A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: A valuable resource for gene localisation and marker-assisted selection

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Jones, David B ^a   Jerry, Dean R ^a   Khatkar, Mehar S ^b   Raadsma, Herman W ^b   Zenger, Kyall R ^a  

^a JAMES COOK UNIVERSITY   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOMINERALIZATION; CONTROLLED STUDY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENE REPRESSION; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC DIFFERENCE; GENETIC DISTANCE; GENETIC HETEROGENEITY; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; MARKER ASSISTED BREEDING; MARKER GENE; MATHEMATICAL COMPUTING; NONHUMAN; PEDIGREE; PINCTADA; PINCTADA MAXIMA; QUANTITATIVE TRAIT LOCUS; SEX DIFFERENCE; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; CHROMOSOME MAP; EXPRESSED SEQUENCE TAG; GENETICS; SYNTENY;

MICROSATELLITE DNA;

ANIMALS; CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; GENETIC LINKAGE; MICROSATELLITE REPEATS; PINCTADA; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RECOMBINATION, GENETIC; SELECTION, GENETIC; SYNTENY;

EID: 84887807684     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-810     Document Type: Article

References (72)

1. Tisdell C, Poirine B. Economics of pearl farming. The pearl oyster 2008, 473-495. Amsterdam, The Netherlands: Elsevier B V, Southgate PC, Lucas JS.
2. Wada KT, Jerry DR. Population genetics and stock improvement. The pearl oyster 2008, 437-471. Amsterdam, The Netherlands: Elsevier B V, Southgate PC, Lucas JS.
3. Kvingedal R, Evans BS, Lind CE, Taylor JJU, Dupont-Nivet M, Jerry DR. Population and family growth response to different rearing location, heritability estimates and genotype × environment interaction in the silver-lip pearl oyster (Pinctada maxima). Aquaculture 2010, 304(1-4):1-6.
4. Jerry DR, Kvingedal R, Lind CE, Evans BS, Taylor JJU, Safari AE. Donor-oyster derived heritability estimates and the effect of genotype x environment interaction on the production of pearl quality traits in the silver-lip pearl oyster, Pinctada maxima. Aquaculture 2012, 338-341:66-71.
5. Saavedra C, Bachere E. Bivalve genomics. Aquaculture 2006, 256(1-4):1-14.
6. Curole JP, Hedgecock D. Bivalve genomics: complications, challenges, and future perspectives. Aquaculture genome technologies 2007, 525-544. Oxford, UK: Blackwell Publishing Ltd.
7. Wada K, Komaru A. Karyotypes in five species of Pteriidae (Bivalvia: Pteriomorphia). Venus 1985, 44(3):183-192.
8. Yu Z, Guo X. Genetic linkage map of the eastern oyster Crassostrea virginica gmelin. Biol Bull 2003, 204(3):327-338.
9. Li L, Guo X. AFLP-based genetic linkage maps of the pacific oyster Crassostrea gigas thunberg. Mar Biotechnol 2004, 6(1):26-36.
10. Hubert S, Hedgecock D. Linkage maps of microsatellite DNA markers for the pacific oyster Crassostrea gigas. Genetics 2004, 168(1):351-362.
11. Lallias D, Beaumont AR, Haley CS, Boudry P, Heurtebise S, Lapègue S. A first-generation genetic linkage map of the european flat oyster Ostrea edulis (L.) based on AFLP and microsatellite markers. Anim Genet 2007, 38(6):560-568.
12. Shi Y, Kui H, Guo X, Gu Z, Wang Y, Wang A. Genetic linkage map of the pearl oyster, Pinctada martensii (dunker). Aquacult Res 2009, 41(1):35-44.
13. Cunha R, Blanc F, Bonhomme F, Arnaud-Haond S. Evolutionary patterns in pearl oysters of the genus Pinctada (Bivalvia: Pteriidae). Mar Biotechnol 2011, 13(2):181-192.
14. Chávez-Villalba J, Soyez C, Huvet A, Gueguen Y, Lo C, Moullac GL. Determination of gender in the pearl oyster Pinctada margaritifera. J Shellfish Res 2011, 30(2):231-240.
15. Jones DB, Jerry DR, Forêt S, Konovalov DA, Zenger KR. Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster. Pinctada maxima. Mar Biotechnol 2013, 15(6):647-658.
16. Konovalov DA, Manning C, Henshaw MT. KINGROUP: a program for pedigree relationship reconstruction and kin group assignments using genetic markers. Mol Ecol Notes 2004, 4(4):779-782.
17. Jones OR, Wang J. COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 2010, 10(3):551-555.
18. Garbe JR, Da YP. Pedigraph user manual version 2.4 2008, Department of Animal Science, University of Minnesota.
19. Sambrook J, Russell DW. Molecular cloning: a laboratory manual 2001, New York: Cold spring harbor laboratory press.
20. Hackett CA, Broadfoot LB. Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 2003, 90(1):33-38.
