Hostname: page-component-78c5997874-g7gxr Total loading time: 0 Render date: 2024-11-15T07:30:54.119Z Has data issue: false hasContentIssue false
  • English
  • Français

Classification and diversity of sacred and American Nelumbo species: the genetic relationships of flowering lotus cultivars in Japan using SSR markers

Published online by Cambridge University Press:  01 May 2009

Nakao Kubo ,
Masashi Hirai ,
Akio Kaneko ,
Daizo Tanaka  and
Kumaji Kasumi
Nakao Kubo*
Affiliation:
Graduate School of Agriculture, Kyoto Prefectural University, Seika, Kyoto619-0244, Japan Kyoto Prefectural Institute of Agricultural Biotechnology, 74 Oji, Kitainayazuma, Seika, Kyoto619-0244, Japan
Masashi Hirai
Affiliation:
Graduate School of Agriculture, Kyoto Prefectural University, Seika, Kyoto619-0244, Japan Kyoto Prefectural Institute of Agricultural Biotechnology, 74 Oji, Kitainayazuma, Seika, Kyoto619-0244, Japan
Akio Kaneko
Affiliation:
Kyoto Botanical Garden, Shimogamo, Sakyo-ku606-0823, Japan
Daizo Tanaka
Affiliation:
Kyoto Flower Center, Seika, Kyoto619-0244, Japan
Kumaji Kasumi
Affiliation:
Kyoto Flower Center, Seika, Kyoto619-0244, Japan
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

The water lotus, genus Nelumbo, contains two species, the sacred (Nelumbo nucifera) and American lotuses (Nelumbo lutea). Hundreds of flowering lotus cultivars are currently known. However, their classification is unclear. For the classification of Nelumbo cultivars, in addition to 35 simple sequence repeat (SSR) markers recently developed, we have developed 17 and 16 of new Nelumbo SSR markers from SSR-enriched genomic libraries and expressed sequence tag (EST) data, respectively. Out of these 68 SSRs, along with SSRs recently published by others, 52 showed clear polymorphisms in 98 Nelumbo samples. A total of 300 alleles were observed, ranging from 2 to 11 alleles per locus, with an average of 5.77. Alleles specific for the American lotus-derived cultivars and a cluster of the American lotus-derived cultivars on a neighbour-joining tree confirmed genetic differences between N. lutea and N. nucifera. In addition, a possible differentiation between Chinese and Japanese cultivars was also suggested. Parentage analysis using the SSR markers confirmed four known parentages and predicted currently-unknown parentages of six cultivars. The present data have demonstrated that site-specific, co-dominant SSR markers enable more accurate classification, identification and comparison of Nelumbo species.

Keywords

lotusneighbour-joining treeNelumbosimple sequence repeat (SSR)
Type
Research Article
Information
Plant Genetic Resources , Volume 7 , Issue 3 , December 2009 , pp. 260 - 270
Copyright
Copyright © NIAB 2009

