Volume 9, Issue 4 (2018)
JMBS 2018, 9(4): 611-619 |
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1- Fisheries Department, Natural Resources & Marine Sciences Faculty, Tarbiat Modares University, Tehran, Iran, Fisheries Department, Natural Resources & Marine Sciences Faculty, Tarbiat Modares University, Nasr Bridge, Jalal-Al-Ahmad Highway, Tehran, Iran , kalbassi_m@madares.ac.ir
2- Aquaculture Research Center South of Iran, Iranian Fisheries Science Research Institute, Agricultural Research Education & Extension Organization (AREEO), Ahwaz, Iran
3- Genetic Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
4- Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
2- Aquaculture Research Center South of Iran, Iranian Fisheries Science Research Institute, Agricultural Research Education & Extension Organization (AREEO), Ahwaz, Iran
3- Genetic Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
4- Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
Abstract: (4026 Views)
Aims: Continuous monitoring of aquatic genetic diversity among different populations in fish hatcheries is an essential requirement to maintain the viability and sustainability of aquaculture industry. The aim of this study was cloning, sequencing, and detection of major histocompatibility complex (MHC) class II β in silver carp.
Materials and Methods: In this experimental study, the polymorphism of MHC class II β in 138 species of silver carp was studied in 4 different hatcheries of Iran (Guilan, Mazandaran, Golestan, and Khuzestan provinces) in addition to an imported group from China. By polymerase chain reaction (PCR), Hymo-DAB gene amplification was performed and the different haplotypes of the samples were analyzed by single-strand conformation polymorphism (SSCP) method and the sequences obtained with ClustalW2 were matched in Geneious 4.8.5 software and the phylogeny tree of the sequences was plotted.
Findings: The PCR reaction of the MHC-DAB II genome of the silver carp with a weight of about 350bp without side band was obtained in the samples, indicating the amplification of t Hymo-DAB1*01/DAB2*1 gene in silver carp. The highest and lowest diversity of haplotypes was observed in populations of Khuzestan and Mazandaran. The mean difference between synonymous site (dS) and nonsynonymous site (dN) of alleles was 0.25 and 0.30, respectively, with the ratio of 1.2. The highest allelic richness was observed in samples imported from China (5) and the lowest allelic richness was among Mazandaran species (3.8).
Conclusion: Haplotype diversity in silver carp belongs to Hymo-DAB1*01/DAB2*1 gene and among different groups of this species, the highest haplotype diversity is in the Khuzestan population and the highest allelic richness is related to samples imported from China.
Materials and Methods: In this experimental study, the polymorphism of MHC class II β in 138 species of silver carp was studied in 4 different hatcheries of Iran (Guilan, Mazandaran, Golestan, and Khuzestan provinces) in addition to an imported group from China. By polymerase chain reaction (PCR), Hymo-DAB gene amplification was performed and the different haplotypes of the samples were analyzed by single-strand conformation polymorphism (SSCP) method and the sequences obtained with ClustalW2 were matched in Geneious 4.8.5 software and the phylogeny tree of the sequences was plotted.
Findings: The PCR reaction of the MHC-DAB II genome of the silver carp with a weight of about 350bp without side band was obtained in the samples, indicating the amplification of t Hymo-DAB1*01/DAB2*1 gene in silver carp. The highest and lowest diversity of haplotypes was observed in populations of Khuzestan and Mazandaran. The mean difference between synonymous site (dS) and nonsynonymous site (dN) of alleles was 0.25 and 0.30, respectively, with the ratio of 1.2. The highest allelic richness was observed in samples imported from China (5) and the lowest allelic richness was among Mazandaran species (3.8).
Conclusion: Haplotype diversity in silver carp belongs to Hymo-DAB1*01/DAB2*1 gene and among different groups of this species, the highest haplotype diversity is in the Khuzestan population and the highest allelic richness is related to samples imported from China.
