Investigation the efficiency of molecular markers to assess genetic diversity of Iranian tea clones

Document Type : Research Paper

Authors

1 Faculty of Agricultural sciences, University of Guilan

2 Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran

3 Assistant Professor, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Lahijan, Iran

4 Assistant Professor, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Lahijan, Iran.

Abstract

Objective
The genetic diversity of the 20 tea populations collected from the Tea Research Organization of Iran was evaluated using 20 microsatellite markers and 10 RAPD markers.
 
Materials and methods
Plant materials in this experiment were 20 tea clones selected from the Tea Research Institute of the Iran. DNA extraction from young leaf samples of tea populations was performed with a few changes using the CTAB method. In this study, 20 microsatellite markers and 10 RAPD markers were used to study the genetic variation of tea populations.
 
Results
The results showed that SSR and RAPD markers produced 105 and 160 polymorphic bands, respectively.Among the microsatellite markers, the MSE0143 and the MSG0681 primers with 9 bands and the MSG0610 primer with 2 bands produced the highest and the least number of amplified bands. MSG0681, MSE0113, MSG0403 markers with the highest amount of observed allele, effective allele, Nei index, Shannon index and PIC were identified as the most effective markers for analyzing genetic diversity in the studied tea genotypes. Among the RAPD markers, the OS-03 primer with 19 bands produced the highest number of bands and the OR-12 primer with 13 bands produced the least number of bands.
 
Conclusions
By comparing the mean PIC of the two marker systems, the microsatellite markers were more effective than RAPD markers. For example, the mean PIC value for SSR markers was measured 0.66 across the tea germplasm. By comparing QND and EMI indices, we found that microsatellite markers were superior to RAPD markers. Also, by comparing the results of cluster analysis of two markers, the microsatellite markers were better able to classify individuals based on their geographic origin.

Keywords

References

Ahuja P, Gulati A, Singh R et al. (2013) Science of Tea Technology. Scientific Publishers.
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, 171-184.
Bhardwaj P, Sharma R, Kumar R et al. (2014) SSR marker based DNA fingerprinting and diversity assessment in superior tea germplasm cultivated in Western Himalaya. In: Proc Indian Natn Sci Acad. pp. 157-162.
Boonerjee S, Islam MN, Hoque M et al. (2013) Genetic diversity analysis of eighteen tea (Camellia sinensis L.) clones of Bangladesh through RAPD. Plant Tissue Cult Biotechnol 23, 189-199.
Chen L, Yamaguchi S (2002) Genetic diversity and phylogeny of tea plant (Camellia sinensis) and its related species and varieties in the section Thea genus Camellia determined by randomly amplified polymorphic DNA analysis. J Hortic Sci Biotechnol 77, 729-732.
Cregan P, Schaap T (2010) Application of DNA Markers for Identification and Breeding of Perennial Fruit Crops I. Plant Breed Rev 76, 195.
Hartl DL, Clark AG, Clark AG (1997) Principles of population genetics. Sinauer associates Sunderland.
Heidari S, Marashi H, Farsi M et al. (2009) Assessment of genetic structure and variation of native Berberis populations of Khorasan provinces (Iran) using AFLP markers versus morphological markers. Iran J Biotechnol 7, 101-107.
Kaundun SS, Zhyvoloup A, Park Y-G (2000) Evaluation of the genetic diversity among elite tea (Camellia sinensis var. sinensis) accessions using RAPD markers. Euphytica 115, 7-16.
Kordrostami M, Rabiei B, Kumleh H (2016) Association analysis, genetic diversity and haplotyping of rice plants under salt stress using SSR markers linked to SalTol and morpho-physiological characteristics. Plant Syst Evol 302, 871-890.
Lai J-A, Yang W-C, Hsiao J-Y (2001) An assessment of genetic relationships in cultivated tea clones and native wild tea in Taiwan using RAPD and ISSR markers. Bot Bul Acad Sin 42, 93-100.
Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Sunderland, MA: : Sinauer Associates, Inc., 1998. Pp.
Melchinger A (1999) Genetic diversity and heterosis. The genetics and exploitation of heterosis in crops. Crop Sci Soc Am, Madison, 99-118.
Naghavi MR, Qarayazi B, Hosseini Salekdeh Q (2009) Molecular markers. Tehran University Press.
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci 70, 3321-3323.
Nili A, Rabiei B, Allahgholipour M et al. (2017) Assessing molecular diversity and genetic relationships among rice (Oryza sativa L.) varieties. Cereal Res 7, 33-50.
Poehlman JM (2013) Breeding field crops. Springer Science & Business Media.
Powell W, Morgante M, Andre C et al. (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2, 225-238.
Quartz (2016) Annual per capita tea consumption worldwide as of 2016, by leading countries (in pounds). In Statista - The Statistics Portal.
Rezaee E, Mirlohi M, Hassanzadeh A et al. (2016) Factors affecting tea consumption pattern in an urban society in Isfahan, Iran. J Educ Health Promot 5, 1-5.
Roy S, Chakraborty B (2009) Genetic diversity and relationships among tea (Camellia sinensis) cultivars as revealed by RAPD and ISSR based fingerprinting. Indian J Biotechnol 8, 370-376.
Shannon CE (2001) A mathematical theory of communication. ACM SIGMOBILE Mob Comput Commun Rev 5, 3-55.
Sivapalan P, Kulasegaram S, Kathiravetpillai A (1986) Handbook on tea. Tea Research Institute of Sri Lanka.
Tan L-Q, Peng M, Xu L-Y et al. (2015) Fingerprinting 128 Chinese clonal tea cultivars using SSR markers provides new insights into their pedigree relationships. Tree Genet Genomes 11, 90.
Taniguchi I (2014) Development of Genomic Resources and Core Collections of Germplasm for Tea Breeding University of Tsukuba.
Varshney RK, Chabane K, Hendre PS et al. (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173, 638-649.
Wachira FN, Kamunya S, Karori S et al. (2013) The tea plants: botanical aspects. In: Tea in health and disease prevention. Elsevier. pp. 3-17.
Wang RJ, Gao XF, Kong XR et al. (2016) An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers. Springer Plus 5, 1152.
Weising K, Nybon H, Wolff K et al. (2005) DNA fingerprinting in plants: Principles, Methods, and Applications. Boca Raton: CRC Press, 472 pp.
Xu Y (2010) Molecular Plant Breeding., CABI Publishing.
Yao M-Z, Ma C-L, Qiao T-T et al. (2012) Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers. Tree Genet Genomes 8, 205-220.
Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 12, 563-584.
Zhang Y, Zhang X, Chen X et al. (2018) Genetic diversity and structure of tea plant in Qinba area in China by three types of molecular markers. Hereditas 155, 22.
 
 
Agricultural Biotechnology Journal
Volume 11, Issue 2
Volume 11, No 2
September 2019
Pages 79-100

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