Journal of Plant Biotechnology

  • 제47권2호
  • /
  • Pages.124-130
  • /
  • 2020
  • /
  • 1229-2818(pISSN)
  • /
  • 2384-1397(eISSN)
한국식물생명공학회 (The Korean Society of Plant Biotechnology)
권호 표지
DOI QR코드

DOI QR Code

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

  • Park, Hyungjun (Department of Environmental Horticulture, University of Seoul) ;
  • Kim, Sujung (Department of Environmental Horticulture, University of Seoul) ;
  • Nie, Hualin (Department of Environmental Horticulture, University of Seoul) ;
  • Kim, Jiseong (Department of Environmental Horticulture, University of Seoul) ;
  • Lee, Jeongeun (Department of Environmental Horticulture, University of Seoul) ;
  • Kim, Sunhyung (Department of Environmental Horticulture, University of Seoul)
  • 투고 : 2020.06.04
  • 심사 : 2020.06.11
  • 발행 : 2020.06.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

The sweet potato (Ipomoea batatas [L.] Lam.) is the sixth-most important crop in the world following rice, wheat, potato, maize, and cassava. Four varieties ('Beniharuka', 'Annobeni', 'Pungwonmi', 'Hogammi') and their Japanese cultivars are broadly distributed in South Korea. In the Korean marketplace, sweet potatoes are classified by color and shape, not by variety, making it necessary to differentiate varieties for uniform production and consumption. In this study, molecular markers were developed to distinguish the four varieties of sweet potato using SNPs and genotyping-by-sequencing (GBS) analysis via a tetra-primer amplification refractory mutation system (ARMS)-PCR. The results revealed that three variety-specific fragments (164 bp and 241 bp of SNP 04-27457768 and 292 bp of SNP 03-16195623) were amplified in the 'Beniharuka', 'Pungwonmi', and 'Annobeni' sweet potato varieties. There were instances where some varieties produced three bands within the gel electrophoresis, indicating heterozygosity at the given SNPs loci. DNA sequencing analysis also confirmed the results of electrophoresis at the SNPs loci. Overall, these molecular markers would provide a useful, rapid, and, simple evaluation method for the Korean sweet potato marketplace, where the mixing of varieties is a serious issue.

