Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
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Current status of sweetpotato genomics research

고구마 유전체 연구현황 및 전망

  • Yoon, Ung-Han (Genomics Division, National Academy of Agricultural Science) ;
  • Jeong, Jae Cheol (Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Kwak, Sang-Soo (Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Yang, Jung-Wook (Bioenergy Crop Research Institute, National Institute of Crop Science) ;
  • Kim, Tae-Ho (Genomics Division, National Academy of Agricultural Science) ;
  • Lee, Hyeong-Un (Bioenergy Crop Research Institute, National Institute of Crop Science) ;
  • Nam, Sang-Sik (Bioenergy Crop Research Institute, National Institute of Crop Science) ;
  • Hahn, Jang-Ho (Genomics Division, National Academy of Agricultural Science)
  • 윤웅한 (국립농업과학원 유전체과) ;
  • 정재철 (한국생명공학연구원 식물시스템공학연구센터) ;
  • 곽상수 (한국생명공학연구원 식물시스템공학연구센터) ;
  • 양정욱 (국립식량과학원 바이오에너지작물연구소) ;
  • 김태호 (국립농업과학원 유전체과) ;
  • 이형운 (국립식량과학원 바이오에너지작물연구소) ;
  • 남상식 (국립식량과학원 바이오에너지작물연구소) ;
  • 한장호 (국립농업과학원 유전체과)
  • Received : 2015.09.11
  • Accepted : 2015.09.16
  • Published : 2015.09.30
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Abstract

Sweetpotato [Ipomoea batatas (L.) Lam] grows well in harsh environmental conditions, and is cultivated as one of the top seven food crops in the world. Recently, sweetpotato is drawing interest from people as a healthy food because it is high in dietary fiber, vitamins, carotenoids and overall nutrition value. However, few studies have been conducted on sweetpotato genome sequencing in spite of its importance. This review is aimed at increasing the efficiency of sweetpotato genome sequencing research as well as establishing a base for gene utilization in order to control useful traits. Recently, animal and plant genome sequencing projects increased significantly. However, sweetpotato genome sequencing has not been performed due to polyploidy and heterogeneity problems in its genome. Meanwhile research on its transcriptome has been conducted actively. Recently, a draft of the diploid sweetpotato genome was reported in 2015 by Japanese researchers. In addition, the Korea-China-Japan Trilateral Research Association of Sweetpotato (TRAS) has conducted research on gene map construction and genome sequencing of the hexaploid sweetpotato Xushu 18 since 2014. The Bill & Melinda Gates Foundation launched the 'sweetpotato genomic sequencing to develop genomic tools for Sub-Sahara Africa breeding program'. The chloroplast genome sequence acquired during sweetpotato genome sequencing is used in evolutionary analyses. In this review, the trend of research in the sweetpotato genome sequencing was analyzed. Research trend analysis like this will provide researchers working toward sweetpotato productivity and nutrient improvement with information on the status of sweetpotato genome research. This will contribute to solving world food, energy and environmental problems.

고구마는 척박한 환경에서도 생육이 가능한 세계 7대 농작물로 식량뿐만 아니라 사료용, 전분 등의 산업용으로도 중요하다. 최근 고구마는 항산화물질, 식이섬유질 등을 고함유하는 건강식품으로 각광을 받고 있다. 그러나 고구마 유전체 해독에 관한 연구는 고구마의 중요도에 비해 많이 이루어지지 않고 있다. 본 총설의 목적은 고구마 유전체 연구 동향분석을 통하여 유전체 해독 연구의 효율성 증대 및 유용형질 유전자의 실용화 연구를 위한 기반구축을 모색하는데 있다. 최근 NGS 분석을 통한 동식물 유전체해독이 급진적으로 많이 이루어지고 있다. 고구마 유전체 해독의 경우는 다배수성 문제와 이질유전체 문제로 유전체 완전해독 연구가 이루어지지 않고 있으며 반면 전사체 분석 연구는 활발히 이루어지고 있는 실정이다. 최근 2015년 일본 연구자들에 의해 2배체 고구마의 유전체 해독 초안이 보고되었다. 한중일 고구마 연구협의회(Trilateral Research Association of Sweetpotato, TRAS)에 의해 6배체 고구마 Xushu 18의 유전자지도 작성 및 유전체 해독 연구가 2014년부터 이루어지고 있다. 빌게이츠재단(Bill & Melinda Gates Foundation)은 사하라사막 남쪽 아프리카지역의 기근과 영양문제를 해결하기 위해 고구마 유전체 기반 분자육종을 위한 분자도구 개발에 관한 프로젝트를 미국을 중심으로 한 컨소시엄을 구성하여 출범하였다. 고구마 유전체 해독과정 중에 분석된 고구마 엽록체 유전체 분석을 통하여 진화학적 해석연구가 이루어지고 있다. 본 총설을 통하여 고구마 유전체 해독 연구동향을 살펴보았다. 이러한 연구 동향 분석은 고구마의 생산성 및 기능성 향상 등의 실용화 연구를 수행하는 연구자들에게 최근의 연구현황을 제공할 수 있을 것이며 세계적인 식량, 에너지, 환경문제의 해결에 크게 기여 할 것으로 생각된다.

