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Journal of Heredity Advance Access published online on August 7, 2009
Journal of Heredity, doi:10.1093/jhered/esp070
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© The American Genetic Association. 2009. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Development of Novel EST–SSRs from Sacred Lotus (Nelumbo nucifera Gaertn) and Their Utilization for the Genetic Diversity Analysis of N. nucifera

Lei Pan, Qiuju Xia, Zhiwu Quan, Honggao Liu, Weidong Ke, and Yi Ding

From the Key Laboratory of Ministry of Education for Plant Development Biology, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China (Pan, Xia, Quan, Liu, and Ding); and the Wuhan National Germplasm Repository for Aquatic Vegetables, Wuhan Institute of Vegetable Sciences, Wuhan 430065, People's Republic of China (Ke)

Address correspondence to Yi Ding at the address above, or e-mail: yiding{at}whu.edu.cn.

Expressed sequence tags (ESTs) provide a valuable resource for the development of simple sequence repeat (SSR) or microsatellite markers. This study identified SSRs within ESTs from Nelumbo nucifera (lotus or sacred lotus), developed markers from them, and assessed the potential of those markers for diversity analysis. Within 2207 ESTs from N. nucifera downloaded from GenBank, 1483 unigenes (303 contigs and 1180 singletons) were identified. After eliminating for redundancy, 125 SSR-containing ESTs were derived, and 71 unique SSRs were detected with an average density of one SSR per 13.04 kb. Dinucleotide repeats were the dominant motif in N. nucifera, whereas the sequences AG/TC/GA/CT, AAG/TTC/GAT/AGA, and AAAGCC were the most frequent of di-, tri-, and hexanucleotide motifs, respectively. The AG/TC (40.85%) and AAG (5.63%) motifs were predominant for the di- and trinucleotide repeats, respectively. Sixty-two SSR-containing ESTs were suitable for primer design. From these sequences, 23 EST–SSR markers were developed and were applied to 39 cultivated varieties of N. nucifera, 10 accessions of wild N. nucifera, and 1 accession of Nelumbo lutea (American lotus). Genetic diversity and genetic relationships were examined by constructing unweighted pair-group method with arithmetic average dendrograms and principal coordinates analysis plots based on SSR polymorphisms. Results indicated genetic differentiation between cultivated and wild lotus and between seed lotus cultivars and rhizome lotus cultivars. These EST–SSR markers will be useful for further studies of the evolution and diversity of Nelumbo.

Key Words: expressed sequence tags • genetic diversity • microsatellite • Nelumbo nucifera

Corresponding Editor: J. Perry Gustafson

Received January 19, 2009
Revised June 24, 2009
Accepted July 14, 2009


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