Subject:
Agricultural Biotechnology
Received: 2016/11/30 | Accepted: 2017/06/5 | Published: 2018/12/21
Received: 2016/11/30 | Accepted: 2017/06/5 | Published: 2018/12/21
References
1. Kirk H, Freeland JR. Applications and implications of neutral versus non-neutral markers in molecular ecology. Int J Mol Sci. 2011;12(6):3966-88. [Link] [DOI:10.3390/ijms12063966]
2. Reed DH, Frankham R. Correlation between fitness and genetic diversity. Conserv Biol. 2003;17(1):230-7. [Link] [DOI:10.1046/j.1523-1739.2003.01236.x]
3. Sunnucks P, Wilson AC, Beheregaray LB, Zenger K, French J, Taylor AC. SSCP is not so difficult: The application and utility of single‐stranded conformation polymorphism in evolutionary biology and molecular ecology. Mol Ecol. 2000;9(11):1699-710. [Link] [DOI:10.1046/j.1365-294x.2000.01084.x]
4. Brumfield RT, Beerli P, Nickerson DA, Edwards SV. The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol. 2003;18(5):249-56. [Link] [DOI:10.1016/S0169-5347(03)00018-1]
5. Meyers LA, Bull JJ. Fighting change with change: Adaptive variation in an uncertain world. Trends Ecol Evol. 2002;17(12):P551-7. [Link] [DOI:10.1016/S0169-5347(02)02633-2]
6. Hedrick PW. Balancing selection and MHC. Genetica. 1999;104(3):207-14. [Link] [DOI:10.1023/A:1026494212540]
7. Doherty PC, Zinkernagel RM. Enhanced immunological surveillance in mice heterozygous at the H-2 gene complex. Nature. 1975;256(5512):50-2. [Link] [DOI:10.1038/256050a0]
8. Penn DJ. The scent of genetic compatibility: Sexual selection and the major histocompatibility complex. Ethology. 2002;108(1):1-21. [Link] [DOI:10.1046/j.1439-0310.2002.00768.x]
9. Kruiswijk CP, Hermsen T, Van Heerwaarden J, Dixon B, Savelkoul HF, Stet RJ. Major histocompatibility genes in the Lake Tana African large barb species flock: Evidence for complete partitioning of class II B, but not class I, genes among different species. Immunogenetics. 2005;56(12):894-908. [Link] [DOI:10.1007/s00251-005-0767-5]
10. De Eyto E, McGinnity P, Consuegra S, Coughlan J, Tufto J, Farrell K, et al. Natural selection acts on Atlantic salmon Major Histocompatibility (MH) variability in the wild. Proc Biol Sci. 2007;274(1611):861-9. [Link] [DOI:10.1098/rspb.2006.0053]
11. Nei M, Hughes AL. Polymorphism and evolution of the major histocompatibility complex loci in mammals. In: Selander RK, Clark AG, Whittam TS, editors. Evolution at the molecular level. Oxford: Oxford University Press, Incorporated; 1991. p. 222. [Link]
12. Larson WA, Seeb JE, Dann TH, Schindler DE, Seeb LW. Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon. Mol Ecol. 2014;23(22):5448-61. [Link] [DOI:10.1111/mec.12949]
13. Ujvari B, Belov K. Major Histocompatibility Complex (MHC) markers in conservation biology. Int J Mol Sci. 2011;12(8):5168-86. [Link] [DOI:10.3390/ijms12085168]
14. Chargé R, Teplitsky C, Sorci G, Low M. Can sexual selection theory inform genetic management of captive population? A review. Evolut Appl. 2014;7(9):1120-33. [Link] [DOI:10.1111/eva.12229]
15. Landry C, Bernatchez L. Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar). Mol Ecol. 2001;10(10):2525-39. [Link] [DOI:10.1046/j.1365-294X.2001.01383.x]
16. Sommer S. The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front Zool. 2005;2:16. [Link] [DOI:10.1186/1742-9994-2-16]
17. Hashimoto K, Nakanishi T, Kurosawa Y. Isolation of carp genes encoding major histocompatibility complex antigens. Proc Natl Acad Sci U S A. 1990;87(17):6863-7. [Link] [DOI:10.1073/pnas.87.17.6863]
18. Ono H, O'hUigin C, Vincek V, Stet RJ, Figueroa F, Klein J. New beta chain-encoding Mhc class II genes in the carp. Immunogenetics. 1993;38(2):146-9. [Link] [DOI:10.1007/BF00190902]