21. Green P, Falls K, Crooks S. Documentation for CRI-MAP 1990, St Louis: Washington University, http://compgen.rutgers.edu/Crimap/Default.aspx.
22. Liu X, Grosz M. Linkage mapping software user's guide 2006, Monsanto Company: St-Louis.
23. Keats BJB, Sherman SL, Morton NE, Robson EB, Buetow KH, Cartwright PE, Chakravarti A, Francke U, Green PP, Ott J. Guidelines for human linkage maps an international system for human linkage maps (ISLM, 1990). Ann Hum Genet 1991, 55(1):1-6.
24. Kosambi D. The estimation of map distances from recombination values. Ann Eugen 1944, 12:172-175.
25. Liu RH, Meng JL. MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data. Yi Chuan 2003, 25(3):317-321.
26. de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T. CarthaGène: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics 2005, 21(8):1703-1704.
27. Cartwright DA, Troggio M, Velasco R, Gutin A. Genetic mapping in the presence of genotyping errors. Genetics 2007, 176(4):2521-2527.
28. Chakravarti A, Lasher LK, Reefer JE. A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 1991, 128(1):175-182.
29. Liao M, Zhang L, Yang G, Zhu M, Wang D, Wei Q, Zou G, Chen D. Development of silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) genetic maps using microsatellite and AFLP markers and a pseudo-testcross strategy. Anim Genet 2007, 38(4):364-370.
30. Danzmann R. LINKMFEX: LINKage analysis package for outcrossed families with male or female EXchange of the mapping parent, ver. 2.3 2006, Ontario, Canada, http://www.uoguelph.ca/~rdanzman/software/LINKMFEX.zip.
31. Sokal RR, Rohlf FJ. Biometry: the principles and practise of statistics in biological research 2012, New York: W. H. Freeman and Co., 4.
32. Haldane J. Sex ratio and unisexual sterility in hybrid animals. J Genet 1922, 12(2):101-109.
33. Ott J. Analysis of human genetic linkage (third edition) 1999, Baltimore: Johns Hopkins University Press.
34. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B (Methodological) 1995, 57(1):289-300.
35. Khatkar M, Nicholas F, Collins A, Zenger K, Cavanagh J, Barris W, Schnabel R, Taylor J, Raadsma H. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 2008, 9(1):187.
36. Hill WG, Robertson A. Linkage disequilibrium in finite populations. Theoret Appl Genet 1968, 38(6):226-231.
37. Lewontin R. The interaction of selection and linkage. I. general considerations; heterotic models. Genetics 1964, 49(1):49.
38. Abecasis GR, Cookson WOC. GOLD-Graphical overview of linkage disequilibrium. Bioinformatics 2000, 16(2):182-183.
39. Guo X, Li Q, Wang Q, Kong L. Genetic mapping and QTL analysis of growth-related traits in the pacific oyster. Mar Biotechnol 2012, 14(2):218-226.
40. Schwarz-Sommer Z, de Andrade Silva E, Berndtgen R, Lönnig W-E, Müller A, Nindl I, Stüber K, Wunder J, Saedler H, Gübitz T, et al. A linkage map of an F2 hybrid population of Antirrhinum majus and A. molle. Genetics 2003, 163(2):699-710.
41. McGoldrick D, Hedgecock D. Fixation, segregation and linkage of allozyme loci in inbred families of the pacific oyster Crassostrea gigas (thunberg): implications for the causes of inbreeding depression. Genetics 1997, 146(1):321-334.
42. Launey S, Hedgecock D. High genetic load in the pacific oyster Crassostrea gigas. Genetics 2001, 159(1):255-265.
43. Li L, Xiang J, Liu X, Zhang Y, Dong B, Zhang X. Construction of AFLP-based genetic linkage map for zhikong scallop, Chlamys farreri Jones et Preston and mapping of sex-linked markers. Aquaculture 2005, 245(1-4):63-73.
44. Wada H, Naruse K, Shimada A, Shima A. Genetic linkage map of a fish, the Japanese medaka Oryzias latipes. Mol Mar Biol Biotech 1995, 4(3):269-274.
45. Zenger KR, McKenzie LM, Cooper DW. The first comprehensive genetic linkage map of a marsupial: the tammar wallaby (Macropus eugenii). Genetics 2002, 162(1):321-330.
46. Hansson B, Åkesson M, Slate J, Pemberton JM. Linkage mapping reveals sex-dimorphic map distances in a passerine bird. Proc R Soc B Biol Sci 2005, 272(1578):2289-2298.
47. Miles L, Isberg S, Glenn T, Lance S, Dalzell P, Thomson P, Moran C. A genetic linkage map for the saltwater crocodile (Crocodylus porosus). BMC Genomics 2009, 10(1):339.
48. Lien S, Gidskehaug L, Moen T, Hayes B, Berg P, Davidson W, Omholt S, Kent M. A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns. BMC Genomics 2011, 12(1):615.
49. Zhang Z, Parsch J. Positive correlation between evolutionary rate and recombination rate in drosophila genes with male-biased expression. Mol Biol Evol 2005, 22(10):1945-1947.
