Genetic Analysis of Litchi (Litchi Chinensis Sonn.) in Southern China by Improved Random Amplified Polymorphic DNA (RAPD) and Inter-simple Sequence Repeat (ISSR)

Overview

Journal Mol Biol Rep

Specialty Molecular Biology

Date 2014 Sep 25

PMID 25249227

Citations 3

Authors

Yan Long

Jingliang Cheng

Zhiqiang Mei

Ling Zhao

Chunli Wei

Shelly Fu

Md Asaduzzaman Khan

Junjiang Fu

Affiliations

Soon will be listed here.

Abstract

Litchi (Litchi chinensis Sonn., L. chinensis), a type of tree growing in most areas of southern China, produces an edible fruit that is also a source of traditional medicine. Genetic identification of litchi species or cultivars using molecular markers is very important. In this study, a total of six litchi samples from Fujian, Hainan, Guangdong, Guangxi and Sichuan province, as well as one wild Dimocarpus confinis (D. confinis) sample from Guangxi province were collected for genetic analysis. The cluster dendrograms were constructed for genetic analysis on the basis of DNA amplification results by RAPD and ISSR. The improved RAPD amplified DNA with consistent and clear banding patterns. A total of 176 bands were found, indicating a 72.7 % polymorphism in L. chinensis DNA samples. Significant genetic distances were found among the different species or cultivars, with an index of similarity coefficient ranging from 0.59 to 0.87. Similar to RAPD results, ISSR analysis of the L. chinensis DNA samples showed a range of 0.70-0.93 similarity coefficients. The genetic distance between Hainan sample and Sichuan samples was the farthest, which is consistent with their geographic distance. Furthermore, the index of similarity coefficient between D. confinis and L. chinensis was 0.35-0.41 by RAPD and 0.38-0.48 by ISSR, indicating that these two species have significant genetic difference. This study reveals the high level of genetic differences between different litchi species or cultivars, and confirms the significance of the improved RAPD method in genetic characterization of organisms. Taken together, the improved RAPD combined with ISSR analysis can be used frequently for the genetic diversity, germplasm resources preservation, molecular-assisted breeding, and genetic characterization of various organisms.

Citing Articles

Genetic Analysis of L. by Random Amplified Polymorphic DNA (RAPD) and Intersimple Sequence Repeat (ISSR).

Li J, Gao G, Li B, Li B, Lu Q Genet Res (Camb). 2022; 2022:2409324.

PMID: 35528220 PMC: 9038437. DOI: 10.1155/2022/2409324.

Molecular authentication of Tetrastigma hemsleyanum from its adulterant species using ISSR, CAPS, and ITS2 barcode.

Peng X, Wu X, Ji Q, Yang R, Li Y Mol Biol Rep. 2016; 43(8):785-94.

PMID: 27245064 DOI: 10.1007/s11033-016-4023-x.

Genetic Authentication of Gardenia jasminoides Ellis var. grandiflora Nakai by Improved RAPD-Derived DNA Markers.

Mei Z, Zhou B, Wei C, Cheng J, Imani S, Chen H Molecules. 2015; 20(11):20219-29.

PMID: 26569205 PMC: 6331946. DOI: 10.3390/molecules201119687.

References

Pachuau L, Atom A, Thangjam R . Genome classification of Musa cultivars from northeast India as revealed by ITS and IRAP markers. Appl Biochem Biotechnol. 2014; 172(8):3939-48. DOI: 10.1007/s12010-014-0827-0. View

Khadivi-Khub A, Soorni A . Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers. Mol Biol Rep. 2014; 41(6):4007-16. DOI: 10.1007/s11033-014-3269-4. View

Varela E, Lima J, Galdino A, Pinto L, Bezerra W, Nunes E . Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from internal transcribed spacer sequences from nuclear ribosomal DNA. Phytochemistry. 2003; 65(1):59-69. DOI: 10.1016/j.phytochem.2003.08.005. View

Agarwal M, Shrivastava N, Padh H . Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 2008; 27(4):617-31. DOI: 10.1007/s00299-008-0507-z. View

Duan X, Wu G, Jiang Y . Evaluation of the antioxidant properties of litchi fruit phenolics in relation to pericarp browning prevention. Molecules. 2007; 12(4):759-71. PMC: 6149334. DOI: 10.3390/12040759. View

