FINGERPRINTING OF SWEETPOTATO GERMPLASM USING AFLP, RAPD, AND SAMPL ANALYSIS

AMINA A. MOHAMED, MERVAT M. M. EL FAR, M. E. SAAD

Abstract


The ability to improve productivity and agronomic traits of sweetpotato through breeding programs depends on assessing the genetic variation of their germplasm and genetic relationship to other genotypes. In addition, studying genetic diversity supports the conservation of genetic resources. In this study, three different DNA-based markers, random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and selective amplification of microsatellite polymorphic loci (SAMPL) were used for fingerprinting and detecting genetic variation for ten germplasm of sweetpotato. Results indicated that RAPD assays using 18 primers produced 213 bands, 145 of which were polymorphic with a percentage of 68.1%. AFLP using five primers yielded 344 amplified products with a percentage of 71.8% polymorphism. SAMPL using two primers combinations amplified 132 bands in which 85 being polymorphic representing 64.4%. Genetic relationship was estimated using Dice’s coefficient values between different accessions, ranging from 0.655 to 0.939 in RAPD, 0.749 to 0.936 in AFLP, and 0.742 to 0.928 for SAMPL. The UPGMA algorithm was used for grouping all germplasm based on their genetic distances. In total, the three molecular marker systems were compared on the basis of multiplex ratio, marker index and average heterozygosity and revealed that AFLP was the bestsuited molecular assay for fingerprinting and assessing genetic relationships. All analysis confirmed the relatively high genetic diversity present in sweetpotato germplasm used. Also, distinct DNA fingerprinting profile could be obtained with all the three molecular marker systems. These results clearly indicate the usefulness of DNA fingerprinting for the identification of sweetpotato germplasm, and their potentiality to eliminate accessions duplicates from gene banks around the world.

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Arizio, C. M., N. Hompanera, E. Y. Suarez and M. M. Manifesto (2009). Genotypic identification and diversity evaluation of a sweet potato (Ipomoea batatas (L). Lam) collection using microsatellites. Plant Genetic Resources, 7: 135-138.

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

Cao, Q. H., J. Li. A. Tang, W. Gruneberg, K. Huamani and D. Ma (2014). Ploidy level and molecular phylogenic relationship among novel Ipomoea interspecific hybrids. Czech J. Genet. Plant Breed., 50: 32-38.

Connolly, A. G., I. D. Godwin, M. Cooper and I. H. DeLacy (1994). Interpretation of randomly amplified polymorphic DNA marker data for fingerprinting sweet potato (Ipomoea batatas L.) genotypes. Theor. Appl. Genet., 88: 332-336.

Costa, R., G. Pereira., I. Garrido, M. M. Tavaresde-Sousa and F. Espinosa (2016). Comparison of RAPD, ISSR and AFLP molecular markers to reveal and classify orchardgrass (Dactylis glomerata L.) germplasm variations. PloS one, 11: 1-15.

da Silva, A. V. C., L. N. T. Andrade, A. R. C. Rabbani, M. U. C. Nunes and L. R. Pinheiro (2014). Genetic diversity of sweet potatoes collection from North-eastern Brazil. African Journal of Biotechnology, 13: 1109-1116.

Doyle, J. J. and J. L. Doyle. (1990) Isolation of plant DNA from fresh tissue. Focus, 12: 13-15.

Elameen, A., S. Fjellheim, A. Larsen, O. A. Rognli, L. Sundheim, S. Msollaand and S. S. Klemsdal (2008). Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP. Genetic Resources and Crop Evolution, 55: 397-408.

EL-Bastawesy, A., A. L. Hareedy and M. M. M. El-Far. (2008). Chemical and technological evaluation of some sweetpotato varities. Arab Univ. J. Agric. Sci., 16: 87-96.

FAO, http://faostat.fao.org. (2014).

Gichuki, S. T., M. Berenyi, D. Zhang, M. Hermann, J. Schmidt, J. Glössl and K. Burg (2003). Genetic diversity in sweetpotato [Ipomoea batatas (L.) Lam.] in relationship to geographic sources as assessed with RAPD markers. Genetic Resources and Crop Evolution, 50: 429-437.