50. Staelens J, Rombaut D, Vercauteren I, Argue B, Benzie J, Vuylsteke M. High-density linkage maps and sex-linked markers for the black tiger shrimp (Penaeus monodon). Genetics 2008, 179(2):917-925.
51. Huxley JS. Sexual difference of linkage in Gammarus chevreuxi. J Genet 1928, 20(2):145-156.
52. Singer A, Perlman H, Yan Y, Walker C, Corley-Smith G, Brandhorst B, Postlethwait J. Sex-specific recombination rates in zebrafish (Danio rerio). Genetics 2002, 160(2):649-657.
53. Isberg SR, Johnston SM, Chen Y, Moran C. First evidence of higher female recombination in a species with temperature-dependent sex determination: the saltwater crocodile. J Hered 2006, 97(6):599-602.
54. Ahmed M, Sparks AK. A preliminary study of chromosomes of two species of oysters (Ostrea lurida and Crassostrea gigas). J Fish Res Board Can 1967, 24(10):2155-2159.
55. Sakamoto T, Danzmann RG, Gharbi K, Howard P, Ozaki A, Khoo SK, Woram RA, Okamoto N, Ferguson MM, Holm L-E, et al. A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics 2000, 155(3):1331-1345.
56. Franch R, Louro B, Tsalavouta M, Chatziplis D, Tsigenopoulos CS, Sarropoulou E, Antonello J, Magoulas A, Mylonas CC, Babbucci M, et al. A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Genetics 2006, 174(2):851-861.
57. Donis-Keller H, Green P, Helms C, Cartinhour S, Weiffenbach B, Stephens K, Keith TP, Bowden DW, Smith DR, Lander ES. A genetic linkage map of the human genome. Cell 1987, 51(2):319-337.
58. Berset-Brändli L, Jaquiéry J, Broquet T, Ulrich Y, Perrin N. Extreme heterochiasmy and nascent sex chromosomes in European tree frogs. Proc R Soc B Biol Sci 2008, 275(1642):1577-1585.
59. Mank JE. The evolution of heterochiasmy: the role of sexual selection and sperm competition in determining sex-specific recombination rates in eutherian mammals. Genet Res 2009, 91(5):355.
60. Lynn A, Schrump S, Cherry J, Hassold T, Hunt P. Sex, not genotype, determines recombination levels in mice. Am J Hum Gen 2005, 77(4):670-675.
61. Hassold T, Hunt P. To err (meiotically) is human: the genesis of human aneuploidy. Nat Rev Genet 2001, 2(4):280-291.
62. Tease C, Hultén MA. Inter-sex variation in synaptonemal complex lengths largely determine the different recombination rates in male and female germ cells. Cytogenet Genome Res 2004, 107(3-4):208-215.
63. Weiss IM, Schönitzer V, Eichner N, Sumper M. The chitin synthase involved in marine bivalve mollusk shell formation contains a myosin domain. FEBS Lett 2006, 580(7):1846-1852.
64. Liu HL, Liu SF, Ge YJ, Liu J, Wang XY, Xie LP, Zhang RQ, Wang Z. Identification and characterization of a biomineralization related gene PFMG1 highly expressed in the mantle of Pinctada fucata. Biochemistry 2007, 46(3):844-851.
65. Suzuki M, Saruwatari K, Kogure T, Yamamoto Y, Nishimura T, Kato T, Nagasawa H. An acidic matrix protein, Pif, is a key macromolecule for nacre formation. Science 2009, 325(5946):1388-1390.
66. Kinoshita S, Wang N, Inoue H, Maeyama K, Okamoto K, Nagai K, Kondo H, Hirono I, Asakawa S, Watabe S. Deep sequencing of ESTs from nacreous and prismatic layer producing tissues and a screen for novel shell formation-related genes in the pearl oyster. PLoS One 2011, 6(6):e21238.
67. Metzler RA, Evans JS, Killian CE, Zhou D, Churchill TH, Appathurai NP, Coppersmith SN, Gilbert PUPA. Nacre protein fragment templates lamellar aragonite growth. J Am Chem Soc 2010, 132(18):6329-6334.
68. Shen X, Belcher A, Hansma P, Stucky G, Morse D. Molecular cloning and characterization of lustrin A, a matrix protein from shell and pearl nacre of Haliotis rufescens. J Biol Chem 1997, 272(51):32472-32481.
69. Fan W, Hu Y, Li C, Xie L, Zhang R. Cloning, characterization, and expression analysis of calreticulin from pearl oyster Pinctada fucata. Tsinghua Sci Technol 2008, 13(4):466-473.
70. Yano M, Nagai K, Morimoto K, Miyamoto H. A novel nacre protein N19 in the pearl oyster Pinctada fucata. Biochem Biophys Res Commun 2007, 362(1):158-163.
71. Sonesson AK. Genomic selection for aquaculture: principles and procedures. Next generation sequencing and whole genome selection in aquaculture 2011, 151-164. Ames, Iowa: Blackwell Publishing Ltd, Liu Z.
72. Du ZQ, Ciobanu DC, Onteru SK, Gorbach D, Mileham AJ, Jaramillo G, Rothschild MF. A gene-based SNP linkage map for pacific white shrimp. Litopenaeus vannamei. Anim Genet 2010, 41(3):286-294.