Abstract
A number of Pacific oyster (Crassostrea gigas) with golden shell background color were obtained which show great potential to develop a niche market. To improve the selective breeding progress of true-breeding strains with complete golden oysters, research was conducted to identify genetic markers linked to the shell color locus. An F1-segregating population was obtained by crossing two oysters with golden shell and white shell. Genomic DNA from eight progenies with golden shell and eight progenies with white shell were equally pooled for amplified fragment length polymorphism (AFLP) screening. In bulked segregant analysis, six out of 225 selective primer pair combinations produced seven polymorphic fragments tightly linked to shell color across the segregating population. The seven AFLP markers were all derived from the golden dam and mapped onto a single linkage group flanking the shell color locus. In conversion of the AFLPs into single-locus PCR-based markers, a sequence-characterized amplified region (SCAR) marker, named SCARJ8-2, a single nucleotide polymorphism (SNP) marker, named SNPL2-4, and a simple sequence repeat (SSR) marker, named SSRO11-2, were obtained. These markers obtained in this study will be useful for marker-assisted selection of the Pacific oyster.
Similar content being viewed by others
References
Adamkewicz L, Castagna M (1988) Genetics of shell color and pattern in the bay scallop Argopecten irradians. J Hered 79:14–17
Alfnes F, Guttormsen AG, Steine G, Kolstad K (2006) Consumers' willingness to pay for the color of salmon: a choice experiment with real economic incentives. Am J Agric Econ 88:1050–1061
Araneda C, Neira R, Iturra P (2005) Identification of a dominant SCAR marker associated with colour traits in Coho salmon (Oncorhynchus kisutch). Aquaculture 247:67–73
Araneda C, Lam N, Díaz NF, Cortez S, Pérez C, Neira R, Iturra P (2009) Identification, development, and characterization of three molecular markers associated to spawning date in Coho salmon (Oncorhynchus kisutch). Aquaculture 296:21–26
Bradeen J, Simon P (1998) Conversion of an AFLP fragment linked to the carrot Y2 locus to a simple, codominant, PCR-based marker form. Theor Appl Genet 97:960–967
Brake J, Evans F, Langdon C (2004) Evidence for genetic control of pigmentation of shell and mantle edge in selected families of Pacific oysters, Crassostrea gigas. Aquaculture 229:89–98
Brugmans B, van der Hulst RG, Visser RG, Lindhout P, van Eck HJ (2003) A new and versatile method for the successful conversion of AFLP™ markers into simple single locus markers. Nucleic Acids Res 31:e55
Cho YG, Blair MW, Panaud O, McCouch SR (1996) Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained polyacrylamide gels. Genome 39:373–378
Cole TJ (1975) Inheritance of juvenile shell colour of the oyster drill Urosalpinx cinerea. Nature 257:794–795
FAO (Food and Agriculture Organization) (2014) Fishery and aquaculture statistics 2012. Food and Agriculture Organization of the United Nations, Rome
Felip A, Young WP, Wheeler PA, Thorgaard GH (2005) An AFLP-based approach for the identification of sex-linked markers in rainbow trout (Oncorhynchus mykiss). Aquaculture 247:35–43
Ge J, Li Q, Yu H, Kong L (2014) Identification and mapping of a SCAR marker linked to a locus involved in shell pigmentation of the Pacific oyster (Crassostrea gigas). Aquaculture 434:249–253
Ge J, Li Q, Yu H, Kong L (2015) Mendelian inheritance of golden shell color in the Pacific oyster Crassostrea gigas. Aquaculture 441:21–24
Guo X, Li Q, Wang QZ, Kong LF (2012) Genetic mapping and QTL analysis of growth-related traits in the Pacific oyster. Mar Biotechnol 14:218–226
Heath D (1975) Colour, sunlight and internal temperatures in the land-snail Cepaea nemoralis (L.). Oecologia 19:29–38
Innes DJ, Haley LE (1977) Inheritance of a shell-color polymorphism in the mussel. J Hered 68:203–204
Kang JH, Kang HS, Lee JM, An CM, Kim SY, Lee YM, Kim JJ (2013) Characterizations of shell and mantle edge pigmentation of a Pacific oyster, Crassostrea gigas, in Korean Peninsula. Asian-Australas J Anim Sci 26:1659–1664
Kobayashi T, Kawahara I, Hasekura O, Kijima A (2004) Genetic control of bluish shell color variation in the Pacific abalone, Haliotis discus hannai. J Shellfish Res 23:1153–1156
Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Li Q, Chen L, Kong L (2009) A genetic linkage map of the sea cucumber, Apostichopus japonicus (Selenka), based on AFLP and microsatellite markers. Anim Genet 40:678–685
Lindberg DR, Pearse JS (1990) Experimental manipulation of shell color and morphology of the limpets Lottia asmi (Middendorff) and Lottia digitalis (Rathke)(Mollusca: Patellogastropoda). J Exp Mar Biol Ecol 140:173–185