Gichuru, V., V. Aritua, G. W. Lubega, R. Edema, E. Adipala and P. R. Rubaihayo (2006). A preliminary analysis of diversity among East African sweetpotato landraces using morphological and simple sequence repeats (SSR) markers. In II Inter. Symp. on Sweetpotato and Cassava: Innovative Tech. for Commercialization, 703: 159-164.

Hartl, D. L. and A. G. Clark (1997). Principles of Population Genetics (Vol. 116). Sunderland: Sinauer Associates.

He, G., C. S. Prakash and R. L. Jarret. (1995). Analysis of genetic diversity in a sweetpotato (Ipomoea batatas) germplasm collection using DNA amplification fingerprinting. Genome, 38: 938-945.

He, X. Q., Q. C. Liu, K. Ishiki, H. Zhai, and Y. P. Wang. (2006). Genetic diversity and genetic relationships among Chinese sweetpotato landraces revealed by RAPD and AFLP markers. Breeding Science, 56: 201-207.

He, X. Q., Q. C. Liu, K. Ishiki, H. Zhai, and Y. Wang (2007). ISSR analysis of genetic diversity and relationships among sweet potato (Ipomoea batatas) landraces in China. Plant Genetic Resources Newsletter (Bioversity International/FAO). 150: 35-1.

Hu, J., M. Nakatani, A. G. Lalusin, T. Kuranouchi and T. Fujimura (2003). Genetic analysis of sweetpotato and wild relatives using inter-simple sequence repeats (ISSRs). Breeding Science, 53: 297-304.

Jacoby, A., M. T. Labuschagne and C. D. Viljoen (2003). Genetic relationships between Southern African Solanum retroflexum Dun. and other related species measured by morphological and DNA markers. Euphytica, 132: 109-113.

Karimi, H. R. and S. Kafkas (2011). Genetic relationships among Pistacia species studied by SAMPL markers. Plant Systematics and Evolution, 297: 207-212.

Karuri, H. W., E. M. Ateka, R. Amata, A. B. Nyende, A. W. T. Muigai, E. Mwasame and S. T. Gichuki (2010). Evaluating diversity among Kenyan sweet potato genotypes using morphological and SSR markers. Int. J. Agric. Biol., 12: 33-38.

Lee, H. M., Y. Park, T. H. Jun, S. W. Kwon, I. S. Choi, Y. C. Kim, R. Gupta, M. N. Chung, S. H. Kim, P. Yan, Y. Wang and S. T. Kim (2015). Direct sequencing of RAPD products provides a set of SCAR markers for discrimination of sweet potato cultivars. Plant Omics, 8: 195-200.

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

Liu, D. G., Z. H. A. O. Ning, Z. H. A. I. Hong, X. X. Yu, J. I. E. Qin, L. J. Wang and Q. C. Liu (2012). AFLP fingerprinting and genetic diversity of main sweetpotato varieties in China. Journal of Integrative Agriculture, 11: 1424-1433.

Luo, K., L. Hui-xiang, W. Zheng-dan, W. Xue-li, Y. Wang, T. Dao-bin, W. Ji-chun and Z. Kai (2016). Genetic diversity and population structure analysis of main sweet potato breeding parents in Southwest China. Scientia Agricultura Sinica, 49: 593-608

Mantel, N. (1967). The detection of dis-ease clustering and a generalized regression approach. Cancer research, 27: 209-220.

Morgante, M., A. Rafalski, P. Biddle, S. Tingey and A. M. Olivieri (1994). Genetic mapping and variability of seven soybean simple sequence repeat loci. Genome, 37: 763-769.

Moulin, M. M., R. Rodrigues, L. S. A. Gonçalves, C. P. Sudré and M. G. Pereira (2012). A comparison of RAPD and ISSR markers reveals genetic diversity among sweet potato landraces (Ipomoea batatas (L.) Lam.). Acta Scientiarum Agronomy, 34: 139-147.

