AFLP fingerprints of Pyropia yezoensis (Bangiales, Rhodophyta) populations revealed the important effect of farming protocols on genetic diversity

Yuan Cao; Wen-Jun Wang; Fu-Li Liu; Zhou-Rui Liang; Xiu-Tao Sun; Xiao-Lei Li; Teng-Qin Sun; Fei-Jiu Wang

doi:10.1515/bot-2017-0073

Article

AFLP fingerprints of Pyropia yezoensis (Bangiales, Rhodophyta) populations revealed the important effect of farming protocols on genetic diversity

Yuan Cao , Wen-Jun Wang , Fu-Li Liu , Zhou-Rui Liang , Xiu-Tao Sun , Xiao-Lei Li , Teng-Qin Sun and Fei-Jiu Wang

Published/Copyright: March 27, 2018

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From the journal Botanica Marina Volume 61 Issue 2

Abstract

Continuous and intensive selective breeding reduces the genetic diversity of cultivated Pyropia stock, thereby increasing its susceptibility to diseases, and hindering the sustainable development of the Pyropia industry. To develop new Pyropia germplasms with desirable agronomic traits, a new Pyropia yezoensis strain, “Huangyou No. 1” was bred from a wild subtidal population. In this study, the genetic diversity of this strain was analyzed using AFLP. Totally, 249 loci were obtained, of which 248 were polymorphic with a polymorphism rate of 99.6%, using seven primer pairs. The intra-population polymorphism rates of the populations Wild 1 and Wild 2 were the highest (47.39% and 59.44%, respectively), while they were relatively low (20.88–24.5%) in the cultivated populations. The genetic distances between the breeding Pyropia populations cultivated in the same aquaculture farm were low. Specifically, the F₂ offspring of “Huangyou No. 1” and the control cultivar, cultivated using the “never-drying” protocol, were genetically distant from the other populations, including that from the same seedlings, yet cultivated using the “periodic-drying” protocol. The never-drying cultivation protocol had a high likelihood of influencing genetic diversity of Pyropia yezoensis.

Keywords: AFLP; farming protocol; genetic diversity; molecular marker; Pyropia yezoensis

Acknowledgements

This work was supported by the Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2015A02), Primary Research & Development Plan of Shandong Province (2016GSF115038), National Natural Science Foundation of China (31672630), China Agriculture Research System (CARS-50), National Science and Technology Infrastructure Project (2012–2017), and Science and Technology Plan of Changdao (2016–2018).

References

Allen, A.M., M.O. Winfield, A.J. Burridge, R.C. Downie, H.R. Benbow, G.L.A. Barker, P.A. Wilkinson, J. Coghill, C. Waterfall, A. Davassi, G. Scopes, A. Pirani, T. Webster, F. Brew, C. Bloor, S. Griffiths, A.R. Bentley, M. Alda, P. Jack, A.L. Phillips and K.J. Edwards. 2017. Characterization of a Wheat Breeders’ Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol. J. 15: 390–401.10.1111/pbi.12635Search in Google Scholar

Baselga, I., O. Zafra, E. Pérez Lago, R. Francisco-Álvarez, G. Rodriguez-Tarduchy and C. Santos. 2017. An AFLP based method for the detection and identification of indigenous yeast in complex must samples without a microbiological culture. Int. J. Food Microbiol. 241: 89–97.10.1016/j.ijfoodmicro.2016.09.014Search in Google Scholar

Bassam, B.J., G. Caetano-Anolles and P.M. Gresshoffp. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196: 80–83.10.1016/0003-2697(91)90120-ISearch in Google Scholar

Botstein, D.R., R.L. White, M. Skolnick and R.W. Davis. 1980. Construction of a geneticlinkage map in man using restriction fragment length polymorphism. Am. J. Hum. Genet. 32: 314–331.Search in Google Scholar

Cao, Y., W.J. Wang, Z.R. Liang, F.L. Liu, X.T. Sun, H.Q. Yao, X.L. Li and F.J. Wang. 2016. Genetic and nutrient analysis of new P. yezoensis strain “Huangyou No.1”. Guangxi Sci. 23: 131–137.Search in Google Scholar

Chen, Y.X., Z.H. Zuo, X. Chen, C.G. Wang and L. Liang-Ju. 2007. Analysis genetic diversity of Porphyra haitanensis using AFLP. J. Xiamen Univ. (Nat. Sci.) 46: 831–835.Search in Google Scholar

Grodzicker, T., J. Williams, P. Sharp and J. Sambrook. 1974. Physical mapping of temperature-sensitive mutations of adenoviruses. Cold Spring Harb Symp Quant Biol 39: 439–446.10.1101/SQB.1974.039.01.056Search in Google Scholar

Gupta, S.K. and T. Gopalakrishna. 2009. Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi). Genome 52: 120–128.10.1139/G08-107Search in Google Scholar PubMed

He, J.Y., L.W. He, X. Zhang, G.H. Pan, P. Xu, J.Y. Zhu, B. Zhang and G.C. Wang. 2010. Analysis of genetic diversity of P. yezoensis using AFLP. Oceanologia Et Limnologia Sinica 41: 489–494.Search in Google Scholar

Li, S.Y. 1989. Studies on the ecological characteristics and application of P. yezoensis monospore and seeding. Mar. Sci. Bulletin 30: 81–92.Search in Google Scholar