19. Van Erp SH, Egberts E, Stet RJ. Characterization of class II A and B genes in a gynogenetic carp clone. Immunogenetics. 1996;44(3):192-202. [Link] [DOI:10.1007/BF02602585]
20. Aurelle D, Berrebi P. Genetic structure of brown trout (Salmo trutta, L.) populations from south-western France: Data from mitochondrial control region variability. Mol Ecol. 2001;10(6):1551-61. [Link] [DOI:10.1046/j.1365-294X.2001.01293.x]
21. Liu ZJ, Cordes JF. DNA marker technologies and their applications in aquaculture genetics. Aquaculture. 2004;238(1-4):1-37. [Link] [DOI:10.1016/j.aquaculture.2004.05.027]
22. Kumari N, Thakur SK, Kumar D, Kumari K. Single Strand Conformation Polymorphism (SSCP) - a review. Indian Res J Genet Biotechnol. 2015;7(1):27-34. [Link]
23. Gasser RB, Hu M, Chilton NB, Campbell BE, Jex AJ, Otranto D, et al. Single Strand Conformation Polymorphism (SSCP) for the analysis of genetic variation. Nat Protoc. 2006;1(6):3121-8. [Link] [DOI:10.1038/nprot.2006.485]
24. Konnai S, Nagaoka Y, Takesima S, Onuma M, Aida Y. Technical note: DNA typing for ovine MHC DRB1 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). J Dairy Sci. 2003;86(10):3362-5. [Link] [DOI:10.3168/jds.S0022-0302(03)73939-3]
25. Fisheries and Aquaculture Department. FishStatJ - software for fishery statistical time series [Internet]. Rome: Food and Agriculture Organization of the United Nations; 2016 [cited 10 June 2016]. Available from: http://www.fao.org/fishery/statistics/software/fishstatj/en [Link]
26. Hillis DM. Molecular systematics. 2nd Edition. Hillis DM, Moritz C, Mable BK, University David M Hillis, editors. Oxford: Oxford University Press, Incorporated; 1996. [Link]
27. Yu H, Tan S, Zhao H, Li H. MH-DAB gene polymorphism and disease resistance to Flavobacterium columnare in grass carp (Ctenopharyngodon idellus). Gene. 2013;526(2):217-22. [Link] [DOI:10.1016/j.gene.2013.05.019]
28. Benbouza H, Jacquemin JM, Baudoin JP, Mergeai G. Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnol Agron Soc Environ. 2006;10(2):77-81. [Link]
29. Drummond AJ, Ashton B, Buxton S, Cheung M, Heled J, Kearse M, et al. Geneious, 4.8.5 [Internet]. 2010 [cited 20 June 2016]. Available from: https://www.geneious.com/products/prime/resources/download/previous-versions/ [Link]
30. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870-4. [Link] [DOI:10.1093/molbev/msw054]
31. Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25(11):1451-2. [Link] [DOI:10.1093/bioinformatics/btp187]
32. Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER, et al. Nomenclature for the major histocompatibility complexes of different species: A proposal. Immunogenetics. 1990;31(4):217-9. [Link] [DOI:10.1007/BF00204890]
33. Goudet J. FSTAT, a program to estimate and test gene diversities and fixation indices version 2.9.3 [Internet]. Lausanne: UNIL, Université de Lausanne; 2001 [cited 15 May 2016]. Available from: http://www.citeulike.org/user/argosmarulanda/article/7617994 [Link]
34. Johansson ML, Clifford K, Fodness B, Vazquez NA, Banks MA. 2012. Mate selection in captive-breeding rockfishes Sebastes spp.: Inference from parentage analysis and the major histocompatibility complex (MHC). Mar Ecol Prog Ser. 2012;460:195-206. [Link] [DOI:10.3354/meps09803]
35. Evans ML, Neff BD, Heath DD. Behavioural and genetic analyses of mate choice and reproductive success in two Chinook salmon populations. Can J Fish Aquat Sci. 2013;70(2):263-70. [Link] [DOI:10.1139/cjfas-2012-0415]
36. Penn D, Potts W. MHC-disassortative mating preferences reversed by cross-fostering. Proc Biol Sci. 1998;265(1403):1299-306. [Link] [DOI:10.1098/rspb.1998.0433]
