Plant Genetic Resources

Research Article

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

Nakao Kuboa1a2 c1, Masashi Hiraia1a2, Akio Kanekoa3, Daizo Tanakaa4 and Kumaji Kasumia4

a1 Graduate School of Agriculture, Kyoto Prefectural University, Seika, Kyoto 619-0244, Japan

a2 Kyoto Prefectural Institute of Agricultural Biotechnology, 74 Oji, Kitainayazuma, Seika, Kyoto 619-0244, Japan

a3 Kyoto Botanical Garden, Shimogamo, Sakyo-ku 606-0823, Japan

a4 Kyoto Flower Center, Seika, Kyoto 619-0244, Japan


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.

(Received March 08 2009)

(Accepted April 05 2009)

(Online publication May 01 2009)


c1 Corresponding author. E-mail: