Marker-assisted Selection in Fish: A Review
Asian Journal of Fisheries and Aquatic Research,
Page 1-11
DOI:
10.9734/ajfar/2019/v3i430038
Abstract
The important economical traits like body growth, resistance to diseases, meat quality, etc. highly influence the profitability of food animals including fishes. The main target of every selective breeding programme is to produce improved traits offspring’s. However, improvement of performance traits through traditional phenotype-based selection needs several generations to optimise these characters. Marker-Assisted Selection (MAS) is a type of indirect method of selection of better performing breeding individuals. MAS is beneficial when the traits are difficult, expensive to measure and has both low heritability and recessive traits. MAS facilitates the exploitation of existing genetic diversity in breeding populations and can be used to improve desirable traits in livestock. MAS depends on identifying the link between a genetic marker and Quantitative Traits Loci (QTL). The distance between marker and target traits determines the association of the marker with the QTL. After identifying the markers linked to QTL, they can be used in the selective breeding programme to select the brooders having better genetic potential for the targeted trait. Improvement of performance traits through MAS is fast and more accurate and allows us to understand the genetic mechanism affecting performance traits.
Keywords:
- Marker-assisted selection
- quantitative traits loci
- genetic diversity
- trait.
How to Cite
Eze, F. (2019). Marker-assisted Selection in Fish: A Review. Asian Journal of Fisheries and Aquatic Research, 3(4), 1-11. https://doi.org/10.9734/ajfar/2019/v3i430038
References
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Ribaut JM, Ragot M. Marker-assisted selection to improve drought adaptation in maize: The backcross approach, perspectives, limitations and alternatives. J Exp Bot. 2007;58:351-360.
Sax K. The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics. 1923;8:522-560.
Brumlop S, Finckh MR. Applications and potentials of marker assisted selection (MAS) in plant breeding. 2011;178.
Available:http://www.bfn.de/0502_skripten.html
Bardakci F, Skibinski DOF. Application of the RAPD technique in tilapia fish species and subspecies identification. 1994;73:117–123.
DOI:10.1038/hdy.1994.110.
Alarcon JA, Alvarez MC. Genetic identification Sparidae species by isozyme markers. Applications to Interspecific Hybrids. Aquaculture. 1999;173:95-103.
Vogel B, Van Aken J. Smart breeding - Marker-assisted selection: A non-invasive biotechnology alternative to genetic engineering of plant varieties Amsterdam, the Netherlands. 2009;28.
Boopathi NM. Marker-assisted selection. In genetic mapping and marker assisted selection: Basics, practice and benefits. 2013a;173–186.
DOI:10.1007/978-81-322-0958-4
Xu Y, Beachell H, McCouch SR. A marker based approach to broadening the genetic base of rice in the USA. Crop Sci. 2008;44:1947–1959.
Nichols KM, Bartholomew J, Thorgaard GH. Mapping multiple genetic loci associated with Ceratomyxa shasta resistance in Oncorhynchus mykiss. Dis. Aquat. Org. 2003;56:145–154.
Yanchuk AD. The role and implications of biotechnology in forestry. Food and agriculture organization of the United Nations, Unasylva. 2002;(30):18–22.
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One. 1990;7:e37135.
Bernardo R. Prediction of maize single-cross performance using RFLPs and Biotechnology in Agriculture and Food; 1994.
Available:http://tandfonline.com/doi/book/10.1081/EEBAF.
Xie C, Xu X. Efficiency of multistage marker-assisted selection in the improvement of multiple quantitative traits. Heredity. 1998;80:489-498.
Ryman N, Utter F. Population genetics and fishery management University of Washington Press, Seattle. 1987;420.
Anderson JL, Marí AR, Braasch I, Amores A, Hohenlohe P, Batzel P. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAPD mapping and population genomics. 2001;3:427-437.
Cnaani A, Zilberman N, Tinman S, Hulata G, Ron M. Genome-scan analysis for quantitative trait loci in an F-2 tilapia hybrid. Mol Genet Genomics. 2003;272(2):162-172.
Willcox MC, Khairallah M, Bergvinson D, Crossa J, Deutsch JA, Edmeades GO, Gonzalez-de-Leon D, Jiang C, Jewell DC, Mihm JA, Williams WP, Hoisington DA. Selection for resistance to southwestern corn borer using marker assisted and conventional backcrossing. Crop Sci. 2002;42:1516–1528.
