Abstract
Fifty-one novel EST-derived microsatellite markers were developed from 23,803 expressed sequence tags in the Pacific oyster, Crassostrea gigas. Polymorphisms of these loci were evaluated in a population of 48 individuals. The allele number ranges from 3 to 11, averaging 5.9 alleles per locus. The observed and expected heterozygosity values range from 0.023 to 0.875 (averaging 0.412) and 0.239 to 0.978 (averaging 0.681), respectively. Twenty-one of the 51 markers accord with Hardy–Weinberg equilibrium (HWE), and the rest show significant departure from HWE after Bonferroni correction, apparently due to heterozygote deficiency, suggesting likely occurrence of null alleles at loci and/or subpopulation of the sample. Cross-amplification was examined in C. hongkongensis and C. arikensis and the results show that 23 and 18 loci, respectively, have a reasonable polymorphism in the two species. These EST-SSR markers will be useful in studies of population genetics, linkage mapping and other aspects for this species.
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References
Bassam BJ, Caetano-Anollés G, Gresshoff PM (1991) Fast and sensitive silver 136 staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83
Bouck A, Vision T (2007) The molecular ecologist’s guide to expressed sequence tags. Mol Ecol 16:907–924
Food and agriculture organization (FAO) (2008) Fisheries and Aquaculture Department, Global Aquaculture production. ftp://ftp.fao.org/fi/STAT/summary/a-6.pdf
Hedgecock D, Li G, Hubert S, Bucklin K, Ribes V (2004) Widespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster, Crassostrea gigas. J Shellfish Res 23:379–385
Huvet A, Boudry P, Ohresser M (2000) Variable microsatellites in the Pacific oyster Crassostrea gigas and other cupped oyster species. Anim Genet 31:71–72
Li Q, Wan JM (2005) SSRHunter: development of a local searching software for SSR sites. Hereditas 27:808–810
Li G, Hubert S, Bucklin K, Ribes V, Hedgecock D (2003) Characterization of 79 microsatellite DNA markers in the Pacific oyster Crassostrea gigas. Mol Ecol Notes 3:228–232
Liu ZJ, Cordes JF (2004) DNA marker technologies and their applications in aquaculture genetics. Aquculture 238:1–37
McGoldrick D, Hedgecock D, English LJ, Baoprasertkul P, Ward RD (2000) The transmission of microsatellite alleles in Australian and north American stocks of the Pacific oyster (Crassostrea gigas): selection and null alleles. J Shellfish Res 19:779–788
Pemberton JM, Slate J, Bancroft DR, Barrett JA (1995) Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies. Mol Ecol 4:249–252
Qiu X, Li X, Liu S, Wang X, Meng X (2008) Eleven polymorphic simple sequence repeat markers from expressed sequence tags of Pacific oyster Crassostrea gigas EST database. Conserv Genet doi:10.1007/s10592-008-9724-9
Reece KS, Ribeiro WL, Gaffney PM, Carnegie RB, Allen SK (2004) Microsatellite marker development and analysis in the eastern oyster (Crassostrea virginica): confirmation of null alleles and non-Mendelian segregation ratios. J Hered 95:346–352
Roberts S, Romano C, Gerlach G (2005) Characterization of EST derived SSRs from the bay scallop, Argopecten irradians. Mol Eco Notes 5:567–568
Rousset F (2008) GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Res 8:103–106
Serapion J, Kucuktas H, Feng JN, Liu ZJ (2004) Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar Biotechnol 6:64–377
Wang Y, Ren R, Yu Z (2008) Bioinformatic mining of EST-SSR loci in the Pacific oyster, Crassostrea gigas. Anim Genet 39:287–289
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
Acknowledgments
This work was financially supported by a 863 Program from Ministry of Sciences and Technology of China (No. 2006AA10A409), a Natural Science Foundation of China (no. 30570242) and a Science Foundation of Guangdong Province (8251030101000001). The authors thank Xiaocui He and Rui Ren for their technical assistance and sample collection.
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Yu, Z., Wang, Y. & Fu, D. Development of Fifty-one novel EST-SSR loci in the Pacific oyster, Crassostrea gigas by data mining from the public EST database. Conservation Genet Resour 2 (Suppl 1), 13–18 (2010). https://doi.org/10.1007/s12686-009-9127-3
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DOI: https://doi.org/10.1007/s12686-009-9127-3