Identification, inheritance, and variation of microsatellite markers in the black scallop Mimachlamys varia

Biochemical Genetics

Volumn 49, Issue 3-4, 2011, Pages 139-152

  Arias, Alberto ^a   Freire, Ruth ^a   De La Roche, Juan Pablo ^b   Román, Guillermo ^b   Méndez, Josefina ^a   Insua, Ana ^a  

^a UNIVERSITY OF A CORUÑA   (Spain)

^b Centro Oceanográfico de A Coruña   (Spain)

Author keywords

Genetic diversity; Microsatellite markers; Mimachlamys varia; Population differentiation; Segregation analysis

Indexed keywords

ANIMAL TISSUE; ARTICLE; FEMALE; GENE FREQUENCY; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HETEROZYGOSITY; INHERITANCE; MALE; MICROSATELLITE MARKER; MIMACHLAMYS VARIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; POPULATION DIFFERENTIATION; SCALLOP; SEGREGATION ANALYSIS; SPAIN;

ANIMALS; BASE SEQUENCE; CHROMOSOME SEGREGATION; GENE FREQUENCY; GENETIC VARIATION; GENOMIC LIBRARY; GENOTYPE; HEREDITY; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PECTINIDAE; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SPAIN;

MIMACHLAMYS VARIA;

EID: 79954581500     PISSN: 00062928     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10528-010-9394-4     Document Type: Article

References (49)