Moreau L, Lamarie S, Charcosset A, Gallais A. Economic efficiency of one molecular marker assisted selection for the mall quality traits in barley. Mol Breeding. 2000;3:427-437.
Davies J, Berzonsky W, Leach G. A comparison of marker-assisted and phenotypic selection for high grain protein content in spring wheat. 2006;152:117-134.
Flint-Garcia SA, Darrah LL, McMullen MD, Hibbard BE. Phenotypic versus genomic selection in an established commercial layer breeding program. Genetics Selection Evolution. 2003;45:29.
Dreher K, Khairallah M, Jean-Marcel R, Monis M. Money matters (I): Costs of field and laboratory procedures associated with convenlional and marker assisted maize breeding at CIMMYT. Molecular Breeding 2002;I I:221-234.
Dudley JW. Molecular markers in plant improvement: Manipulation of genes affecting quantitative traits. Crop Sci. 1993;33:660–668.
Jackson TR, Ferguson MM, Danzmann RG, Fishback AG, Ihssen PE, O’Connell M, Crease TJ. Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynnchus mykiss) half-sib families. Heredity. 1998;80:143–151.
Robison BD, Wheeler PA, Sundin K, Sikka P, Thorgaard GH. Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss). J. Heredity. 2001;92:16–22.
Sakamoto T, Danzmann RG, Okamoto N, Ferguson MM, Ihssen PE. Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss). Aquaculture. 1999;173:33–43.
Ozaki A, Sakamoto T, Khoo S, Nakamura K, Coimbra MR, Akutsu T. Okamoto N. Quantitative Trait Loci (QTL) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss). Mol. Genet. Genomics. 2001;265:23–31.
Liu Z, Karsi A, Li P, Cao D, Dunham R. An AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family. Genetics 2003;165:687–694.
Mackay TFC. The genetic architecture of quantitative traits. Annu Rev Genet. 2001;35:303-339.
Groen AF, Crooijmans RPMA, Van Kampen AJA, Van der Beek S, Van der Poel JJ, Groenen MAM. Microsatellite polymorphism in commercial broiler and layer lines. Proc 5th World Congr Genet Appl Livestock Prod. 2000;21:95-98.
Paterson A, Lander SE, Hevit JD, Peterson S. Lincoln SE, Lanksley SD. Resolution of quantitative traits into mendelian factors by using a complete linkage map of Restriction Fragment Length Polymorphisms. Nature. 1988;325:721-726.
Jacob HJ, Lindpainter K, Lincoln SE, Kusumi RK, Mao YP, Ganten D, Dzau VJ, Lander ES. Genetic mapping of a gene causing hypersensitive rat. Cell. 1991;67:213-224.
Sonesson A. Within-family marker-assisted selection for aquaculture species. Genet Sel Evol. 2007;39:301–18.
Postlethwait JH, Johnson SL, Midson CN, Talbot WS, Gates M, Ballinger EW, Africa D, Andrews R, Carl T, Eisen JS. A genetic linkage map for the zebrafish. Science. 1994;264:699-703.
Shimoda N, Knapik EW, Ziniti J, Sim C, Yamada E, Kaplan S, Jackson D, de Sauvage F, Jacob H, Fishman MC. Zebrafish genetic map with 2000 microsatellite markers. Genomics. 1999;58: 219-232.
Sakamoto T, Danzmann RG, Gharbi K, Howard P, Ozaki A, Khoo SK. A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics. 2000;155:1331-1345.
Kocher TD, Lee WJ, Sobolewska H, Penman D, McAndrew B. A genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus). Genetics. 1998;148:1225–1232.
Kause A, Paananen T, Ritola O, Koskinen H. Direct and indirect selection of visceral lipid weight, fillet weight, and fillet percentage in a rainbow trout breeding program. Journal of Anim Sci. 2003;85:3218-3227.
Sonesson AK. A combination of walk-back and optimum contribution selection for fish – a simulation study. Genet. Sel. Evol. 2003;37:587–599.
Perry GM, Danzmann RG, Ferguson MM, Gibson JP. Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout (Oncorhynchus mykiss). Heredity. 2001;86:333– 341.
Sakamoto T, Danzmann RG, Okamoto N, Ferguson MM, Ihssen PE. Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss). Aquaculture. 1999;173:33–43.
