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Journal of Applied Phycology

, Volume 23, Issue 1, pp 35–45 | Cite as

An AFLP-based survey of genetic diversity and relationships of major farmed cultivars and geographically isolated wild populations of Saccharina japonica (Phaeophyta) along the northwest coasts of the Pacific

  • Ti Feng Shan
  • Shao Jun PangEmail author
  • Yu Rong Zhang
  • Irina M. Yakovleva
  • Anna V. Skriptsova
Article

Abstract

The genetic diversity and relationships of six representative cultivars and six geographically isolated wild populations of Saccharina japonica along the northwest coasts of the Pacific Ocean were investigated using AFLP markers. A total of 547 bands were generated across all samples by ten primer combinations. At the cultivar or population level, the percentage of polymorphic loci (P), gene diversity (H), and Shannon’s information index (I) was highest in Dalian population (P 59.05%; H 0.2057; I 0.3062) and lowest in Lianjiang cultivar (P 9.87%; H 0.0331; I 0.0497). At the species level, P, H, and I were 85.01%, 0.1948, and 0.3096, respectively. Unique bands were detected in all the six wild populations, with Dalian being the most. In comparison, only Yanza cultivar possessed one unique band. The G ST value was 0.6226 and the gene flow (N m ) was 0.1515, indicating strong genetic differentiation among cultivars and populations. Two UMPGA dendrograms were constructed based on the Dice similarity coefficients among individuals and on genetic distances among cultivars and populations, which generally revealed three major clades corresponding to three countries. Analysis of molecular variance revealed that a larger proportion (60.21%) of the total genetic variation was attributable to differences among cultivars and populations. The Mantel test suggested that genetic differentiation was positively correlated with geographic distance (r = 0.7962, P = 0.011) in the six wild populations, agreeing with the isolation by distance model. On the whole, low to moderate genetic diversity within cultivars and populations (except Dalian population) and high genetic differentiation among cultivars and populations were detected.

Keywords

AFLP Cultivar Genetic differentiation Genetic diversity Population structure Saccharina japonica 

Notes

Acknowledgements

The authors wish to thank Hyung Geun Kim and Kyu Sam Han from Kangnung-Wonju National University for collecting the algal samples, Su Qin Gao, Shi Guo Li, Chun Hua Song, and Jing Pu Zhang for the great help in sample handling and some of the experimental work. Special thanks go to the anonymous reviewers for their invaluable suggestions and comments. This investigation was financially supported by the following programs: (1) the 863 Hi-Tech Research and Development Program of China (2006AA10A412;2006AA10A416); (2) a project from the Chinese Academy of Sciences (KSCX2-YW-N-47-07); (3) a project from the Ministry of Science and technology of China (2006DKA30470-017); (4) a China–Russia bilateral cooperation program between the Chinese Academy of Sciences and the Far East Branch of Russian Academy of Sciences (program no. 2008-21#); (5) a project from Ministry of Agriculture of China (200903030).