Liu Z, Cordes J (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238:1–37
Liu X, Wu F, Zhao H, Zhang G, Guo X (2009) A novel shell color variant of the Pacific abalone Haliotis discus hannai Ino subject to genetic control and dietary influence. J Shellfish Res 28:419–424
Liu F, Yao J, Wang X, Hu Z, Duan D (2011) Identification of SCAR marker linking to longer frond length of Saccharina japonica (Laminariales, Phaeophyta) using bulked-segregant analysis. J Appl Phycol 23:709–713
Michelmore RW, Paran I, Kesseli R (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci 88:9828–9832
Nakamura K, Ozaki A, Akutsu T, Iwai K, Sakamoto T, Yoshizaki G, Okamoto N (2001) Genetic mapping of the dominant albino locus in rainbow trout (Oncorhynchus mykiss). Mol Genet Genomics 265:687–693
Nell JA (2001) The history of oyster farming in Australia. Mar Fish Rev 63:14–25
Petersen JL, Baerwald MR, Ibarra AM, May B (2012) A first-generation linkage map of the Pacific lion-paw scallop (Nodipecten subnodosus): initial evidence of QTL for size traits and markers linked to orange shell color. Aquaculture 350:200–209
Piao Z, Deng Y, Choi S, Park Y, Lim Y (2004) SCAR and CAPS mapping of CRb, a gene conferring resistance to Plasmodiophora brassicae in Chinese cabbage (Brassica rapa ssp. pekinensis). Theor Appl Genet 108:1458–1465
Qin Y, Liu X, Zhang H, Zhang G, Guo X (2007) Identification and mapping of amplified fragment length polymorphism markers linked to shell color in bay scallop, Argopecten irradians irradians (Lamarck, 1819). Mar Biotechnol 9:66–73
Savelkoul P, Aarts H, De Haas J, Dijkshoorn L et al (1999) Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol 37:3083–3091
Shahinnia F, Sayed-Tabatabaei BE (2009) Conversion of barley SNPs into PCR-based markers using dCAPS method. Genet Mol Biol 32:564–567
Sokolova I, Berger VJ (2000) Physiological variation related to shell colour polymorphism in White Sea Littorina saxatilis. J Exp Mar Biol Ecol 245:1–23
Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0: Software for the calculation of genetic linkage maps. Plant Research International, Wageningen
Vos P, Hogers R, Bleeker M, Reijans M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Wada K, Komaru A (1990) Inheritance of white coloration of the prismatic layer of shells in the Japanese pearl oyster Pinctada fucata martensii and its importance in the pearl culture industry. Bull Jpn Soc Sci Fish 56:1787–1790
Wang L, Fan C, Liu Y, Zhang Y et al (2014) A genome scan for quantitative trait loci associated with Vibrio anguillarum infection resistance in Japanese flounder (Paralichthys olivaceus) by bulked segregant analysis. Mar Biotechnol 16:513–521
Winkler F, Estevez B, Jollan L, Garrido J (2001) Inheritance of the general shell color in the scallop Argopecten purpuratus (Bivalvia: Pectinidae). J Hered 92:521–525
Wittwer CT (2009) High-resolution DNA melting analysis: advancements and limitations. Hum Mutat 30:857–859
Xiao Q, Wibowo TA, Wu X-L, Michal JJ et al (2007a) A simplified QTL mapping approach for screening and mapping of novel AFLP markers associated with beef marbling. J Biotechnol 127:177–187
Xiao S, Xu J, Li Y, Zhang L et al (2007b) Generation and mapping of SCAR and CAPS markers linked to the seed coat color gene in Brassica napus using a genome-walking technique. Genome 50:611–618
Yu Z, Guo X (2003) Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin. Biol Bull 204:327–338
Yuan T, He MX, Huang LM (2012) Identification of an AFLP fragment linked to shell color in the noble scallop chlamys nobilis reeve. J Shellfish Res 31:33–37
Zhang Z, van Parijs FRD, Xiao B (2014) The status of AFLP in the genomics era and a pipeline for converting AFLPs into single-locus markers. Mol Breeding 34:1245–1260
Zheng H, Zhang T, Sun Z, Liu W, Liu H (2012) Inheritance of shell colours in the noble scallop Chlamys nobilis (Bivalve: Pectinidae). Aquac Res 1:1–7
Zhong X, Li Q, Yu H, Kong L (2013) Development and validation of single-nucleotide polymorphism markers in the Pacific Oyster, Crassostrea gigas, using high-resolution melting analysis. J World Aquacult Soc 44:455–465
Acknowledgments
This study was supported by the National High Technology Research and Development Program (2012AA10A405-6), and grants from the 973 Program (2010CB126406) and the National Natural Science Foundation of China (31372524).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Ge, J., Li, Q., Yu, H. et al. Identification of Single-Locus PCR-Based Markers Linked to Shell Background Color in the Pacific Oyster (Crassostrea gigas). Mar Biotechnol 17, 655–662 (2015). https://doi.org/10.1007/s10126-015-9652-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10126-015-9652-x