Nei, M. and W. Li (1979). Mathematical model for studying genetic varia-tion in terms of restriction endonu-cleases. Proc. Natl. Acad. Sci. USA, 76: 5269-5273

Ngailo, S., H. Shimelis, J. Sibiya, B. Amelework and K. Mtunda (2016). Genetic diversity assessment of Tanzanian sweetpotato genotypes using simple sequence repeat markers. South African Journal of Botany, 102: 40-45.

Powell, W., M. Morgante, C. Andre., M. Hanafey, J. Vogel, S. Tingey and A. Rafalski. (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding, 2: 225-238.

Sagredo, B., P. Hinrichsen, H. López, A. Cubillos and C. Muñoz (1998). Genetic variation of sweetpotatoes (Ipomoea batatas L.) cultivated in Chile determined by RAPDs. Euphytica, 101: 193-198.

Shannon, C. E. (1949). Communication theory of secrecy systems. Bell System Technical Journal, 28: 656-715.

Tairo, F., E. Mneney and A. Kullaya (2008). Morphological and agronomical characterization of sweet potato [Ipomoea batatas (L.) Lam.] germplasm collection from Tanzania. African Journal of Plant Science, 2: 077-085.

Teulat, B., C. Aldam, R. Trehin, P. Lebrun, J. H. A. Barker, G. M. Arnold, A. Karp., L. Baudouin and F. Rognon (2000). An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs. Theor. Appl. Genet., 100: 764-771.

The World Bank (2011). World Development Report: Conflict, Security and Development. The International Bank for Reconstruction and Development TheWorld Bank. Washington (USA), 416.

Tonk, F. A., R. R. A. Giachino, C. Sönmez, S. Yüce, E. Bayram, I. Telci and M. A. Furan (2011). Characterization of various Hypericum perforatum clones by hypericin and RAPD analyses. Int. J. Agric. Biol, 13: 31-37.

Tosti, N. and V. Negri (2002). Efficiency of three PCR-based markers in assessing genetic variation among cowpea (Vigna unguiculata subsp. unguiculata) landraces. Genome, 45: 268-275.

Tseng, Y. T., H. F. Lo and S. Y. Hwang (2002). Genotyping and assessment of genetic relationships in elite polycross breeding cultivars of sweet potato in Taiwan based on SAMPL polymorphisms. Botanical Bulletin of Academia Sinica, 43: 99-105.

Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman and M. Kuiper (1995). AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research, 23: 4407-4414.

Wang, Z., L. Jun, L. Zhongxia, H. Lifei, C. Xinliang, F. Boping, L. Yujun, C. Jingyi and Z. Xiongjian (2011). Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC Plant Biology, 11: 139-148.

Williams, J. G., A. R. Kubelik, K. J. Livak, J. A. Rafalski and S. V. Tingey (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18: 6531-6535.

Witsenboer, H., R. W. Michelmore and J. Vogel (1997). Identification, genetic localization and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp). Genome, 40: 923-936.

Yeh, F. C., R. C. Yang, T. B. Boyle, Z. H. Ye and J. X. Mao (1997). POPGENE, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada, 10. Zhang, D. P., D. Carbajulca, L. Ojeda, G. Rossel, S. Milla, C. Herrera and M. Ghislain (1999). Microsatellite analysis of genetic diversity in sweetpotato varieties from Latin America. CIP Program Report, 2000: 295-301.

Zhang, D., J. Cervantes, Z. Huamán, E. Carey and M. Ghislain (2000). Assessing genetic diversity of sweet potato (Ipomoea batatas (L.) Lam.) cultivars from tropical America using AFLP. Genetic Resources and Crop Evolution, 47: 659-665.

Zhang, D., M. Ghislain, Z. Huamán, A. Golmirzaie and R. Hijmans (1998). RAPD variation in sweetpotato (Ipomoea batatas (L.) Lam) cultivars from South America and Papua New Guinea. Genetic Resources and Crop Evolution, 45: 271-277.


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