References

  1. Anderson EK, North WJ (1966) In situ studies of spore production and dispersal in the giant kelp Macrocystis. In: Young EG, McLochlan JL (eds) Proc Int Seaweed Symp, vol 5. Pergamon, Oxford, pp 73–86Google Scholar
  2. Bassam JB, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83CrossRefPubMedGoogle Scholar
  3. Bensch S, Åkesson M (2005) Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol 14:2899–2914CrossRefPubMedGoogle Scholar
  4. Billot C, Engel CR, Rousvoal S, Kloareg B, Valero M (2003) Current patterns, habitat discontinuities and population genetic structure: the case of the kelp Laminaria digitata in the English Channel. Mar Ecol Prog Ser 253:111–121CrossRefGoogle Scholar
  5. Boland W, Marner FJ, Jaenicke L, Müller DG, Folster E (1983) Comparative receptor study in gamete chemotaxis of the seaweeds Ectocarpus siliculosus and Cutleria multifida: an approach to interspecific communication of algal gametes. Eur J Biochem 134:97–103CrossRefPubMedGoogle Scholar
  6. Bonin A, Ehrich D, Manel S (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Mol Ecol 16:3737–3758CrossRefPubMedGoogle Scholar
  7. Caballero A, Quesada H, Rolan-Alvarez E (2008) Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 179:539–554CrossRefPubMedGoogle Scholar
  8. Cheng SH, Cao LY, Yang SH, Zhai HQ (2004) Forty years’ development of hybrid rice: China’s experience. Rice Sci 11:225–230Google Scholar
  9. Coyer JA, Olsen JL, Stam TW (1997) Genetic variability and spatial separation in the sea palm kelp Postelsia palmaeformis (Phaeophyceae) as assessed with M13 fingerprints and RAPDs. J Phycol 33:561–568CrossRefGoogle Scholar
  10. Dayton PK (1973) Dispersion, dispersal, and persistence of the annual intertidal alga, Postelsia palmaeformis Ruprecht. Ecology 54:433–438CrossRefGoogle Scholar
  11. Dice LR (1945) Measures of the amount of ecological association between species. Ecology 26:297–302CrossRefGoogle Scholar
  12. Engelen AH, Olsen JL, Breeman AM, Stam WT (2001) Genetic differentiation in Sargassum polyceratium (Fucales: Phaeophyceae) around the island of Curacao (Netherlands Antilles). Mar Biol 139:267–277CrossRefGoogle Scholar
  13. Erting L, Daugbjerg N, Pedersen PM (2004) Nucleotide diversity within and between four species of Laminaria (Phaeophyceae) analyzed using partial LSU and ITS rDNA sequences and AFLP. Eur J Phycol 39:243–256CrossRefGoogle Scholar
  14. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50PubMedGoogle Scholar
  15. Fang TC, Wu CY, Jiang Y, Li TT, Ren GZ (1962) The breeding of a new breed of Haidai (Laminaria japonica Aresch.) and its preliminary genetic analysis. Acta Bot Sin 10:197–209, (in Chinese with English abstract)Google Scholar
  16. Fang TC, Cui JJ, Ou YL, Dai JX, Wang ML (1983) Breeding of the new variety “Danhai No. 1” of Laminaria japonica by using a female haploid clone of the kelp. J Shandong Coll Oceanol 13:63–70, (in Chinese with English abstract)Google Scholar
  17. Fei XG (2004) Solving the coastal eutrophication problem by large scale seaweed cultivation. Hydrobiologia 512:145–151CrossRefGoogle Scholar
  18. Féral JP (2002) How useful are the genetic markers in attempts to understand and manage marine biodiversity? J Exp Mar Biol Ecol 268:121–145CrossRefGoogle Scholar
  19. Hellberg ME (1994) Relationships between inferred levels of gene flow and geographic distance in a philopatric coral, Balanophyllia elegans. Evolution 48:1829–1854CrossRefGoogle Scholar
  20. Hellberg ME (1995) Stepping-stone gene flow in the solitary coral Balanophyllia elegans: equilibrium and nonequilibrium at different spatial scales. Mar Biol Berl 123:573–581CrossRefGoogle Scholar
