Investigation of Genetic Diversity and Structure Analysis of Different Citrus Genotypes Using ISSR Markers

Abouzari, Abouzar; Dadras, Ahmad Reza; Golein, Behrouz; Tajvar, Yahya

doi:10.52547/pgr.7.2.2

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Volume 7, Issue 2 (2021)

pgr 2021, 7(2): 13-24

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Investigation of Genetic Diversity and Structure Analysis of Different Citrus Genotypes Using ISSR Markers

Abouzar Abouzari ^*

, Ahmad Reza Dadras

, Behrouz Golein

, Yahya Tajvar

Crop and Horticultural Science Research Department, Mazandaran Agricultural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sari, Iran , a.abouzari@areeo.ac.ir

Abstract: (9721 Views)

In breeding programs, it is necessary having knowledge of the relatedness and genetic diversity in germplasm pools. The spread of cultivated regions and the high levels of production indicates citrus importance in the global economy. Therefore, 110 citrus genotypes were evaluated using 12 ISSR markers. Overall, 154 polymorphic bands were scored with an average of 12.8 alleles per primer. The polymorphism percentage ranged from 57 for the ISSR1 to 82 for the ISSR9. Averages of polymorphic information content (PIC), marker index (MI), gene diversity index (Nei), Shannon index (I) and number of effective alleles (Ne) were 0.48 ± 0.002, 6.14 ± 1.17, 0.42 ± 0.11, 0.61 ± 0.12 and 1.78 ± 0.27, respectively. Based on genetic diversity statistics, the studied population had high genetic diversity, and four markers (ISSR11, ISSR9, ISSR4, and ISSR5) had more potential for differentiation of genotypes. Cluster analysis and model-based structure analysis, divided the genotypes into five groups and four subpopulations based on the Neighbor-Joining method (NJ) and Bayesian approach, respectively. Based on both analyses, grouping of unknown genotypes and control cultivars in the same group probably confirms the assumption of a common genetic background between these genotypes. Results from the two analyses showed that Pummelo (C. maxima), Mandarin (C. reticulate), and Citron (C. medica), as three true citrus species, separated in different groups. In addition to the three true species, at least one species or another genus of citrus relatives is involved in the genetic makeup of the studied population. In this study, although both used analyses were effective in completing each other's information, by considering the degree of genetic mixing and the information of the origin of the genotypes, the effectiveness of model-based structure analysis in evaluating genetic relationships could be achieved.

Keywords: ISSR markers, Population structure analysis, Citrus, Phylogenetic relationships

Full-Text [PDF 671 kb] (1611 Downloads)

Type of Study: Research | Subject: Molecular genetics

References

1. Abouzari, A., Solouki, M., Golein, B., Fakheri, B.A., Sabouri, A. and Dadras, A.R. (2020). Unraveling the cryptic genetic variation and population structure of the citrus genotypes with unknown origin. Genetika, 52: 291-309.

2. Ahmed, S., Rattanpal, H., Kumari, P. and Singh, J. (2017) Study of genetic variability in Citrus fruit crop by molecular markers a review. Indian Journal of Pure & Applied Biosciences, 5: 111-128. [DOI:10.18782/2320-7051.2480]

3. Aziznia, R., Badakhshan, H., Javadi, T. and Zamani, S. (2020). Assessment of diversity in barley genotypes (Hordeum vulgare L.) based on beta-glucan content and issr markers. Plant Genetic Researches, 6(2): 97-110 (In Persian).

4. Awad, M.A., El-Alakmy, H.A., Abdalla, M.M. and ElDeep, M.D. (2019). Distinguishing of zygotic and nucellar seedlings in citrus rootstocks using issr technique. Sinai Journal of Applied Sciences, 8: 1-8.

5. Barkley, N.A., Roose, M.L., Krueger, R.R. and Federici, C.T. (2006). Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theoretical and Applied Genetics, 112: 1519-1531.

6. Bayer, R.J., Mabberley, D.J., Morton, C., Miller, C.H., Sharma, I.K., Pfeil, B.E., Rich, S., Hitchcock, R. and Sykes, S. (2009). A molecular phylogeny of the orange subfamily (Rutaceae: Aurantioideae) using nine cpDNA sequences. American Journal of Botany, 96: 668-685.

7. Bornet, B. and Branchard, M. (2001). Nonanchored inter simple sequence repeat (ISSR) markers: reproducible and specific tools for genome fingerprinting. Plant Molecular Biology Reporter, 19: 209-215.

8. Curk, F., Ancillo, G., Ollitrault, F., Perrier, X., Jacquemoud-Collet, J.P., Garcia-Lor, A., Navarro, L. and Ollitrault, P. (2015). Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties. PLOS ONE, 10: e0125628.

9. Edwards, K., Johnstone, C. and Thompson, C. (1991). A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Research, 19: 1349.

10. Evanno, G., Regnaut, S. and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14: 2611-2620.

11. Falush, D., Stephens, M. and Pritchard, J.K. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164: 1567-1587.

12. Fang, D. and Roose, M. (1997). Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theoretical and Applied Genetics, 95: 408-417.