1. SF Altschul TL Madden AA Schaffer JH Zhang Z Zhang W Miller DJ Lipman 1997 Gapped Blast and PSI-Blast: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402 9254694 10.1093/nar/25.17.3389 1:CAS:528:DyaK2sXlvFyhu7w%3D (Pubitemid 27359211)
2. HS An JY Park YG Lee DS Lee C Lee 2005 Ten polymorphic microsatellite loci in the giant scallop (Mizuhopecten yessoensis) Mol Ecol Notes 5 806 808 10.1111/j.1471-8286.2005.01069.x 1:CAS:528:DC%2BD28Xjs1WhsA%3D%3D (Pubitemid 43277974)
3. A Arias R Freire J Méndez A Insua 2009 Intron characterization and their potential as molecular markers for population studies in the scallops Aequipecten opercularis and Mimachlamys varia Hereditas 142 46 57 10.1111/j.1601-5223.2008.02075.x
4. A Arias R Freire J Méndez A Insua 2010 Isolation and characterization of microsatellite markers in the queen scallop Aequipecten opercularis and their application to a population genetic study Aquat Living Resour 23 199 207 10.1051/alr/2010011 1:CAS:528:DC%2BC3cXhtFCrtb%2FF
5. F Balloux N Lugon-Moulin 2002 The estimation of population differentiation with microsatellite markers Mol Ecol 11 155 165 11856418 10.1046/j.0962-1083.2001.01436.x (Pubitemid 34140159)
6. AR Beaumont CM Beveridge 1984 Electrophoretic survey of genetic variation in Pecten maximus, Chlamys opercularis, Chlamys varia and Chlamys distorta from the Irish Sea Mar Biol 81 299 306 10.1007/BF00393224 1:CAS:528: DyaL2MXhsVKntb4%3D
7. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) Genetix 4.05, logiciel sous Windows pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France). Available from http://www.genetix.univ-montp2.fr/genetix/genetix.htm
8. G Benson 1999 Tandem repeats finder: a program to analyze DNA sequences Nucleic Acids Res 27 573 580 9862982 10.1093/nar/27.2.573 1:CAS:528: DyaK1MXhtVKmtrg%3D (Pubitemid 29210025)
9. JAH Benzie C Smith-Keune 2006 Microsatellite variation in Australian and Indonesian pearl oyster Pinctada maxima populations Mar Ecol Prog Ser 314 197 211 10.3354/meps314197 1:CAS:528:DC%2BD28Xot1Kis7s%3D (Pubitemid 43989689)
10. N Billote PJL Lagoda AM Risterucci FC Baurens 1999 Microsatellite- enriched libraries: applied methodology for the development of SSR markers in tropical crops Fruits 54 277 288
11. JF Brookfield 1996 A simple new method for estimating null allele frequency from heterozygote deficiency Mol Ecol 5 453 455 8688964 1:STN:280:DyaK28zivFeqtQ%3D%3D (Pubitemid 126594621)
12. GK Chambers ES MacAvoy 2000 Microsatellites: consensus and controversy Comp Biochem Physiol B 126 455 476 11026658 10.1016/S0305-0491(00)00233-9 1:STN:280:DC%2BD3cvns1WhtA%3D%3D (Pubitemid 30628375)
13. MP Chapuis A Estoup 2007 Microsatellite null alleles and estimation of population differentiation Mol Biol Evol 24 621 631 17150975 10.1093/molbev/msl191 1:CAS:528:DC%2BD2sXjtleku7c%3D (Pubitemid 46355787)
14. DA Chistiakov B Hellemans FAM Volckaert 2006 Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics Aquaculture 255 1 29 10.1016/j.aquaculture. 2005.11.031 1:CAS:528:DC%2BD28Xlt1aht7s%3D (Pubitemid 43782863)
15. KJ Edwards JHA Barker A Daly C Jones A Karp 1996 Microsatellite libraries enriched for several microsatellite sequences in plants BioTechniques 20 758 760 8723911 1:CAS:528:DyaK28XislCjt7k%3D (Pubitemid 126507844)
16. CM Elfstrom CT Smith KC Jones JE Seeb 2005 Characterization of 16 polymorphic microsatellite loci in weathervane scallop Patinopecten caurinus Mol Ecol Notes 5 514 516 10.1111/j.1471-8286.2005.00974.x 1:CAS:528: DC%2BD2MXhtVOhtbrN (Pubitemid 41716833)
17. M Fernández-Moreno A Arias-Pérez R Freire J Méndez 2008 Genetic analysis of Aequipecten opercularis and Mimachlamys varia (Bivalvia: Pectinidae) in several Atlantic and Mediterranean localities, revealed by mitochondrial PCR-RFLPs: a preliminary study Aquac Res 39 474 481 10.1111/j.1365-2109.2008.01899.x (Pubitemid 351421788)
18. J Fernández-Tajes J Méndez 2007 Identification of the razor clam species Ensis arcuatus, E. siliqua, E. directus, E. macha, and Solen marginatus using PCR-RFLP analysis of the 5S rDNA region J Agric Food Chem 55 7278 7282 17691804 10.1021/jf0709855 (Pubitemid 47492278)
19. EM Gosling GM Burnell 1988 Evidence for selective mortality in Chlamys varia (L) transplant experiments J Mar Biol Assoc UK 68 251 258 10.1017/S0025315400052164
20. Goudet J (2001) Fstat, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Institut d'Ecologie, Université de Lausanne, Dorigny, Switzerland. Available from http://www2.unil.ch/popgen/ softwares/fstat.htm
21. TA Hall 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symp Ser 41 95 98 1:CAS:528:DC%2BD3cXhtVyjs7Y%3D
22. D Hedgecock G Li S Hubert K Bucklin V Ribes 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 (Pubitemid 39283063)
23. PW Hedrick 2005 A standardized genetic differentiation measure Evolution 59 1633 1638 16329237 1:CAS:528:DC%2BD2MXhtVKlt7bO (Pubitemid 41266769)
24. M Hui Z Bao A Zhan X Hu W Lu D Chang J Hu 2006 Ten polymorphic dinucleotide microsatellite markers of the noble scallop Chlamys nobilis Mol Ecol Notes 6 1033 1035 10.1111/j.1471-8286.2006.01420.x 1:CAS:528: DC%2BD2sXmsl2rsg%3D%3D (Pubitemid 44807932)