  21. Jones DF (1945) Heterosis resulting from degenerative changes. Genetics 30:527–542Google Scholar
  22. Kiula BA, Lyimo NG, Botha AM (2008) Association between AFLP-based genetic distance and hybrid performance in tropical maize. Plant Breed 127:140–144CrossRefGoogle Scholar
  23. Kusumo HT, Druehl LD (2000) Variability over space and time in the genetic structure of the winged kelp Alaria marginata. Mar Biol 136:397–409CrossRefGoogle Scholar
  24. Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398Google Scholar
  25. Li XJ, Cong YZ, Yang GP, Shi YY, Qu SC, Li ZL, Wang GW, Zhang ZZ, Luo SJ, Dai HL, Xie JZ, Jiang GL, Liu JL, Wang TY (2007) Trait evaluation and trial cultivation of Dongfang No. 2, the hybrid of a male gametophyte clone of Laminaria longissima (Laminariales, Phaeophyta) and a female one of L. japonica. J Appl Phycol 19:139–151CrossRefPubMedGoogle Scholar
  26. Li BJ, Shi YY, Yang GP, Che S, Li XJ, Cong YZ (2008a) Microsatellite DNA variation of the gametophyte clones isolated from introduced Laminaria japonica (Phaeophyta) and L. longissima of China and varieties derived from them. J Integr Plant Biol 50:352–359CrossRefPubMedGoogle Scholar
  27. Li XJ, Liu JL, Cong YZ, Qu SC, Zhang ZZ, Dai HL, Luo SJ, Han XB, Huang SS, Wang QY, Liang GJ, Sun J, Jin Y, Wang DQ, Yang GP (2008b) Breeding and trial cultivation of Dongfang No. 3, a hybrid of Laminaria gametophyte clones with a more than intraspecific but less than interspecific relationship. Aquaculture 280:76–80CrossRefGoogle Scholar
  28. Li XJ, Yang GP, Shi YY, Cong YZ, Che S, Qu SC, Li ZL (2008c) Prediction of the heterosis of Laminaria hybrids with the genetic distance between their parental gametophyte clones. J Appl Phycol 20:1097–1102CrossRefGoogle Scholar
  29. Li SG, Shan TF, Hou HS, Pang SJ (2009) Genetic analyses of principal farmed cultivars of Laminaria japonica in China (I): AFLP analyses of self-breeding F1 of nine cultivars. J Fish Sci China 16:214–220 (in Chinese with English abstract)Google Scholar
  30. Lu TT, Willliams SL (1994) Genetic diversity and genetic structure in the brown alga Halidrys dioica (Fucales: Cystoseiraceae) in Southern California. Mar Biol 121:363–371CrossRefGoogle Scholar
  31. Lüning K, Müller DG (1978) Chemical interaction in sexual reproduction of several Laminariales (Phaeophyceae): release and attraction of spermatozoids. Z Pflanzenphysiol 89:333–341Google Scholar
  32. Maier I, Müller DG (1986) Sexual pheromones in algae. Biol Bull 170:145–175CrossRefGoogle Scholar
  33. Martin JM, Talbert LE, Lanning SP, Blake NK (1995) Hybrid performance in wheat as related to parental diversity. Crop Sci 35:104–108CrossRefGoogle Scholar
  34. Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12:106–117CrossRefPubMedGoogle Scholar
  35. Miller MP (1997) Tools for population genetic analyses (TFPGA) 1.3: a Windows program for the analysis of allozyme and molecular population genetic data. Computer software distributed by authorGoogle Scholar
  36. Müller DG (1981) Sexuality and sexual attraction. In: Lobban CS, Wynne JJ (eds) The biology of seaweeds. Bot. Monogr., vol. 17, pp 661–674Google Scholar
  37. Müller DG, Gassman G, Lüning K (1979) Isolation of a spermatozoid-releasing and -attracting substance from female gametophytes of Laminaria digitata. Nature 279:430–431CrossRefPubMedGoogle Scholar
  38. Müller DG, Maier I, Gassman G (1985) Survey on sexual pheromone specificity in Laminariales (Phaeophyceae). Phycologia 24:475–484CrossRefGoogle Scholar
  39. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A 70:3321–3323CrossRefPubMedGoogle Scholar
  40. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  41. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York, pp 159–166Google Scholar
