Identification of lotus cultivars using DNA fingerprinting

Jianhua Xue1 Li Jiang2 Xiaolin Ma2 Yanhong Bing1 Sichen Zhao2 Keping Ma1

(1.State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093)
(2.Yuanmingyuan Administration, Haidian District, Beijing, Beijing 100084)

【Abstract】DNA fingerprinting is a fast and accurate method for cultivar identification, which can overcome the limitation of morphological traits. We used DNA fingerprinting to identify 72 lotus (Nelumbo) cultivars collected from the Resources Garden of the Yuanmingyuan Park in Beijing. We used 1,409 samples of N. nucifera and 58 samples of N. lutea as a genetic background reference. Fifteen out of 104 pairs of nucleus microsatellite primers (n SSR) and 2 out of 17 pairs of chloroplast microsatellite primers (cp SSR), for a total of 17 pairs of fluorescent primers, were selected as the barcode for fingerprint identification of the 72 lotus cultivars. For the 15 n SSR primers, 94 alleles were examined (with an average of 6.27). Out of the 94 alleles, 11 belong to N. lutea, 65 belong to N. nucifera, and the remaining 18 alleles could not be identified. The polymorphism information content (PIC) range between 0.389 9 and 0.802 3, with an average value of 0.574 8. For the two pairs of cp SSR primers, 13 haplotypes were examined. Among them, 9 haplotypes belong to N. nucifera and 4 haplotypes belong to N. lutea. Results of identification of all 17 pairs of primer markers showed that 19 cultivars included genes from N. lutea, and 8 cultivars had female parents from N. lutea. There were 36 cultivars (using 12 pairs of primers) which had at least one unique genotype. With a minimum of 8 pairs of primers, 68 cultivars could be distinguished. Among the 72 cultivars, four cultivars in two groups could not be distinguished based on the whole set of 17 primers. Using the core primer combination method, we developed specific DNA fingerprints for each of the 68 lotus cultivars. Based on the above results, we recommended 15 pairs of primers including 13 pairs of n SSR and 2 pairs of cp SSR as the core barcode for lotus cultivar identification.

【Keywords】 DNA fingerprint; microsatellites; Nelumbo; cultivar identification; molecular ID;

【DOI】

【Funds】 National Natural Science Foundation of China (31270262) Special Program for Science and Technology Basic Work (2013FY112300) Program for Beijing Municipal Science & Technology Commission (K2012004S)

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    References

    Archak S, Lakshminarayanareddy V, Nagaraju J(2007)High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa). Electrophoresis, 28, 2396-2405.

    Botstein D, White RL, Skolnick M, Davis RW(1980)Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32, 314-331.

    Chen CW, Cao K, Wang LR, Zhu GR, Fang WC(2011)Molecular ID establishment of main China peach varieties and peach related species. Scientia Agricultura Sinica, 44, 2081-2093. (in Chinese with English abstract)

    Faria MA, Nunes E, Oliveira MBPP(2008)Relative quantification of Vitis vinifera L. varieties in musts by microsatellite DNA analysis. European Food Research and Technology, 227, 845-850.

    Jeffreys AJ, Wilson V, Thein SL(1985a)Individual-specific‘fingerprints’of human DNA. Nature, 316, 76-79.

    Jeffreys AJ, Wilson V, Thein SL (1985b) Hypervariable ‘Minisatellite’ regions in human DNA. Nature, 314, 67-73.

    Kubo N, Hirai M, Kaneko A, Tanaka D, Kasumi K(2009)Development and characterization of simple sequence repeat (SSR) markers in the water lotus(Nelumbo nucifera). Aquatic Botany, 90, 191-194.

    Lai YP, Wang LR, He QL, Zhang ZF, Zhang XM, Du YY, Yu Y(2014)Screening of SSR core primers and fingerprinting construction of Brassica napus L. Southwest China Journal of Agricultural Sciences, 27, 2290-2299. (in Chinese with English abstract)

    Li Y, Svetlana P, Yao JX, Li CS (2014) A review on the taxonomic, evolutionary and phytogeographic studies of the lotus plant (Nelumbonaceae:Nelumbo). Acta Geologica Sinica, 88, 1252-1261.