Li, H.S. 2004. ISSR molecular marker technique and its applications in plant cenetic diversity. Bull. Biol. 39: 19–21.Search in Google Scholar

Li, X.L., W.J. Wang, F.L. Liu, Z.R. Liang, X.T. Sun, H.Q. Yao and F.J. Wang. 2017. Periodical drying or no drying during aquaculture affects the desiccation tolerance of a sublittoral P. yezoensis strain. J. Appl. Phycol. 2: 1–9.10.1007/s10811-017-1227-ySearch in Google Scholar

Liu, F.L. 2011. Population genetic analysis and QTLs study of frond length and width for Saccharina japonica. Ph. D. thesis, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.Search in Google Scholar

Liu, F.L., Z.R. Shao, H.N. Zhang, J.D. Liu, X.L. Wang and D.L. Duan. 2009. QTL mapping for frond length and width in Laminaria japonica Aresch (Laminarales, Phaeophyta) using AFLP and SSR markers. Mar. Biotechnol. 12: 386–394.10.1007/s10126-009-9229-7Search in Google Scholar PubMed

Magdy, M., O. Werner, S.F. Mcdaniel, B. Goffinet and R.M. Ros. 2016. Genomic scanning using AFLP to detect loci under selection in the moss Funaria hygrometrica along a climate gradient in the Sierra Nevada Mountains, Spain. Plant Biol. 18: 280–288.10.1111/plb.12381Search in Google Scholar PubMed

Magne, F. 1993. Importance of basic research in applied phycology. Hydrobiologia 260: 25–29.10.1007/978-94-011-1998-6_3Search in Google Scholar

Saeed, A. and R. Darvishzadeh. 2017. Association analysis of biotic and abiotic stresses resistance in chickpea (Cicer spp.) using AFLP markers. Biotechnol. Biotec. Eq. 31: 698–708.10.1080/13102818.2017.1333455Search in Google Scholar

Shakhatreh, Y., M. Baum, N. Haddad, M. Alrababah and S. Ceccarelli. 2016. Assessment of genetic diversity among Jordanian wild barley (Hordeum spontaneum) genotypes revealed by SSR markers. Genet. Resour. Crop Ev. 63: 813–822.10.1007/s10722-015-0285-8Search in Google Scholar

Tao, W.J. and D.J. Liu. 1998. AFLP technology and its application in plant genome research. World Agriculture 236: 16–19.Search in Google Scholar

Vos, P., R. Hogers, B. Marjo, M. Reijans, T. Lee, M. Hornes, A. Friters, J. Pot, J. Paleman, M. Kuiper and M. Zabeau. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407–4414.10.1093/nar/23.21.4407Search in Google Scholar PubMed PubMed Central

Wang, Y., B.Q. Liu, Q.J. Luo, Z.Q. Fei, L.Q. Pei and Q.Z. Xue. 2000. RAPD analysis of genetic diversity among Porphyra haitaneusis strains. J. Ocean Univ. Qingdao (Natural Sci.) 30: 225–229.Search in Google Scholar

Wang, X., S.Y. Wang, M.M. Wang, Y.D. Wang, C.X. Zhu, Q.Q. Lu, B. Jiang, T. Zhang and J.Y. Zhu. 2013. AFLP genetic diversity analysis of different strains of Pyropia. Jiangsu Agriculture Sci. 41: 38–41.Search in Google Scholar

Wang, R., H.X. Huang, E.L. Yu, Q.H. Chen, Z.J. Liang and T.Q. Wu. 2014. Genetic and gene expression analysis of dm1, a dwarf mutant from Cucurbita maxima Duch. ex Lam, based on the AFLP method. Can. J. Plant Sci. 94: 293–302.10.4141/cjps2013-016Search in Google Scholar

Williams, J.G.K., A.R. Kubelik, K.J. Livak, J.A. Rafalski and S.V. Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531–6535.10.1093/nar/18.22.6531Search in Google Scholar PubMed PubMed Central

Xu, P. 2013. Reproduction and development of major economic marine algae in China. China Agriculture Press, Beijing. pp. 101.Search in Google Scholar

Xu, D., L.S. Song, S. Qin, P. Alessandro, X.G. Fei and C.K. Zeng. 2001. RAPD analysis of genetic diversity among cultivated Porphyra. Chinese High Technology Letters 11: 1–8.Search in Google Scholar

Yang, R., B.Q. Liu, Q.J. Luo, Y.J. Wang and J.M. Bao. 2003. Genetic diversity of Porphyra yezoensis by using AFLP 1. Acta Oceanol. Sin. 22: 453–457.Search in Google Scholar

Yao, H.W., L.D. Zhang, J.Y. Sun and X.X. Liu. 2010. Summary of DNA molecular marker technology. Hebei Fisheries 7: 42–46.Search in Google Scholar

Zabeau, M. and P. Vos. 1993. Selective restriction fragment amplification: a general method for DNA fingerprinting: EP 0534858[P]. 1993-03-31.Search in Google Scholar

Received: 2017-9-29

Accepted: 2018-2-15

Published Online: 2018-3-27

Published in Print: 2018-3-28

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https://doi.org/10.1515/bot-2017-0073

Keywords for this article

AFLP; farming protocol; genetic diversity; molecular marker; Pyropia yezoensis