키워드

참고문헌

  1. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208-218 https://doi.org/10.1007/BF02672069
  2. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314-331
  3. Bovell‐Benjamin AC (2007) Sweet potato: a review of its past, present, and future role in human nutrition. Adv Food Nutr Res 52:1-59 https://doi.org/10.1016/S1043-4526(06)52001-7
  4. Collins A, Ke X (2012) Primer1: primer design web service for tetra-primer ARMS-PCR. Open Bioinformat J 6:55-58 https://doi.org/10.2174/1875036201206010055
  5. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS one 6:e19379 https://doi.org/10.1371/journal.pone.0019379
  6. Ganal MW, Altmann T, Roder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211-217 https://doi.org/10.1016/j.pbi.2008.12.009
  7. Hirakawa H, Okada Y, Tabuchi H, Shirasawa K, Watanabe A, Tsuruoka H, Minami C, Nakayama S, Sasamoto S, Kohara M, Kishida Y, Fujishiro T, Kato M, Nanri K, Komaki A, Yoshinaga M, Takahata Y, Tanaka M, Tabata S, Isobe SN (2015) Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H.B.K) G. Don. DNA Res 22:171-179 https://doi.org/10.1093/dnares/dsv002
  8. Jeong HJ, Jo YD, Park SW, Kang BC (2010) Identification of Capsicum species using SNP markers based on high resolution melting analysis. Genome 53:1029-1040 https://doi.org/10.1139/G10-094
  9. Karuri HW, Ateka EM, Amata R, Nyende AB, Muigai AWT, Mwasame E, Gichuki ST (2010) Evaluating diversity among Kenyan sweet potato genotypes using morphological and SSR markers. Int J Agric Biol 12:33-38
  10. Kim JS, Jang HW, Kim JS, Kim HJ, Kim JH (2012) Molecular identification of Schisandra chinensis and its allied species using multiplex PCR based on SNPs. Genes Genomics 34: 283-290 https://doi.org/10.1007/s13258-011-0201-3
  11. Kim SH, Hamada T (2005) Rapid and reliable method of extracting DNA and RNA from sweetpotato, Ipomoea batatas (L). Lam. Biotech Let 27:1841-1845 https://doi.org/10.1007/s10529-005-3891-2
  12. Kou M, Xu JL, Li Q, Liu YJ, Wang X, Tang W, Yan H, Zhang YG, Ma DF(2017) Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato. J Integr Agric 16:464-470 https://doi.org/10.1016/S2095-3119(16)61405-3
  13. Kriegner A, Cervantes JC, Burg K, Mwanga RO, Zhang D (2003) A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam.] based on AFLP markers. Mol Breed 11:169-185 https://doi.org/10.1023/A:1022870917230
  14. Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics 728398:1-11
  15. Mullis KB, Faloona F (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Meth Enzymol 155:335-350 https://doi.org/10.1016/0076-6879(87)55023-6
  16. Ozias-Akins P, Jarret RL (1994) Nuclear DNA content and ploidy levels in the genus Ipomoea. J Am Soc Hortic Sci 119:110-115 https://doi.org/10.21273/JASHS.119.1.110
  17. Park MJ, Kim MK, In JG Yang DC (2006) Molecular identification of Korean ginseng by amplification refractory mutation system-PCR. Food Res Int 39:568-574 https://doi.org/10.1016/j.foodres.2005.11.004
  18. Poland J, Endelman J, Dawson J, Rutkoski J, Wu S, Manes Y, Dreisigacker S, Crossa J, Sanchez-Villeda H, Sorrells M, Jannink JL (2012) Genomic selection in wheat breeding using genotyping by sequencing. Plant Genome 5:103-113 https://doi.org/10.3835/plantgenome2012.06.0006
  19. Pootakham W, Jomchai N, Ruang-areerate P, Shearman JR, Sonthirod C, Sangsrakru D, Tragoonrung S, Tangphatsornruang S (2015) Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics 105:288-295 https://doi.org/10.1016/j.ygeno.2015.02.002
  20. Roullier C, Duputie A, Wennekes P, Benoit L, Bringas VMF, Rossel G, Tay D, McKey D, Lebot V (2013) Disentangling the origins of cultivated sweet potato (Ipomoea batatas (L.) Lam.). PLoS One 8:e62707 https://doi.org/10.1371/journal.pone.0062707
  21. Ukoskit K, Thompson PG (1997) Autopolyploidy versus allopolyploidy and low-density randomly amplified polymorphic DNA linkage maps of sweetpotato. J Am Soc Hortic Sci 122: 822-828 https://doi.org/10.21273/JASHS.122.6.822
  22. Vos P, Hogers R, Bleeker M, Reijans M, Lee TVD, Hornes M, Friters A, Pot J, Paleman J, Zabeau MKM (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414 https://doi.org/10.1093/nar/23.21.4407
  23. Wang Z, Li J, Luo Z, Huang L, Chen X, Fang B, Li Y, Chen J, Zhang X (2011) Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC plant Biol 11:139 https://doi.org/10.1186/1471-2229-11-139
  24. Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531-6535 https://doi.org/10.1093/nar/18.22.6531
  25. Wu S, Lau KH, Cao Q, Hamilton JP, Sun H, Zhou C, Eserman L, Gemenet DC, Olukolu BA, Wang H, Crisovan E, Godden GT, Jiao C, Wang X, Kitavi M, Manrique-Carpintero N, Vaillancourt B, Wiegert-Rininger K, Yang X, Bao K, Schaff J, Kreuze J, Gruneberg W, Khan A, Ghislain M, Ma D, Jiang J, Mwanga ROM, Leebens-Mack J, Coin LJM, Yencho GC, Buell CR, Fei Z (2018) Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nat Commun 9:1-12 https://doi.org/10.1038/s41467-017-02088-w
  26. Yang J, Moeinzadeh MH, Kuhl H, Helmuth J, Xiao P, Haas S, Liu G, Zheng J, Sun Z, Fan W, Deng G, Wang H, Hu F, Zhao S, Fernie AR, Boerno S, Timmermann B, Zhang P, Vingron M (2017) Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nat Plants 3:696-703 https://doi.org/10.1038/s41477-017-0002-z
  27. Yang S, Li X, Huang F, Huang Y, Liu X, Wu J, Wang Q, Deng Z, Chen R, Zhang M (2018) A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum. PLoS ONE 13:e0197458 https://doi.org/10.1371/journal.pone.0197458
  28. Ye S, Dhillon S, Ke X, Collins AR, Day IN (2001) An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res 29:e88 https://doi.org/10.1093/nar/29.17.e88
  29. Zhang K, Wu Z, Tang D, Lv C, Luo K, Zhao Y, Liu X, Huang Y, Wang J (2016) Development and identification of SSR markers associated with starch properties and $\beta$-carotene content in the storage root of sweet potato (Ipomoea batatas L.). Front Plant Sci 7:223
  30. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeats (SSR)-anchored polymerase chain reaction amplification. Genom 20:176-183 https://doi.org/10.1006/geno.1994.1151