Hostname: page-component-cd9895bd7-dzt6s Total loading time: 0 Render date: 2024-12-23T11:23:57.493Z Has data issue: false hasContentIssue false
  • English
  • Français

Genetic diversity of Dioscorea japonica germplasm in Taiwan revealed by inter-simple sequence repeat DNA markers

Published online by Cambridge University Press:  20 July 2015

Tsai-Li Kung ,
Kuan-Hung Lin  and
Shun-Fu Lin
Tsai-Li Kung
Affiliation:
Department of Agronomy, National Taiwan University, Taipei, Taiwan, Republic of China Taoyuan District Agricultural Research and Extension Station, Council of Agriculture, Taoyuan, Taiwan, Republic of China
Kuan-Hung Lin
Affiliation:
Department of Horticulture and Biotecnology, Chinese Culture University, Taipei, Taiwan, Republic of China
Shun-Fu Lin*
Affiliation:
Department of Agronomy, National Taiwan University, Taipei, Taiwan, Republic of China
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

There are three native varieties of edible yams (Dioscorea japonica Thunb.) in Taiwan, but germplasm has been collected from only a few. To assess the genetic diversity of 99 accessions collected from four geographically diverse regions, inter-simple sequence repeat (ISSR) DNA markers were analysed, and 90.2% of the polymorphic markers in these accessions were found. Genetic similarity among accessions ranged from 30.8 to 74.4%, averaging 48.4%. Cluster analyses revealed four main clusters plus one outlier (Dioscorea alata L.). The varieties oldhamii and pseudojaponica were separated into different clusters and var. japonica was grouped with both varieties. Since var. japonica was found to be genetically similar to var. oldhamii and var. pseudojaponica, we suggest that var. japonica is a hybrid or intermediate variety between the two varieties. Molecular analysis of variance results indicated that variation within counties (95.94%) was predominantly greater than variation among counties (3.63%) and among regions (0.43%). Overall, gene flow (Nm= 0.970) estimated from genetic differentiation (Gst= 0.340) suggests that gene flow among regions is relatively high. The highest genetic diversity (H= 0.191) and Shannon's index (I= 0.312), and a high gene flow (Nm= 3.926) of germplasm in the northern region suggest that this region is a possible centre of dispersal and domestication of yams in Taiwan. This study provided valuable information for germplasm collection and genetic improvement.