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

Borsch, T and Barthlott, W (1994) Classification and distribution of the genus Nelumbo Adans (Nelumbonaceae). Beiträge zur Biologie der Pflanzen 68: 421–450.Google Scholar
Bowcock, AM, Ruiz-Linares, A, Tomfohrde, J, Minch, E, Kidd, JR and Cavalli-Sforza, LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455–457.CrossRefGoogle ScholarPubMed
Chen, Y, Zhou, R, Lin, X, Wu, K, Qian, X and Huang, S (2008) ISSR analysis of genetic diversity in sacred lotus cultivars. Aquatic Botany 89: 311–316.CrossRefGoogle Scholar
Felsenstein, J (2007) PHYLIP (Phylogeny Inference Package) Version 3.67. Seattle, USA: Department of Genome Sciences, University of Washington.Google Scholar
Guo, HB, Li, SM, Peng, J and Ke, WD (2007) Genetic diversity of Nelumbo accessions revealed by RAPD. Genetic Resources and Crop Evolution 54: 741–748.CrossRefGoogle Scholar
Han, YC, Teng, CZ, Chang, FH, Robert, GW, Zhou, MQ, Hu, ZL and Song, YC (2007a) Analyses of genetic relationships in Nelumbo nucifera using nuclear ribosomal ITS sequence data, ISSR and RAPD markers. Aquatic Botany 87: 141–146.CrossRefGoogle Scholar
Han, YC, Teng, CZ, Zhong, S, Zhou, MQ, Hu, ZL and Song, YC (2007b) Genetic variation and clonal diversity in populations of Nelumbo nucifera (Nelumbonaceae) in central China detected by ISSR markers. Aquatic Botany 86: 69–75.CrossRefGoogle Scholar
Han, YC, Teng, CZ, Wahiti, GR, Zhou, MQ, Hu, ZL and Song, YC (2009) Mating system and genetic diversity in natural populations of Nelumbo nucifera (Nelumbonaceae) detected by ISSR markers. Plant Systematics and Evolution 277: 13–20.CrossRefGoogle Scholar
Huang, J (2004) Cultivar identification, classification and assessment of genetic diversity of lotus (Nelumbo) with molecular markers. PhD Thesis, Tottori University.Google Scholar
Huang, J, Tanabe, K and Itai, A (2003) Identification of flowering lotus cultivars by ISSR (inter-simple sequence repeat) markers. Horticultural Research (Japan) 2: 259–264.CrossRefGoogle Scholar
Huang, J, Tanabe, K and Itai, A (2004) Identification of parent-offspring correlation and presumption of pollen parent in lotus with ISSR markers. Horticultural Research (Japan) 3: 251–256.CrossRefGoogle Scholar
Kalinowski, ST, Taper, ML and Marshall, TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16: 1099–1106.CrossRefGoogle ScholarPubMed
Kanazawa, A, Watanabe, S, Nakamoto, T, Tsutsumi, N and Hirai, A (1998) Phylogenetic relationships in the genus Nelumbo based on polymorphism and quantitative variations in mitochondrial DNA. Genes and Genetic Systems 73: 39–44.CrossRefGoogle Scholar
Kaneko, A (2002) Hundreds of Flowering Lotuses. Nakagyo-ku, Kyoto, Japan: Yoshida Printing (in Japanese).Google Scholar
Katori, M, Nomura, K, Watanabe, K and Yoneda, K (2003) Genetic relationships of flowering lotus (Nelumbo spp.) based on RAPD markers. Horticultural Research (Japan) 2: 153–156.CrossRefGoogle Scholar
Kubo, N, Hirai, M, Kaneko, A, Tanaka, D and Kasumi, K (2009) Development and characterization of simple sequence repeat (SSR) markers in the water lotus (Nelumbo nucifera). Aquatic Botany 90: 191–194.CrossRefGoogle Scholar
Minch, E, Ruiz-Linares, A, Goldstein, D, Feldman, M and Cavalli-Sforza, LL (1998) Microsat (Version 1.5): A Computer Program for Calculating Various Statistics on Microsatellite Allele Data. Stanford, USA: Department of Genetics, School of Medicine, Stanford University. Available online only at http://hpgl.stanford.edu/projects/microsat/.Google Scholar
Nunome, T, Negoro, S, Miyatake, K, Yamaguchi, H and Fukuoka, H (2006) A protocol for the construction of microsatellite enriched genomic library. Plant Molecular Biology Reporter 24: 305–312.CrossRefGoogle Scholar
Pan, L, Quan, Z, Li, S, Liu, H, Huang, X, Ke, W and Ding, Y (2007) Isolation and characterization of microsatellite markers in the sacred lotus (Nelumbo nucifera Gaertn.). Molecular Ecology Notes 7: 1054–1056.CrossRefGoogle Scholar
Peng, Y, Han, Y, Wang, L, Teng, C, Zhou, M, Hu, Z and Song, Y (2004) Genetic diversity in lotus (Nelumbo) accessions revealed by AFLP technique. Molecular Plant Breeding 2: 823–827.Google Scholar
Savolainen, V and Chase, MW (2003) A decade of progress in plant molecular phylogenetics. Trends in Genetics 19: 717–724.CrossRefGoogle ScholarPubMed
Tian, HL, Chen, XQ, Wang, JX, Xue, JH, Wen, J, Mitchell, G and Zhou, SL (2008a) Development and characterization of microsatellite loci for lotus (Nelumbo nucifera). Conservation Genetics 9: 1385–1388.CrossRefGoogle Scholar
Tian, HL, Xue, JH, Wen, J, Mitchell, G and Zhou, SL (2008b) Genetic diversity and relationships of lotus (Nelumbo) cultivars based on allozyme and ISSR markers. Scientia Horticulturae (Amsterdam) 116: 421–429.CrossRefGoogle Scholar
Uchida, M (2006) Matao Uchida Anthology, Lotuses in Ogura-ike. Chiyoda-ku, Tokyo, Japan: Nishida Shoten Publishers (in Japanese).Google Scholar
Varshney, RK, Graner, A and Sorrells, ME (2005) Genic microsatellite markers in plants: features and applications. Trends in Biotechnology 23: 48–55.CrossRefGoogle ScholarPubMed
Wang, Q and Zhang, X (2005) Lotus Flower Cultivars in China. Beijing: China Forestry Publishing House.Google Scholar
Watanabe, S (1990) The Fascinating World of Lotus. Chiyoda-ku, Tokyo: Parks and Open Space Association.Google Scholar
Xue, J, Zhuo, L and Zhou, S (2006) Genetic diversity and geographic pattern of wild lotus (Nelumbo nucifera) in Heilongjiang Province. Chinese Science Bulletin 51: 421–432.CrossRefGoogle Scholar
Yeh, FC, Yang, RC, Boyle, TJB, Ye, ZH and Mao, JX (1997) POPGENE, the user-friendly shareware for population genetic analysis. Alberta, Canada: Molecular Biology and Biotechnology Centre, University of Alberta. Available at http://www.ualberta.ca/~fyeh/index.htm.Google Scholar
Zou, YP, Cai, ML, Wang, XD and Xu, BM (1998) RAPD analysis of germplasm in ancient ‘Taizi lotus’ and modern Chinese lotus. Acta Botanica Sinica 40: 163–168.Google Scholar
Supplementary material: Image

Kubo supplementary material

Figure1.jpg

Download Kubo supplementary material(Image)
Image 366.8 KB
Supplementary material: File

Kubo supplementary material

Table2.xls

Download Kubo supplementary material(File)
File 35.8 KB
Supplementary material: File

Kubo supplementary material

Table3.xls

Download Kubo supplementary material(File)
File 43 KB
Supplementary material: File

Kubo supplementary material

Table4.xls

Download Kubo supplementary material(File)
File 15.4 KB