  42. Pang SJ, Wu CY (1996) Study on gametophyte vegetative growth of Undaria pinnatifida and its application. Chin J Oceanol Limnol 14:205–210CrossRefGoogle Scholar
  43. Pang SJ, Hu XY, Wu CY (1997) Intraspecific crossings on Undaria pinnatifida (Harv.) Sur.: a possible time-saving way of strain selection. Chin J Oceanol Limnol 15:227–235CrossRefGoogle Scholar
  44. Perèz R, Kaas R, Campelle F, Arbault S, Barbaroux O (1992) La culture de l’algue Undaria pinnatifida (Harvey) Suringar. In: Perèz R (ed) La Culture des Algues Marines dans le Monde. Service de la Documentation et des Publications (SDP) IFREMER, Brest, pp 425–462Google Scholar
  45. Reed DC, Laur DR, Ebeling AW (1988) Variation in algal dispersal and recruitment: the importance of episodic events. Ecol Monogr 58:321–335CrossRefGoogle Scholar
  46. Reed DC, Amsler CD, Ebeling AW (1992) Dispersal in kelps: factors affecting spore swimming and competency. Ecology 73:1577–1583CrossRefGoogle Scholar
  47. Rohlf FJ (2000) NTSYSpc: numerical taxonomy and multivariate analysis system, version 2.1. Exeter Software, Setauket, New YorkGoogle Scholar
  48. Shan TF, Pang SJ (2009) Assessing genetic identity of sporophytic offspring of the brown alga Undaria pinnatifida derived from mono-crossing of gametophyte clones by use of amplified fragment length polymorphism and microsatellite markers. Phycol Res 57:36–44CrossRefGoogle Scholar
  49. Shi YY, Yang GP, Liu YJ, Liao MJ, Li XJ, Cong YZ (2007) Development of 18 polymorphic microsatellite DNA markers of Laminaria japonica (Phaeophyceae). Mol Ecol Notes 7:620–622CrossRefGoogle Scholar
  50. Shi YY, Yang GP, Liao MJ, Liu YJ, Shang S, Li XJ, Cong YZ (2008) Comparative study on the microsatellite DNA polymorphism of the gametophytes of Laminaria japonica and Laminaria longissima. Periodical Ocean Univer China 38:303–308Google Scholar
  51. Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 36:1349–1368CrossRefGoogle Scholar
  52. Stuber CW, Lincoln SE, Wolff DW, Helentijars T, Lander ES (1992) Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132:823–839PubMedGoogle Scholar
  53. Subudhi KP, Parami PN, Harrison AS, Materne DM, Murphy JP, Nash D (2005) An AFLP-based survey of genetic diversity among accessions of sea oats (Uniola paniculata, Poaceae) from the southeastern Atlantic and Gulf coast states of the United States. Theor Appl Genet 111:1632–1641CrossRefPubMedGoogle Scholar
  54. Sundene O (1962) The implications of transplant and culture experiments on the growth and distribution of Alaria esculenta. Nytt Mag Bot 9:155–174Google Scholar
  55. Tian Z, Yuan B (1989) Report of the breeding of a novel kelp variety, “Zaohoucheng No.1”. Mariculture 1:7–17, (in Chinese)Google Scholar
  56. Tseng CK (2001) Algal biotechnology industries and research activities in China. J Appl Phycol 13:375–380CrossRefGoogle Scholar
  57. Tseng CK, Sun KY, Wu CY (1955) On the cultivation of Haidai (Laminaria japonica Aresch) by summering young sporophytes at low temperature. Acta Bot Sin 4:255–264 (in Chinese with English abstract)Google Scholar
  58. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11:139–151CrossRefPubMedGoogle Scholar
  59. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414CrossRefPubMedGoogle Scholar
  60. Wang XL, Yang YX, Cong YZ, Duan DL (2004) DNA fingerprinting of selected Laminaria (Phaeophyta) gametophytes by RAPD markers. Aquaculture 238:143–153CrossRefGoogle Scholar
  61. Wang XL, Liu CL, Li XJ, Cong YZ, Duan DL (2005) Assessment of genetic diversities of selected Laminaria (Laminariales, Phaeophyta) gametophytes by inter-simple sequence repeat analysis. J Integr Plant Biol 47:753–758CrossRefGoogle Scholar
