Horticulture, Environment, and Biotechnology

, Volume 60, Issue 1, pp 95–103 | Cite as

The establishment of a DNA fingerprinting database for 73 varieties of Lactuca sativa capitate L. using SSR molecular markers

  • Huiyan Zhou
  • Penghang Zhang
  • Jiang Luo
  • Xueying Liu
  • Shuangxi Fan
  • Chaojie Liu
  • Yingyan HanEmail author
Research Report


Head lettuce originating near the Mediterranean coast was introduced to China in the fifth century. It is difficult to identify different varieties of head lettuce due to their close genetic relationships. Simple sequence repeats (SSR) technology is a practical method that has been widely used in variety identification, fingerprint construction and genetic diversity analysis. In this paper, 23 pairs of SSR primers were selected to identify and analyse 73 varieties of head lettuce. The results identified a total of 117 mutated alleles detected in 23 loci, with the number of each loci ranging from 2 to 11, with an average of 5.1 mutated alleles per locus. Additionally, 152 genotypes were detected in 23 loci, with an average of 6.6 genotypes per locus derived from a range of 2–13. The polymorphism information content ranged from 0.071 to 0.702, with an average of 0.499. The selected primer pairs could clearly reflect the genotypic diversity level of the 73 head lettuce varieties tested, and can be used in the detection and analysis of the head lettuce varieties. The results of our sequence analysis also showed that these 73 varieties of head lettuce could be effectively identified by a combination of 19 primer pairs even though the genetic similarity among the 73 varieties ranged from 0.647 to 0.991, with an average of 0.798. Based on a capillary electrophoresis platform, a DNA fingerprinting database of 73 head lettuce varieties was established.


Head lettuce Lactuca sativa L. SSR Variety identification DNA fingerprinting database 



This work was supported by National Natural Science Foundation of China [31401883], the Beijing Innovation Consortium of Agriculture Research System (BAIC08), and the Beijing Municipal National Science Foundation (KZ201610020019).

Supplementary material

13580_2018_102_MOESM1_ESM.jpg (78 kb)
Trend analysis: the variety differentiation of primer pair combination (JPEG 78 kb)
13580_2018_102_MOESM2_ESM.pdf (74 kb)
DNA fingerprints of 73 lettuce varieties (PDF 74 kb)
13580_2018_102_MOESM3_ESM.pdf (102 kb)
Allelic loci of each primer pair (PDF 101 kb)