Somorjai IM, Danzmann RG, Ferguson MM. Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies in rainbow trout (Oncorhynchus mykiss). Genetics. 2001;165:1443–1456.
Martyniuk CJ, Perry GML, Mogahadam HK, Ferguson MM, Danzmann RG. The genetic architecture of correlations among growth related traits and male age at maturation in rainbow trout. Journal of Fish Biol. 2003;63:746–764.
O’Malley KG, Sakamoto T, Danzmann RG, Ferguson MM. Quantitative trait loci for spawning date and body weight in rainbow trout: Testing for conserved effects across ancestrally duplicated chromosomes. J. Hered. 2003;94:273–84.
Reid DP, Szanto A, Glebe B, Danzmann RG, Ferguson MM. QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus). Heredity. 2005;94(2):166-172.
Zimmerman AM, Wheeler PA, Ristow SS, Thorgaard GH. Composite interval mapping reveals three QTL associated with pyloric caeca number in rainbow trout, Oncorhynchus mykiss. Aquaculture. 2005;247:85–95.
Wang CM, Lo LC, Zhu ZY, Yue GH. A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer). BMC Genomics; 2006.
Yu Z, Guo X. Genetic linkage map of the eastern oyster (Crassostrea virginica) Gmelin. Biol. Bull. 2003;204:327–338.
Guo X, Hershberger WK, Cooper K, Chew KK. Artificial gynogenesis with; 2012.
Loukovitis D, Sarropoulou E, Tsigenopoulos CS, Batargias C, Magoulas A, Apostolidis AP, Chatziplis D, Kotoulas G. Quantitative trait loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan. PLoS ONE. 2011;6:e16599.
Wringe B, Devlin R, Ferguson M, Moghadam H, Sakhrani D, Danzmann R. Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss). BMC Genetics. 2010;11(63).
Liu F, Sun F, Xia JH, Li J, Fu GH, Lin G. A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia. Sci Rep. 2014;4:7256.
Yue GH. Recent advances of genome mapping and marker-assisted selection in aquaculture. 2014;15:376–96.
Wang CM, Lo LC, Zhu ZY, Yue GH. A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer). BMC Genomics; 2006.
Wang CM, Lo LC, Feng F, Zhu ZY, Yue GH. Identification and verification of QTL associated with growth traits in two genetic backgrounds of Barramundi (Lates calcarifer). Anim Genet. 2008;39(1):34-39.
Houston RD, Bishop SC, Hamilton A, Guy DR, Tinch AE, Taggart JB, Derayat A, McAndrew BJ, Haley CS. Detection of QTL affecting harvest traits in a commercial Atlantic salmon population. Anim Genet. 2009;40(5):753-755.
Houston RD, Haley CS, Hamilton A, Guy DR, Tinch AE, Taggart JB. Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar). Genetics. 2009;178:1109–15.
Song W, Li Y, Zhao Y, Liu Y, Niu Y, Pang R. Construction of a high density microsatellite genetic linkage map and mapping of sexual and growth-related traits in half-smooth tongue sole (Cynoglossus semilaevis). PLoS One. 2012;7:e52097.
Song W, Pang R, Niu Y, Gao F, Zhao Y, Zhang J. Construction of high density genetic linkage maps and mapping of growth-related quantitative trail loci in the Japanese flounder (Paralichthys olivaceus). PLoS One.7:e50404; 2012
Li J, Boroevich KA, Koop BF, Davidson WS. Comparative genomics identifies candidate genes for Infectious Salmon Anemia (ISA) resistance in Atlantic Salmon (Salmo salar). Mar Biotechnol. 2009;13:232-241.
Wang S, Meyer E, McKay JK, Matz MV. 2b-RAD: a simple and flexible method for genome-wide genotyping. Nat Methods. 2012;9:808–10.
Davidson WS, Koop BF, Jones SJM, Iturra P, Vidal R, Mas A, Jonassen I, Lien S, Omholt SW. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 2009;11:403.
Eshel O, Shirak A, Weller JI, Slossman T, Hulata G, Cnaani A. Fine mapping of a locus on linkage group 23 for sex determination in Nile tilapia (Oreochromis niloticus). Anim Genet. 2011;42:222–4.
Moghadam H, Poissant J, Fotherby H, Haidle L, Ferguson M, Danzmann R. Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). Mol Genet Genomics. 2007;277(6):647-661.
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