SSR fingerprinting of 203 sweetpotato (Ipomoea batatas (L.) Lam.) varieties
MENG Yu-sha, ZHAO Ning, LI Hui, ZHAI Hong, HE Shao-zhen, LIU Qing-chang
Key Laboratory of Sweetpotato Biology and Biotechnolog, Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization of Ministry of Education, China Agricultural University, Beijing 100193, P.R.China
Abstract Simple sequence repeat (SSR) markers have been shown to be a powerful tool for varieties identification in plants. However, SSR fingerprinting of sweetpotato varieties has been a little reported. In this study, a total of 1 294 SSR primer pairs, including 1 215 genomic-SSR and 79 expressed sequence tag (EST)-SSR primer pairs, were screened with sweetpotato varieties Zhengshu 20 and Luoxushu 8 and their 2 F1 individuals randomly sampled, and 273 and 38 of them generated polymorphic bands, respectively. Four genomic-SSR and 3 EST-SSR primer pairs, which showed good polymorphism, were selected to amplify 203 sweetpotato varieties and gave a total of 172 bands, 85 (49.42%) of which were polymorphic. All of the 203 sweetpotato varieties showed unique fingerprint patterns, indicating the utility of SSR markers in variety identification of this crop. Polymorphism information content (PIC) ranged from 0.5824 to 0.9322 with an average of 0.8176. SSR-based genetic distances varied from 0.0118 to 0.6353 with an average of 0.3100 among these varieties. Thus, these sweetpotato varieties exhibited high levels of genetic similarity and had distinct fingerprint profiles. The SSR fingerprints of the 203 sweetpotato varieties have been successfully constructed. The highly polymorphic SSR primer pairs developed in this study have the potential to be used as core primer pairs for variety identification, genetic diversity assessment and linkage map construction in sweetpotato and other plants.
This work was supported by the earmarked fund for the China Agriculture Research System (CARS-11), the National Natural Science Foundation of China (31461143017) and the Science and Technology Planning Project of Guangdong Province, China (2015B020202008).
Corresponding Authors: Correspondence LIU Qing-chang, Tel: +86-10-62733710, E-mail: firstname.lastname@example.org
About author: MENG Yu-sha,E-mail:email@example.com
Cite this article:
MENG Yu-sha, ZHAO Ning, LI Hui, ZHAI Hong, HE Shao-zhen, LIU Qing-chang. SSR fingerprinting of 203 sweetpotato (Ipomoea batatas (L.) Lam.) varieties[J]. Journal of Integrative Agriculture,
2018, 17(01): 86-93.
Akond M, Jin S M, Wang X W. 2012. Molecular characterization of selected wild species and miniature roses based on SSR markers. Scientia Horticulturae, 147, 89-97.
Botstein D, White R L, Skolnick M, Davis R W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32, 314-331.
Caramante M, Corrado G, Monti L M, Rao R. 2011. Simple sequence repeats are able to trace tomato cultivars in tomato food chains. Food Control, 22, 549-554.
Chen H L, Chen X, Tian J, Yang Y, Liu Z X, Hao X Y, Wang L X, Wang S H, Liang J, Zhang L Y, Yin F X, Chen X Z. 2016. Development of gene-based SSR markers in rice bean (Vigna umbellata L.) based on transcriptome data. PLOS ONE, 11, e0151040.
Chen Y N, Dai X G, Hou J, Guan H W, Wang Y X, Li Y, Yin T M. 2016. DNA fingerprinting of oil camellia cultivars with SSR markers. Tree Genetics & Genomes, 12, 1-8.
Guo J P, Pan D R, Xu L P, Yuan Z N. 2003. Establishment of DNA fingerprint and its application to variety identification in sweet potato. Journal of Fujian Agriculture and Forestry University, 32, 19-22. (in Chinese)
Hagenimana V, Low J. 2000. Potential of orange-fleshed sweet potatoes for raising vitamin A intake in Africa. Food and Nutrition Bulletin, 21, 414-418.
Hayden M J, Sharp P J. 2001. Targeted development of informative microsatellite (SSR) markers. Nucleic Acids Research, 29, 1003-1010.
Hundayehu M C, du Toit E, Laurie S M, Steyn M, Greyling R, Myeza N. 2014. Effect of long-term in vitro subculturing on quality degeneration of sweetpotato varieties: Morpho-anatomic assessment and simple sequence repeat (SSR) analysis. In: Low J, Nyongesa M, Quinn S, Parker M, eds., Potato and Sweetpotato in Africa: Transforming the Value Chains for Food and Nutrition Security. CABI Publishing, England. pp. 311-321.
Hwang S Y, Tseng Y T, Lo H F. 2002. Application of simple sequence repeats in determining the genetic relationships of cultivars used in sweet potato polycross breeding in Taiwan. Scientia Horticulturae, 93, 215-224.
Jiang S K, Huang C, Zhang X J, Wang J Y, Chen W F, Xu Z J. 2010. Development of a highly informative microsatellite (SSR) marker framework for rice (Oryza sativa L.) genotyping. Agricultural Sciences in China, 9, 1697-1704.
Jones C J, Edwards K J, Castaglione S, Winfield M O, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A. 1997. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular Breeding, 3, 381-390.
KarihalooJ L. 2015. DNA fingerprinting techniques for plant identification. In: Plant Biology and Biotechnology. Springer, India. pp. 205-221.
Koussao S, Gracen V, Asante I, Danquah E Y, Ouedraogo J T, Baptiste T J, Vianney T M. 2014. Diversity analysis of sweetpotato (Ipomoea batatas (L.) Lam.) germplasm from Burkina Faso using morphological and simple sequence repeats markers. African Journal of Biotechnology, 13, 729-742.