37. Wiegertjes GF, Bongers AB, Voorthuis P, Zandieh Doulabi B, Groeneveld A, Van Muiswinkel WB, et al. Characterization of isogenic carp (Cyprinus carpio L.) lines with a genetically determined high or low antibody production. Anim Genet. 1996;27(5):313-9. [Link] [DOI:10.1111/j.1365-2052.1996.tb00975.x]
38. Langefors A, Lohm J, Grahn M, Andersen O, Von Schantz T. Association between major histocompatibility complex class IIB alleles and resistance to Aeromonas salmonicida in Atlantic salmon. Proc Biol Sci. 2001;268(1466):479-85. [Link] [DOI:10.1098/rspb.2000.1378]
39. Miller KM, Winton JR, Schulze AD, Purcell MK, Ming TJ. Major histocompatibility complex loci are associated with susceptibility of Atlantic salmon to infectious hematopoietic necrosis virus. Environ Biol Fish. 2004;69(1-4):307-16. [Link] [DOI:10.1023/B:EBFI.0000022874.48341.0f]
40. Hetland DL, Jørgensen SM, Skjødt K, Dale OB, Falk K, Xu C, et al. In situ localisation of major histocompatibility complex class I and class II and CD8 positive cells in Infectious Salmon Anaemia Virus (ISAV)-infected Atlantic salmon. Fish Shellfish Immunol. 2010;28(1):30-9. [Link] [DOI:10.1016/j.fsi.2009.09.011]
41. Ristow SS, Grabowski LD, Thompson SM, Warr GW, Kaattari SL, De Avila JM, et al. Coding sequences of the MHC class II beta chain of homozygous rainbow trout (Oncorhynchus mykiss). Dev Comp Immunol. 1999;23(1):51-60. [Link] [DOI:10.1016/S0145-305X(98)00039-1]
42. Peters MB, Turner TF. Genetic variation of the major histocompatibility complex (MHC class II β gene) in the threatened Gila trout, Oncorhynchus gilae gilae. Conserv Genet. 2008;9(2):257-70. [Link] [DOI:10.1007/s10592-007-9336-9]
43. Kuroda N, Figueroa F, O'hUigin C, Klein J. Evidence that the separation of Mhc class II from class I loci in the zebrafish, Danio rerio, occurred by translocation. Immunogenetics. 2002;54(6):418-30. [Link] [DOI:10.1007/s00251-002-0473-5]
44. Godwin UB, Flores M, Quiniou S, Wilson MR, Miller NW, Clem LW, et al. MHC class II A genes in the channel catfish (Ictalurus punctatus). Dev Comp Immunol. 2000;24(6-7):609-22. [Link] [DOI:10.1016/S0145-305X(00)00005-7]
45. Dong ZD, Zhao Y, Zeng QF, Fu Y, Zhou FN, Ji XS, et al. Molecular cloning and polymorphism of the Major Histocompatibility Complex (MHC) class IIB gene of grass carp (Ctenopharyngodon idella). Biochem Genet. 2013;51(1-2):139-46. [Link] [DOI:10.1007/s10528-012-9549-6]
46. Jia Z, Chi X, Li C, Shi L. Development of MHC class I and II B primers in common carp and its molecular characterization. Biochem Genet. 2010;48(7-8):690-5. [Link] [DOI:10.1007/s10528-010-9351-2]
47. Rakus KŁ, Wiegertjes GF, M Stet RJ, J Savelkoul HF, Pilarczyk A, Irnazarow I. Polymorphism of major histocompatibility complex class II B genes in different lines of the common carp (Cyprinus carpio). Aquat Living Resour. 2003;16(5):432-7. [Link] [DOI:10.1016/S0990-7440(03)00057-3]
48. Ortí G, Hare MP, Avise JC. Detection and isolation of nuclear haplotypes by PCR-SSCP. Mol Ecol. 1997;6(6):575-80. [Link] [DOI:10.1046/j.1365-294X.1997.00212.x]
49. Grimholt U, Larsen S, Nordmo R, Midtlyng P, Kjoeglum S, Storset A, et al. MHC polymorphism and disease resistance in Atlantic salmon (Salmo salar); facing pathogens with single expressed major histocompatibility class I and class II loci. Immunogenetics. 2003;55(4):210-9. [Link] [DOI:10.1007/s00251-003-0567-8]
50. Kalinowski ST. Counting alleles with rarefaction: Private alleles and hierarchical sampling designs. Conserv Genet. 2004;5(4):539-43. [Link] [DOI:10.1023/B:COGE.0000041021.91777.1a]
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