13. Golein, A., Ghasemi, M., Fattahi Moghadam, J. and Gholamian, E. (2014). Genetic analysis between unknown Citrus accessions and commercially important cultivars using ISSR marker. Agricultural Biotechnology Journal, 5(4): 111-124 (In Persian).

14. Khiavi, S.J., Hamidoghli, Y., Golein, B. and Sabouri, A. (2015) Evaluation of genetic diversity in acid lime (Citrus aurantifolia swingle) genotypes using AFLP markers. Australian Journal of Crop Science, 9: 996-1002.

15. Kijas, J., Thomas, M., Fowler, J. and Roose, M. (1997). Integration of trinucleotide microsatellites into a linkage map of Citrus. Theoretical and Applied Genetics, 94: 701-706.

16. Krueger, R.R. and Navarro, L. (2007). Citrus Gerplasm Resources. In: Khan, I.A., Ed., Citrus Genetics, Breeding and Biotechnology. pp. 45-140. CABI, London, UK.

17. Li, X., Xie, R., Lu, Z. and Zhou, Z. (2010). The origin of cultivated citrus as inferred from internal transcribed spacer and chloroplast DNA sequence and amplified fragment length polymorphism fingerprints. Journal of the American Society for Horticultural Science, 135: 341-350.

18. Luro, F., Laigret, F., Bové, J.M. and Ollitrault, P. (1995). DNA amplified fingerprinting, a useful tool for determination of genetic origin and diversity analysis in Citrus. HortScience, 30: 1063-1067.

19. Mabberley, D. (2004). Citrus (Rutaceae): a review of recent advances in etymology, systematics and medical applications. Blumea-Biodiversity, Evolution and Biogeography of Plants, 49: 481-498.

20. Moore, G.A. (2001). Oranges and lemons: clues to the taxonomy of Citrus from molecular markers. Trends in Genetics, 17: 536-540.

21. Mirmohammadi Maibody, S.A.M. and Golkar, P. (2019). Application of DNA molecular markers in plant breeding. Plant Genetic Researches, 6(1): 1-30 (In Persian).

22. Munankarmi, N.N., Rana, N., Bhattarai, T., Shrestha, R.L., Joshi, B.K., Baral, B. and Shrestha, S. (2018). Characterization of the genetic diversity of acid lime (Citrus aurantifolia (christm.) swingle) cultivars of eastern Nepal using inter-simple sequence repeat markers. Plants, 7(2): 46-60.

23. Nicolosi, E., Deng, Z., Gentile, A., La Malfa, S., Continella, G and Tribulato, E. (2000). Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theoretical and Applied Genetics, 100: 1155-1166.

24. Novelli, V.M., Machado, M.A. and Lopes, C.R. (2000). Isoenzymatic polymorphism in Citrus spp. and Poncirus trifoliata (L.) Raf.(Rutaceae). Genetics and Molecular Biology, 23: 163-168.

25. Ollitrault, F., Terol, J., Pina, J.A., Navarro, L., Talon, M. and Ollitrault, P. (2010). Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus. American Journal of Botany, 97: e124-e129.

26. Omura, M. and Shimada, T. (2016). Citrus breeding, genetics and genomics in Japan. Breeding Science, 66: 3-17.

27. Pang, X.M., Hu, C.G. and Deng, X.X. (2007). Phylogenetic relationships within Citrus and its related genera as inferred from AFLP markers. Genetic Resources and Crop Evolution, 54: 429-436.

28. Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155: 945-959.

29. Shahsavar, A.R., Ezadpanah, K.A., Tafazoli, A.A. and Seyed Tababaie, B.A. (2004). Evaluation of genetic variability of limes and lemons in the Fars province by morphological traits and inter-simple sequence repeat (ISSR). Journal of Horticultural Science and Technology, 5(4): 177-188 (In Persian).

30. Shahsavar, A., Izadpanah, K., Tafazoli, E. and Tabatabaei, B.S. (2007). Characterization of citrus germplasm including unknown variants by inter-simple sequence repeat (ISSR) markers. Scientia Horticulturae, 112: 310-314.

31. Velasco, R. and Licciardello, C. (2014). A genealogy of the citrus family. Nature Biotechnology, 32: 640-642.

32. Wu, G.A., Terol, J., Ibanez, V., López-García, A., Pérez-Román, E., Borredá, C., Domingo, C., Tadeo, F.R., Carbonell-Caballero, J. and Alonso, R. (2018). Genomics of the origin and evolution of Citrus. Nature, 554: 311-316.

33. Xu, Q., Chen, L.L., Ruan, X., Chen, D., Zhu, A., Chen, C., Bertrand, D., Jiao, W.B., Hao, B.H. and Lyon, M.P. (2013). The draft genome of sweet orange (Citrus sinensis). Nature Genetics, 45: 59-66.

34. Zhang, Y., Yan, H., Jiang, X., Wang, X., Huang, L., Xu, B., Zhang, X. and Zhang, L. (2016). Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers. Hereditas, 153: 4-16.

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‎ 10.52547/pgr.7.2.2

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Abouzari A, Dadras A R, Golein B, Tajvar Y. Investigation of Genetic Diversity and Structure Analysis of Different Citrus Genotypes Using ISSR Markers. pgr 2021; 7 (2) :13-24
URL: http://pgr.lu.ac.ir/article-1-206-en.html

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