    Liu K, Muse SV (2005) Power Marker:an integrated analysis environment for genetic marker analysis. Bioinformatics, 21, 2128-2129.

    Madhou M, Normand F, Bahorun T, Hormaza JI (2013) Fingerprinting and analysis of genetic diversity of litchi (Litchi chinensis Sonn. ) accessions from different germplasm collections using microsatellite markers. Tree Genetics&Genomes, 9, 387-396.

    Miura K, Ikegami S (2012) Photographic Reference Book of World Lotus Flowers. Bensei Publish Company, Tokyo. (in Japan)

    Ming R, Van Buren R, Liu YL, Yang M, Han YP, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li JP, Bowers JE, Tang HB, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao YN, Der JP, Zeng FC, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu QY, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia RZ, Chen NC, Arro J, Wai CM, Wafula E, Spence A, Han YN, Xu LM, Zhang JS, Peery R, Haus MJ, Xiong WW, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du CG, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, de Pamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li SH, Shen-Miller J(2013)Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14, R41.

    Nie XH, You CY, Li XF, Qin JH, Huang C, Guo HL, Wang XQ, Zhao WX, Lin ZX (2014) Construction of DNA fingerprinting and analysis of genetic diversity for Xinluzao cotton varieties. Acta Agronomica Sinica, 40, 2104-2117. (in Chinese with English abstract)

    Song HB, Cui XB, Ma HY, Zhu ZC, Luan FS (2012) Construction of DNA fingerprint database based on SSR marker for varieties (Lines) of Cucumis melo L. Scientia Agricultura Sinica, 45, 2676-2689. (in Chinese with English abstract)

    Tian HL, Chen XQ, Wang JX, Xue JH, Wen J, Mitchell G, Zhou SL (2008) Development and characterization of microsatellite loci for lotus (Nelumbo nucifera). Conservation Genetics, 9, 1385-1388.

    Wang QC, Zhang XY (2005) Lotus Flower Cultivars in China. China Forestry Publishing House, Beijing. (in Chinese)

    Wu ZY, Lu AM, Tang YC, Chen ZD, Li DZ (2003) The Families and Genera of Angiosperms in China. Science Press, Beijing. (in Chinese)

    Xue JH, Dong WP, Zhou SL (2012) Nelumbonaceae:Systematic position and species diversification revealed by the complete chloroplast genome. Journal of Systematics and Evolution, 50, 477-487.

    Xue JH, Wang S, Zhou SL (2012) Polymorphic chloroplast microsatellite loci in Nelumbo (Nelumbonaceae). American Journal of Botany, 99, E240-E244.

    Yang M, Han YN, Van Buren R, Ming R, Xu LM, Han YP, Liu YL (2012) Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar. BMC Genomics, 13, 653.

    Zhang XY, Chen LQ, Wang QC (2011) New Lotus Flower Cultivars in China I. China Forestry Publishing House, Beijing. (in Chinese)

    Zhao JR, Wang FG (2009) Research and Application of Maize Cultivars’DNA Fingerprint Identification Technology. China Agricultural Science and Technology Press, Beijing. (in Chinese)

    Zhao JR, Wang FG, Yi HM, Tian HL, Yang Y (2015) Progress of construction of Chinese maize varieties standard DNAfingerprint database. Crops, 165, 1-6. (in Chinese with English abstract).

    Zhao SJ, Zhu HJ, Lu XQ, He N, Liu WG(2014)Studies on DNA fingerprinting and genetic diversity of seedless watermelon (Citrullus lanatus) varieties using core simple se-quence repeat(SSR)markers. Journal of Agricultural Bio-technology, 22, 188-194. (in Chinese with English abstract)

This Article

ISSN:1005-0094

CN:11-3247/Q

Vol 24, No. 01, Pages 3-11

January 2016

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Abstract

  • 1 Materials and methods
  • 2 Results
  • 3 Discussion
  • Supplementary Material
  • References