  62. Wang D, Wang XL, Li DP, Wang FJ, Duan DL (2006) The genetic analysis and germplasm identification of the gametophytes of Undaria pinnatifida (Phaeophyceae) with RAPD method. J Appl Phycol 18:801–809CrossRefGoogle Scholar
  63. Wright S (1946) Isolation by distance under diverse systems of mating. Genetics 31:39–59Google Scholar
  64. Wright S (1978) Evolution and genetics of populations. Variability within and among natural populations, vol 4. University of Chicago Press, Chicago, 649 ppGoogle Scholar
  65. Wu CY, Lin GH (1987) Progress in the genetics and breeding of economic seaweeds in China. Hydrobiologia 151/152:57–61Google Scholar
  66. Xia P, Wang XL, Li XJ, Zhao YS, Yao L, Duan DL (2005) Genetic study of Kelp “901” strain. Chin J Oceanol Limnol 23:152–157CrossRefGoogle Scholar
  67. Xu RQ, Tomooka N, Vaughan DA (2000) AFLP markers for characterizing the azuki bean complex. Crop Sci 40:808–815CrossRefGoogle Scholar
  68. Yap I, Nelson R (1996) WinBoot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI discussion paper series no. 14. IRRI, ManilaGoogle Scholar
  69. Yeh FC, Yang RC, Boyle T (1999) POPGENE (version 1.3.1). Microsoft Window-based freeware for population genetic analysis. http://www.ualberta.ca/∼fyeh/. University of Alberta and the Centre for International Forestry Research, Edmonton, Canada
  70. Yuan LP (1997) Current status and developing prospects in two-line hybrid rice research in China. Res Agric Modernization 18:1–3 (in Chinese with English abstract)Google Scholar
  71. Yuan LP (2004) Hybrid rice for food security in the world. FAO Rice Conference. FAO, RomeGoogle Scholar
  72. Zhang QS, Tang XX, Cong YZ, Qu SC, Luo SJ, Yang GP (2007a) Breeding of an elite Laminaria variety 90-1 through inter-specific gametophyte crossing. J Appl Phycol 19:303–311CrossRefGoogle Scholar
  73. Zhang XQ, Wang XD, Jiang PD, Hua SJ, Zhang HP, Dutt Y (2007b) Relationship between molecular marker heterozygosity and hybrid performance in intra- and interspecific hybrids of cotton. Plant Breed 126:385–391CrossRefGoogle Scholar
  74. Zhang QS, Shi YY, Cong YZ, Qu SC, Yang GP (2008) AFLP analysis of the gametophyte clones derived from introduced Laminaria (Phaeophyta) and cultured varieties of China. Periodical Ocean Univer China 38:429–435Google Scholar
  75. Zhao MF, Li XH, Yang JB, Xu CJ, Hu RY, Liu DJ, Zhang QF (1999) Relationship between molecular marker heterozygosity and hybrid performance in intra- and inter-subspecific cross of rice. Plant Breed 118:139–144CrossRefGoogle Scholar
  76. Zhao FJ, Wang XL, Liu JD, Duan DL (2007) Population genetic structure of Sargassum thunbergii (Fucales, Phaeophyta) detected by RAPD and ISSR markers. J Appl Phycol 19:409–416CrossRefGoogle Scholar
  77. Zhao FJ, Liu FL, Liu JD, Ang PO Jr, Duan DL (2008) Genetic structure analysis of natural Sargassum muticum (Fucales, Phaeophyta) populations using RAPD and ISSR markers. J Appl Phycol 20:191–198CrossRefGoogle Scholar
  78. Zhou ZG, Shi XZ, Hu YJ, Sun YP (2003) Genetic relationship among brown seaweed Laminaria longissima and various cultivars of L. japonica in China revealed by isozyme and RAPD markers. J Fish Sci China 10:474–480, (in Chinese with English abstract)Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Ti Feng Shan
    • 1
  • Shao Jun Pang
    • 1
    Email author
  • Yu Rong Zhang
    • 2
  • Irina M. Yakovleva
    • 3
  • Anna V. Skriptsova
    • 3
  1. 1.Marine Biological Culture Collection Center, Institute of OceanologyChinese Academy of SciencesQingdaoChina
  2. 2.Fisheries Research Institute of Zhejiang ProvinceZhoushanChina
  3. 3.Institute of Marine BiologyFar Eastern Branch of Russian Academy of SciencesVladivostokRussia

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