J C, Sutherland G R. 1993. Incidence and origin of “null” alleles in the (AC)n microsatellite markers. Am. J. Hum. Genet., 52: 922–927.

Cho Y G, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch S R, Park W D, Ayres N, Cartinhour S. 2000. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet., 100: 713–722.

de Villena, F P M, Sapienza C. 2001. Nonrandom segregation during meiosis: the unfairness of females. Mamm. Genome, 12: 331–339.

Dieringer D, Schlotterer C. 2003. MICROSATELLITE ANALYSER (MSA): a platform independent analysis tool for large microsatellite data sets. Mol. Ecol. Notes, 3: 167–169.

Ellis J R, Burke J M. 2007. EST-SSRs as a resource for population genetic analyses. Heredity, 99: 125–132.

Evans B, Conod N, Elliott N G. 2001. Evaluation of microsatellite primer conservation in abalone. J. Shellfish Res., 20: 1 065–1 070.

Gupta P K, Rustgi S, Sharma S, Singh R, Kumar N, Balyan H S. 2003. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol. Genet. Genomics, 270: 315–323.

Hurst L D, Atlan A, Bengtsson B O. 1996. Genetic conflicts. Q. Rev. Biol., 71: 317–364.

International Human Genome Sequencing Consortium (IHGSC). 2001. Initial sequencing and analysis of the human genome. Nature, 409: 860–920.

Kijima A, Ikeda M, Fujio Y. 1992. Genetic characteristics of the artificial seed populations of abalone. Fish. Genet. Breed. Sci., 18: 53–63. (in Japanese)

Li Q, Park C, Kijima A. 2002. Isolation and characteristics of microsatellite DNA markers in the Pacific abalone, Haliotis discus hannai. J. Shellfish Res., 21: 811–815.

Li Q, Park C, Kijima A. 2003a. Allelic transmission of microsatellites and application to kinship analysis in newly hatched Pacific abalone larvae. Fish. Sci., 69: 883–889.

Li Q, Park C, Kobayashi T, Kijima A. 2003b. Inheritance of microsatellite DNA markers in the Pacific abalone Haliotis discus hannai. Mar. Biotechnol., 5: 331–338.

Li Q, Park C, Endo T, Kijima A. 2004. Loss of genetic variation at microsatellite loci in hatchery strains of the Pacific abalone (Haliotis discus hannai). Aquaculture, 235: 207–222.

Maneeruttanarungroj C, Pongsomboon S, Wuthisuthimethavee S, Klinbunga S, Wilson K J, Swan J, Li Y, Whan V, Chu K H, Li C P, Tong J, Glenn K, Rothschild M, Jerry D, Tassanakajon A. 2006. Development of polymorphic expressed sequence tag-derived microsatellites for the extension of the genetic linkage map of the black tiger shrimp (Penaeus monodon). Anim. Genet., 37: 363–368.

Ng S H S, Chang A, Brown G D, Koop B F, Davidson W S. 2005. Type I microsatellite markers from Atlantic salmon (Salmo salar) expressed sequence tags. Mol. Ecol. Notes, 5: 762–766.

Perez F, Ortiz J, Zhinaula M, Gonzabay, Calderon J, Volckaert F A. 2005. Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Mar. Biotechnol., 7: 554–569.

Primmer C R, Møller A P, Ellegren H. 1995. Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallow Hirundo rustica. Mol. Ecol., 4: 493–498.

Sekino M, Kobayashi T, Hara M. 2006. Segregation and linkage analysis of 75 novel microsatellite DNA markers in pair crosses of Japanese abalone (Haliotis discus hannai) using the 5′-tailed primer method. Mar. Biotechnol., 8: 453–466.

Serapion J, Kucuktas H, Feng J, Liu Z. 2004. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar. Biotechnol., 6: 364–377.

Squirrell J, Hollingsworth P M, Woodhead M, Russell J, Lowe A J, Gibby M, Powell W. 2003. How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol., 12: 1 339–1 348.

Varshney R K, Grane A, Sorrells M E. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol., 23: 48–54.

Vigouroux Y, McMullen M, Hittinger C T, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J. 2002. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc. Natl. Acad. Sci. USA, 99: 9 650–9 655.

Wang H, Li F, Xiang J. 2005. Polymorphic EST-SSR markers and their mode Fenneropenaeus chinensis. Aquaculture, 249: 107–114.

Wang Y, Guo X. 2007. Development and characterization of EST-SSR markers in the eastern oyster Crassostrea virginica. Mar. Biotechnol., 9: 12–23.

Yu H, Li Q. 2008. Exploiting EST databases for the development and characterization of EST-SSRs in the Pacific oyster (Crassostrea gigas). J. Hered., 99: 208–214.

Zane L, Bargelloni L, Patarnello T. 2002. Strategies for microsatellites isolation: a review. Mol. Ecol., 11: 1–16.

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