25. Iglesias P, Louro A, Román G (2008) How does reproduction and recruitment patterns match? The case of Chlamys varia in Ría de Betanzos-Sada, NW Spain. 2nd Mollusc Physiology Conference. September 1-4, Brest, France. Book of abstracts, p 119
26. KJ Jeffery LF Keller P Arcese MW Bruford 2001 The development of microsatellite loci in the song sparrow, Melospiza melodia (Aves) and genotyping errors associated with good quality DNA Mol Ecol Notes 1 11 13 10.1046/j.1471-8278.2000.00005.x 1:CAS:528:DC%2BD3MXlslaksrc%3D (Pubitemid 33691831)
27. S Launey D Hedgecock 2001 High genetic load in the Pacific oyster Crassostrea gigas Genetics 159 255 265 11560902 1:STN:280:DC%2BD3MrhtlSisw%3D%3D (Pubitemid 32917375)
28. YC Li AB Korol T Fahima A Beiles E Nevo 2002 Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review Mol Ecol 11 2453 2465 12453231 10.1046/j.1365-294X.2002.01643.x 1:CAS:528: DC%2BD38Xpsl2ms7o%3D (Pubitemid 35436668)
29. EJ Louis ER Dempster 1987 An exact test for Hardy-Weinberg and multiple alleles Biometrics 43 805 811 3427165 10.2307/2531534 1:STN:280: DyaL1c7gsl2qsQ%3D%3D (Pubitemid 18016766)
30. A Louro DL Roche MJ Campos G Román 2003 Hatchery rearing of the black scallop, Chlamys varia (L.) J Shellfish Res 22 95 99 (Pubitemid 36941159)
31. NF Mathers 1975 Environmental variability at the phosphoglucose isomerase locus in the genus Chlamys Biochem Syst Ecol 3 123 127 10.1016/0305-1978(75) 90015-0
32. DJ McGoldrick D Hedgecock LJ English P Baoprasertkul RD Ward 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 (Pubitemid 32122713)
33. E Meglécz 2007 Microfamily (version 1): a computer program for detecting flanking-region similarities among different microsatellite loci Mol Ecol Notes 7 18 20 10.1111/j.1471-8286.2006.01537.x (Pubitemid 46046573)
34. CR Miller LP Waits 2003 The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): implications for conservation Proc Natl Acad Sci USA 100 4334 4339 12655042 10.1073/pnas. 0735531100 1:CAS:528:DC%2BD3sXivFWjsbg%3D (Pubitemid 36418203)
35. M Nei 1978 Estimation of average heterozygosity and genetic distance from a small number of individuals Genetics 89 583 590 17248844 1:STN:280: DC%2BC3crpt1Kqtg%3D%3D (Pubitemid 8396073)
36. M Raymond F Rousset 1995 Genepop (version 1.2): population genetics software for exact tests and ecumenicism J Hered 86 248 249
37. KS Reece WL Ribeiro PM Gaffney RB Carnegie SK Allen Jr 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 15247315 10.1093/jhered/esh058 1:CAS:528:DC%2BD2cXlsFyisr0%3D (Pubitemid 38963187)
38. WR Rice 1989 Analyzing tables of statistical tests Evolution 43 223 225 10.2307/2409177
39. C Ríos S Sanz C Saavedra JB Pena 2002 Allozyme variation in populations of scallops, Pecten jacobaeus (L.) and P. maximus (L.) (Bivalvia: Pectinidae), across the Almeria-Oran front J Exp Mar Biol Ecol 267 223 244 10.1016/S0022-0981(01)00371-9 (Pubitemid 34074198)
40. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365-386
41. H Sobolewska AR Beaumont 2005 Genetic variation at microsatellite loci in northern populations of the European flat oyster (Ostrea edulis) J Mar Biol Assoc UK 85 955 960 10.1017/S002531540501194X 1:CAS:528:DC%2BD2MXlsFOmtbo%3D (Pubitemid 41044905)
42. CD Soulsbury G Iossa KJ Edwards PJ Baker S Harris 2007 Allelic dropout from a high-quality DNA source Conserv Genet 8 733 738 10.1007/s10592-006-9194-x 1:CAS:528:DC%2BD2sXks1yntrc%3D (Pubitemid 46682971)
43. N Taris S Baron TF Sharbel C Sauvage P Boudry 2005 A combined microsatellite multiplexing and boiling DNA extraction method for high-throughput parentage analyses in the Pacific oyster (Crassostrea gigas) Aquac Res 36 516 518 10.1111/j.1365-2109.2004.01208.x 1:CAS:528: DC%2BD2MXjs1Wisbo%3D (Pubitemid 40428354)
44. C Van Oosterhout WF Hutchinson DPM Wills P Shipley 2004 MicroChecker: software for identifying and correcting genotyping errors in microsatellite data Mol Ecol Notes 4 535 538 10.1111/j.1471-8286.2004.00684.x (Pubitemid 39147523)
45. HP Wagner 1991 Review of the European Pectinidae Vita Marina 41 1 48
46. PC Watts WJ Mallanaphy C McCarthy BD Beukers-Stewart MWJ Mosley AR Brand IJ Saccheri 2005 Polymorphic microsatellite loci isolated from the great scallop, Pecten maximus (Bivalvia: Pectinidae) Mol Ecol Notes 5 902 904 10.1111/j.1471-8286.2005.01107.x 1:CAS:528:DC%2BD28Xjs1Wlsg%3D%3D (Pubitemid 43278006)
47. BS Weir CC Cockerham 1984 Estimating F-statistics for the analysis of population structure Evolution 38 1358 1370 10.2307/2408641 (Pubitemid 16277759)
48. L Zane L Bargelloni T Patarnello 2002 Strategies for microsatellite isolation: a review Mol Ecol 11 1 16 11903900 10.1046/j.0962-1083.2001.01418.x 1:CAS:528:DC%2BD38Xht1Wltbc%3D (Pubitemid 34108467)
49. AB Zhan ZM Bao M Hui ML Wang HB Zhao W Lu XL Hu JJ Hu 2007 Inheritance pattern of EST-SSRs in self-fertilized larvae of the bay scallop Argopecten irradians Ann Zool Fenn 44 259 268 (Pubitemid 47441977)