Keywords

genetic similarityinter-simple sequence repeats (ISSR)varietyyam
Type
Research Article
Information
Plant Genetic Resources , Volume 14 , Issue 3 , September 2016 , pp. 211 - 218
Copyright
Copyright © NIAB 2015 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Araki, H, Harada, T and Yakuwa, T (1983) Some characteristics of interspecific hybrids between Dioscorea japonica and Dioscorea opposita . Journal of the Japanese Society for Horticultural Science 52: 153–158.CrossRefGoogle Scholar
Bousalem, M, Viader, V, Mariac, C, Gomez, R, Hochu, I, Santoni, S and David, J (2010) Evidence of diploidy in the wild Amerindian yam, a putative progenitor of the endangered species Dioscorea trifida (Dioscoreaceae). Genome 53: 371–383.Google Scholar
Excoffier, L and Lischer, HEL (2010) Arlequin Suite Ver 3.5: A New Series of Programs to Perform Population Genetics Analyses under Linux and Windows. 3012 Bern, German: University of Berne Swiss Institute of Bioinformatics.Google ScholarPubMed
Hamrick, JL, Godt, MJW and Sherman-Broyles, SL (1992) Factors influencing levels of genetic diversity in woody plant species. New Forests 6: 95–124.CrossRefGoogle Scholar
Helen, NA (1995) A fast, simple, and efficient miniscale method for the preparation of DNA from tissues of Yam (Dioscorea spp.). Plant Molecular Biology Reporter 13: 214–218.Google Scholar
Huang, TC, Hsiao, JL (2000) Dioscoreaceae. In: Huang, et al. (ed.) Flora of Taiwan, 2nd edn. Vol.5. Taipei: Department of Botany, National Taiwan University, pp. 87–98.Google Scholar
Jaccard, P (1908) Nouvelles recherches sur la distribution firale. Bulletin de la Société Vaudoise des Sciences Naturelles 44: 223–270.Google Scholar
Lay, H, Liu, H, Liao, M, Chen, C, Liu, S and Sheu, B (2001) Genetic identification of Chinese drug materials in yams (Dioscorea spp.) by RAPD analysis. Journal of Food and Drug Analysis 9: 132–138.Google Scholar
Lebot, V (2009) Tropical root and tuber crops: cassava, sweet potato, yams and aroids. In Crop Production Science in Horticulture, vol. 17. Wallingford, UK: CAB Books, CABI, pp. 183–188.Google Scholar
Muthamia, ZK, Morag, FE, Nyende, AB, Mamati, EG and Wanjala, BW (2013) Estimation of genetic diversity of the Kenyan yam (Dioscorea spp.) using microsatellite markers. African Journal of Biotechnology 12: 5845–5851.Google Scholar
Nascimento, WF, Rodrigues, JF, Koehler, S, Gepts, P and Veasey, EA (2013) Spatially structured genetic diversity of the Amerindian yam (Dioscorea trifida L.) assessed by SSR and ISSR markers in Southern Brazil. Genetic Resources and Crop Evolution 60: 2405–2420.CrossRefGoogle Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences 70: 3321–3323.Google Scholar
Reddy, MP, Sarla, N and Siddiq, EA (2002) Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128: 9–17.Google Scholar
Rohlf, FJ (2000) NTSYS-pc. Numerical Taxonomy and Multivariate Analysis System, Version 2.10. New York: Applied Biostatistics.Google Scholar
Scarcelli, N, Tostain, S, Mariac, C and Agbangla, C (2006) Genetic nature of yams (Dioscorea spp.) domesticated by farmers in Benin (West Africa). Genetic Resources and Crop Evolution 53: 121–130.Google Scholar
Shannon, CE and Weaver, W (1949) The Mathematical Theory of Communication. Urbana: Univsersity of Illinois Press.Google Scholar
Slatkin, M and Barton, NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43: 1349–1368.CrossRefGoogle ScholarPubMed
Tamiru, M, Mass, BL and Pawelzik, E (2008) Characterizing diversity in composition and pasting properties of tuber flour in yam germplasm (Dioscorea spp.) from Southern Ethiopia. Journal of the Science of Food and Agriculture 88: 1675–1685.Google Scholar
Wu, Z, Leng, C, Tao, Z, Wei, Y and Jiang, C (2009) Genetic diversity of Dioscorea alata based on ISSR analysis. China Journal of Chinese Materia Medica 34: 3017–3020.Google Scholar
Wu, Z, Li, X, Lin, X, Jiang, W, Tao, Z, Mantri, N and Bao, X (2014) Genetic diversity analysis of yams (Dioscorea spp.) cultivated in China using ISSR and SRAP markers. Genetic Resources and Crop Evolution 61: 639–650.CrossRefGoogle Scholar
Yeh, FC, Yang, RC, Boyle, TBJ, Ye, ZH and Mao, JX (1999) POPGENE version 1.31 Microsoft Window-based Freeware for Population Genetic Analysis: Quick User Guide. Canada: University of Alberta, Edmonton.Google Scholar
Zhou, Y, Zhou, C, Yao, H, Liu, Y and Tu, R (2008) Amplification of ISSR markers in detection of genetic variation among Chinese yam (Dioscorea opposita Thunb.) cultivars. Life Science Journal 5: 6–12.Google Scholar
Zietkiewicz, E, Rafalski, A and Labuda, D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genome 20: 176–183.Google Scholar
Supplementary material: File

Kung supplementary material

Table S1

Download Kung supplementary material(File)
File 239.1 KB
Supplementary material: File

Kung supplementary material

Table S2

Download Kung supplementary material(File)
File 60.9 KB