Kumar M, Ponnuswami V, Nagarajan P, Jeyakumar P, Senthil N. 2013. Molecular characterization of ten mango cultivars using simple sequences repeat (SSR) markers. African Journal of Biotechnology, 12, 6568-6573.
Li H, Zhao N, Yu X X, Liu Y X, Zhai H, He S Z, Li Q, Ma D F, Liu Q C. 2014. Identification of QTLs for storage root yield in sweetpotato. Scientia Horticulturae, 170, 182-188.
Li Q, Liu Q C, Zhai H, Ma D F, Wang X, Li X Q, Wang Y P. 2008. Genetic diversity in main parents of sweetpotato in China as revealed by ISSR marker. Acta Agronomica Sinica, 34, 972-977. (in Chinese)
Li R J, Zhai H, Kang C, Liu D G, He S Z, Liu Q C. 2015. De novo transcriptome sequencing of the orange-fleshed sweetpotato and analysis of differentially expressed genes related to carotenoid biosynthesis. International Journal of Genomics, 2015, 843802.
Liu D G, Zhao N, Zhai H, Yu X X, Jie Q, Wang L J, He S Z, Liu Q C. 2012. AFLP fingerprinting and genetic diversity of main sweetpotato varieties in China. Journal of Integrative Agriculture, 11, 1424-1433.
Louarn S, Torp A M, Holme I B, Andersen S B, Jensen B D. 2007. Database derived microsatellite markers (SSRs) for cultivar differentiation in Brassica oleracea. Genetic Resources and Crop Evolution, 54, 1717-1725.
Lu S Y, Liu Q C, Li W J. 1998. Sweetpotato Breeding. China Agriculture Press, Beijing, China. pp. 7-17. (in Chinese)
Lu X Z, Ni J L, Li L, Wang X F, Ma H, Zhang X J, Yang J B. 2014. Construction of rice variety identity using SSR fingerprint and commodity information. Acta Agronomica Sinica, 40, 823-829. (in Chinese)
Luo Z X, Fang B P, Li R, Wang Z Y, Huang L F, Chen J Y, Zhang X J, Li Y J, Chen X L, Huang S H. 2014. Construction of DNA fingerprint database based on EST-SSR markers for sweet potato germplasm. Journal of Plant Genetic Resource, 15, 810-814. (in Chinese)
Moisan-Thiery M, Marhadour S, Kerlan M C, Dessenne N, Perramant M, Gokelaere T, Hingrat L. 2005. Potato cultivar identification using simple sequence repeats markers (SSR). Potato Research, 48, 191-200.
Nagy S, Poczai P, Cernák I, Gorji A M, Heged?s G, Taller J. 2012. PICcalc: An online program to calculate polymorphic information content for molecular genetic studies.Biochemical Genetics, 50, 670-672.
Ngailo S, Shimelis H, Sibiya J, Amelework B, Mtunda K. 2016. Genetic diversity assessment of Tanzanian sweetpotato genotypes using simple sequence repeat markers. South African Journal of Botany, 102, 40-45.
Powell W, Machray G C, Provan J. 1996. Polymorphism revealed by simple sequence repeats. Trends in Plant Science, 1, 215-222.
Prakash C S, He G H, Jarret R L. 1996. DNA marker-based study of genetic relatedness in United States sweetpotato cultivars. Journal of the American Society for Horticultural Science, 121, 1059-1062.
Rodriguez-Bonilla L, Cuevas H E, Montero-Rojas M, Bird-Pico F, Luciano-Rosario D, Siritunga D. 2014. Assessment of genetic diversity of sweetpotato in PuertoRico. PLOS ONE, 9, e116184.
Rohlf F J. 1992. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System. Setauket, New York.
Saghai-Maroof M A, Soliman K M, Jorgensen R A, Allard R W. 1984. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences of the United States of America, 81, 8014-8018.
Dos Santos L F, Fregapani R M, Falcao L L, Togawa R C, do Carmo Costa M M, Lopes U V, Gramacho K P, Alves R M, Micheli F, Marcellino L H. 2016. First microsatellite markers developed from cupuassu ESTs: Application in diversity analysis and cross-species transferability to Cacao. PLOS ONE, 11, e0151074.
Srinivas T. 2009. Economics of sweetpotato production and marketing. In: Loebenstein G, Thottappilly G, eds., The Sweetpotato. Springer, New York. pp. 235-267.
Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
Team R C. 2013. R: A Language and Environment for Statistical Computing. Computing Team, RDCVienna, Austria.
Wang C B, Guo W Z, Zhang T Z, Li Y E, Liu H M. 2009. AutoSSR: An improved automatic software for SSR analysis from large-scale EST sequences. Cotton Science, 21, 243-247. (in Chinese)
Wang H Y, Zhai H, Wang Y P, He S Z, Liu Q C. 2009. RAPD fingerprints and genetic variations of the 30 main sweetpotato varieties in China. Molecular Plant Breeding, 5, 879-884.
Yada B, Brown-Guedira G, Alajo A, Ssemakula G N, Mwanga R O M, Yencho G C. 2015. Simple sequence repeat marker analysis of genetic diversity among progeny of a biparental mapping population of sweetpotato. Hortscience, 50, 1143-1147.
Yang X S, Su W J, Wang L J, Lei J, Chen S S, Liu Q C. 2015. Molecular diversity and genetic structure of 380 sweetpotato accessions as revealed by SSR markers. Journal of Integrative Agriculture, 14, 633-641.
Yeh F C, Boyle T J B. 1997. Sample genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian Journal of Botany, 129, 157.
Zhao N, Yu X X, Jie Q, Li H, Li H, Hu J, Zhai H, He S Z, Liu Q C. 2013. A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweetpotato. Molecular Breeding, 32, 807-820.