Hsu C, Lin C, Huang C, Lin Y, Chou J, Tsia Y . Induction of apoptosis and cell cycle arrest in human colorectal carcinoma by Litchi seed extract. J Biomed Biotechnol. 2012; 2012:341479. PMC: 3470890. DOI: 10.1155/2012/341479. View

Noh J, Kim H, Park C, Fujii H, Yokozawa T . Hypolipidaemic and antioxidative effects of oligonol, a low-molecular-weight polyphenol derived from lychee fruit, on renal damage in type 2 diabetic mice. Br J Nutr. 2010; 104(8):1120-8. DOI: 10.1017/S0007114510001819. View

Fu J, Yang L, Khan M, Mei Z . Genetic characterization and authentication of Lonicera japonica Thunb. by using improved RAPD analysis. Mol Biol Rep. 2013; 40(10):5993-9. DOI: 10.1007/s11033-013-2703-3. View

Hess J, Kadereit J, Vargas P . The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Mol Ecol. 2000; 9(7):857-68. DOI: 10.1046/j.1365-294x.2000.00942.x. View

10.

Huang F, Zhang R, Yi Y, Tang X, Zhang M, Su D . Comparison of physicochemical properties and immunomodulatory activity of polysaccharides from fresh and dried litchi pulp. Molecules. 2014; 19(4):3909-25. PMC: 6270829. DOI: 10.3390/molecules19043909. View

11.

Mei Z, Fu S, Yu H, Yang L, Duan C, Liu X . Genetic characterization and authentication of Dimocarpus longan Lour. using an improved RAPD technique. Genet Mol Res. 2014; 13(1):1447-55. DOI: 10.4238/2014.March.6.3. View

12.

Sharma P, Joshi N, Sharma A . Isolation of genomic DNA from medicinal plants without liquid nitrogen. Indian J Exp Biol. 2010; 48(6):610-4. View

13.

Noormohammadi Z, Hasheminejad-Ahangarani Farahani Y, Sheidai M, Ghasemzadeh-Baraki S, Alishah O . Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers. Genet Mol Res. 2013; 12(1):256-69. DOI: 10.4238/2013.January.30.12. View

14.

Su D, Zhang R, Hou F, Zhang M, Guo J, Huang F . Comparison of the free and bound phenolic profiles and cellular antioxidant activities of litchi pulp extracts from different solvents. BMC Complement Altern Med. 2014; 14:9. PMC: 3893551. DOI: 10.1186/1472-6882-14-9. View

15.

Wang X, Yuan S, Wang J, Lin P, Liu G, Lu Y . Anticancer activity of litchi fruit pericarp extract against human breast cancer in vitro and in vivo. Toxicol Appl Pharmacol. 2006; 215(2):168-78. DOI: 10.1016/j.taap.2006.02.004. View

16.

Xu L, Xue J, Wu P, Wang D, Lin L, Jiang Y . Antifungal activity of hypothemycin against Peronophythora litchii in vitro and in vivo. J Agric Food Chem. 2013; 61(42):10091-5. DOI: 10.1021/jf4030882. View

17.

G Williams J, Kubelik A, Livak K, Rafalski J, Tingey S . DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990; 18(22):6531-5. PMC: 332606. DOI: 10.1093/nar/18.22.6531. View

18.

Ichinose T, Musyoka T, Watanabe K, Kobayashi N . Evaluation of antiviral activity of Oligonol, an extract of Litchi chinensis, against betanodavirus. Drug Discov Ther. 2014; 7(6):254-60. DOI: 10.5582/ddt.2013.v7.6.254. View

19.

Yang D, Chang Y, Chen Y, Liu S, Hsu C, Lin J . Antioxidant effect and active components of litchi (Litchi chinensis Sonn.) flower. Food Chem Toxicol. 2012; 50(9):3056-61. DOI: 10.1016/j.fct.2012.06.011. View

20.

Noh J, Park C, Yokozawa T . Treatment with oligonol, a low-molecular polyphenol derived from lychee fruit, attenuates diabetes-induced hepatic damage through regulation of oxidative stress and lipid metabolism. Br J Nutr. 2011; 106(7):1013-22. DOI: 10.1017/S0007114511001322. View