  1. Aljumaili S, Rafi M, Latif M et al (2018) Genetic diversity of aromatic rice germplasm revealed by SSR markers. Hindawi BioMed Res Int. Google Scholar
  2. Bao L, Lin G, Zhao D et al (2016) Analysis of complex agronomic traits of the new main rice CMS lines. J Sichuan Agric Univ 34:14–18. Google Scholar
  3. Baraket G, Chatti K, Saddoud O et al (2011) Comparative assessment of SSR and AFLP markers for evaluation of genetic diversity and conservation of fig, Ficus carica L., genetic resources in Tunisia. Plant Mol Biol Rep 29:121–184. CrossRefGoogle Scholar
  4. Beharav A, Maras M, Kitner M et al (2010) Comparison of three genetic similarity coefficients based on dominant markers from predominantly self-pollinating species. Biol Plant 54:54–60. CrossRefGoogle Scholar
  5. Boriss H, Brunke H (2005) Commodity profile: lettuce. University of California.
  6. Bradley F, Barbara B, Martin D (2009) The organic gardener’s handbook of natural pest and disease control. Emmaus, Rodale, p 129. ISBN 978-1-60529-677-7Google Scholar
  7. Chen J, Mao R, Hu X et al (2016) Identification of SSR markers linked to high oleic content in peanut (Arachis hypogaea L.) by RIL population. J Peanut Sci 45:1–7. Google Scholar
  8. Cheng B, Xia J, Gong J et al (2011) Application of capillary electrophoress detection with fluorescent SSR markers in rice DNA fingerprint identification. Chin J Rice Sci 6:672–676. Google Scholar
  9. Cristofani YM, Novelli VM, Bastianel M et al (2011) Transferability and level of heterozygosity of microsatellite markers in citrus species. Plant Mol Biol Rep 29:418–423. CrossRefGoogle Scholar
  10. Guimarães A, Amaral Júnior A, Almeida F et al (2018) Population structure and impact of recurrent selection on popcorn using EST-SSR markers. Genet Plant Breed Acta Sci Agron 40:e35218. CrossRefGoogle Scholar
  11. Hendre PS, Aggarwal RK (2014) Development of genic and genomic SSR markers of robusta coffee (Coffea canephora Pierre Ex A. Froehner). PLoS ONE 9:e113661. CrossRefGoogle Scholar
  12. Hong J, Kwon Y, Mishra R et al (2015) Construction of EST-SSR databases for effective cultivar identification and their applicability to complement for lettuce (Lactuca sativa L.) distinctness test. Am J Plant Sci 06:113–125. CrossRefGoogle Scholar
  13. Ishii T, Xu Y, McCouch S (2001) Nuclear- and Chloroplast-microsatellite variation in A-genome species of rice. Genome 44:658–666. CrossRefGoogle Scholar
  14. Jemelková M, Kitner M, Křístková E et al (2015) Biodiversity of Lactuca aculeata germplasm assessed by SSR and AFLP markers, and resistance variation to Bremia lactucae. Biochem Syst Ecol 61:344–356. CrossRefGoogle Scholar
  15. (2018) Kings seeds-vegetable seeds | A leading supplier of vegetable seeds and flowers seeds |
  16. Kuang M, Yang W, Xu H (2011) Construction of DNA fingerprinting and analysis of genetic diversity with SSR markers for cotton major cultivars in China. Sci Agric Sin 44:20–27. Google Scholar
  17. Lai Y, Wang P, Fan G et al (2013) Genetic diversity and association analysis using SSR markers in barley. Sci Agric Sin 02:233–242. Google Scholar
  18. Luo R, Wu W, Zhang Y et al (2010) SSR marker and its application to crop genetics and breeding. Genomics Appl Biol 29:137–143Google Scholar
  19. Luo W, Zhang L, Yang K et al (2013) Construction of genetic linkage map using SSR molecular markers in azuki bean (Vigna angularis Ohwi and Ohashi). Sci Agric Sin 17:3534–3544. Google Scholar
  20. Rauscher G, Simko L (2013) Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes. BMC Plant Biol 13:1–11. CrossRefGoogle Scholar
  21. Schulman A (2007) Molecular markers to assess genetic diversity. Euphytica 158:313–321. CrossRefGoogle Scholar
  22. Simoons FJ (1991) Food in China: a cultural and historical inquiry. CRC Press, Boco Raton, pp 147–148. ISBN 0-8493-8804-XGoogle Scholar
  23. Souza R, Rezende R, Hachmann T et al (2017) Head lettuce production in greenhouse under fertigation with nitrogen and potassium silicate. Acta Sci Agron 39:211. CrossRefGoogle Scholar
  24. Sun J, Liu T, Guo B et al (2006) Development of SSR primers from EST sequences and their application in germplasm identification of Porphyra lines (Rhodophyta). Eur J Phycol 41:329–336. CrossRefGoogle Scholar
  25. Sun Q, Ma W, Ma S et al (2011) Characteristics of SSRs derived from ESTs and development of EST-SSR markers in Litchi (Litchi chinensis Sonn.). Sci Agric Sin 19:4037–4049. Google Scholar
  26. Swapna M, Sivaraju K, Sharma RK et al (2011) Single-strand conformational polymorphism of EST-SSRs: a potential tool for diversity analysis and varietal identification in sugarcane. Plant Mol Biol Rep 29:505–513. CrossRefGoogle Scholar
  27. Tian D, Lin Y, Liu H et al (2013) Fingerprinting analysis of 123 rice varieties based on the new SSR core markers. Mol Plant Breed 11:20–29Google Scholar
  28. Wang F, Zhao J, Guo J et al (2003) Series of research on establishing DNA fingerprinting pool of Chinese new maize cultivars. The establishment of a standard SST system fitting for maize cultivars’ identification. J Maize Sci 11:3–6. Google Scholar
  29. Wang X, Jiang S, Shang’guan L et al (2010) Development of EST-derived SSR markers for pear and evaluation of their application in pear genetic diversity analysis. Sci Agric Sin 24:5079–5087. Google Scholar
  30. Wang J, Du J, Liu J et al (2016) Genetic diversity analysis of 36 Alfalfa accessions based on SSR markers. Chin J Grassl 2:20–25. Google Scholar
  31. Wang L, Chen D, Huang C et al (2017) Application of SSR molecular marker technique in plant research. J Anhui Agric Sci 45:123–126. Google Scholar
  32. Wang S, Wang B, Huang X et al (2018) Association analysis between microsatellite loci and phenotypic traits in Lactuca sativa L. North Hortic 5:1–6. CrossRefGoogle Scholar
  33. Wu S (2016) Analysis of genetic diversity of gliadins in Thinopyrum elongatum. J Henan Agric Sci 3:34–38. Google Scholar
  34. Wu M, Niu Q, Tian Y et al (2014) SSR primers screening and analyzing for watermelon variety identification. Crops 05:38–42. Google Scholar
  35. Xiao J, Zhao J, Liu M et al (2015) Genome-wide characterization of simple sequence repeat (SSR) loci in Chinese Jujube and Jujube SSR primer transferability. PLoS ONE 10:e0127812. CrossRefGoogle Scholar
  36. Xu S, Yan T, Zhong R et al (2017) Analysis on genetic differences between parents of two-line medium indica hybrid rice by SSR markers. Agric Sci Technol 18:1800–1804Google Scholar
  37. Zeng L, Kwon T, Liu X et al (2004) Genetic diversity analysed by microsatellite markers among rice (Oryza sativa L.) genotypes with different adaptations to saline soils. J Plant Sci 166:1275–1285. CrossRefGoogle Scholar
  38. Zhang Q, Li J, Zhao Y et al (2012) Evaluation of genetic diversity in Chinese wild apple species along with apple cultivars using SSR markers. Plant Mol Biol Rep 29:418–423. Google Scholar
  39. Zhang G, You Y, Lou Y et al (2016) Characteristic analysis of EST-SSR markers in head lettuce (Lactuca sativa). Agric Sci Technol 17:2682–2685Google Scholar
  40. Zhao J, Wang F, Guo J et al (2003) Series of research on establishing DNA fingerprinting pool of Chinese new maize cultivars-confirmation of a set of SSR core primer pairs. J Maize Sci 11:3–5Google Scholar

Copyright information

© Korean Society for Horticultural Science 2018

Authors and Affiliations

  • Huiyan Zhou
    • 1
  • Penghang Zhang
    • 1
  • Jiang Luo
    • 1
  • Xueying Liu
    • 1
  • Shuangxi Fan
    • 1
  • Chaojie Liu
    • 1
  • Yingyan Han
    • 1
    Email author
  1. 1.Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina

Personalised recommendations