Keywords

References

  1. Ahn YS, Chung MN, Jeang BC, Lee JS, Oh YH (2002a) A New Sweetpotato variety Resistance to Fusarium Wilt, "Singeonmi". Korean J. Breed. Sci. 34:381-382
  2. Ahn YS, Jeang BC, Chung MN, Lee JS, Oh YH (2002b) New Variety Developed : A New Purple-Flesh and High Anthocyanin Sweetpotato Variety, "Sinjami". Korean J. Breed. Sci. 34: 379-380
  3. Ahn YS, Chung MN, Lee JS, Jeang BC (2006) A New Sweetpotato variety for Food and Processing, "Juhwangmi". Korean J. Breed. Sci. 38:69-70
  4. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815 https://doi.org/10.1038/35048692
  5. Austin DF, Huam Z (1996) A synopsis of Ipomoea (Convolvulaceae) in the America. Taxon 45:3-38 https://doi.org/10.2307/1222581
  6. Bovell-Benjamin AC (2007) Sweetpotato: 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
  7. Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035-1039 https://doi.org/10.1038/ng.919
  8. Cargill (2014) Food security: The challenge, 1-3
  9. Cervantes-Flores JC, Yencho GC, Kriegner A, Pecota KV, Faulk MA, Mwanga ROM, Sosinski BR (2008) Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers. Mol Breed 21:511-532 https://doi.org/10.1007/s11032-007-9150-6
  10. Food and Agriculture Organization of the United Nations (FAO) (2015) The state of food insecurity in the world, 8-18
  11. 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 sweetpotato, Ipomoea trifida (H.B.K.) G. Don. DNA Res 22:171-179 https://doi.org/10.1093/dnares/dsv002
  12. International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711-716 https://doi.org/10.1038/nature11543
  13. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800 https://doi.org/10.1038/nature03895
  14. International Wheat Genome Sequencing Consortium (IWGSC) (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788 https://doi.org/10.1126/science.1251788
  15. Jeong JC, Ji CY, Park SC, Lee HS, Kwak SS (2015) Comparative transcriptome analysis of sweetpotato and its land races in response to oxidative stress. Proceeding Book of Annual Academic Meeting of Korean Society for Plant Biotechnology (Korean Culture Training Institute, June 18-19, 2015). p59.
  16. Kim CY, Ahn YO, Kim SH, Kim YH, Lee HS, Catanach AS, Jacobs JME, Conner AJ, Kwak SS (2010) The sweetpotato IbMYB1 gene as a potential visible marker for sweetpotato intragenic vector system. Physiol Plantarum 139:229-240
  17. Kim MD, Ahn YO, Kim YH, Kim CY, Lee JJ, Jeong JC, Lee HS, Mok IJ, Kwak SS (2009) Strategies of development of environmentally firendly industrial sweetpotato on marginal lands by molecular breeding. J Plant Biotechnol 36:197-201 https://doi.org/10.5010/JPB.2009.36.3.197
  18. Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107: 22032-22037 https://doi.org/10.1073/pnas.1009526107
  19. Kim SH, Ahn YO, Ahn MJ, Jeong JC, Lee HS, Kwak SS (2013) Cloning and characterization of an Orange gene that increases carotenoid accumulation and salt stress tolerance in transgenic sweetpotato cultures. Plant Physiol Biochem 70:445-454 https://doi.org/10.1016/j.plaphy.2013.06.011
  20. Kriegner A, Cervantes JC, Burg K, Mwanga ROM, 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
  21. Lee JS, Ahn YS, Chung MN, Kim HS, Jeong KH, Bang JK, Song YS, Shim HK, Han SK, Suh SJ (2010) A New Sweetpotato Cultivar for Use of Bioethanol 'Daeyumi'. Korean J. Breed. Sci. 42:674-678
  22. Li AX, Liu QC, Wang QM, Zhang LM, Zhai H, Liu SZ (2010) Establishment of molecular linkage maps using SRAP markers in sweetpotato. Acta Agron. Sin. 36:1286-1295
  23. Monden Y, Hara T, Okada Y, Jahana O, Kobayashi A, Tabuchi H, Onaga S, Tahara M (2015) Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing. Breed Sci 65:145-153 https://doi.org/10.1270/jsbbs.65.145
  24. Park SC, Kim SH, Park SY, Lee HU, Lee JS, Bae JY, Ahn MJ, Kim YH, Jeong JC, Lee HS, Kwak SS (2015a) Enhanced accumulation of carotenoids in sweetpotato plants overexpressing IbOr-Insgene in purple-fleshed sweetpotato cultivar. Plant Physiol Biochem 86:82-90 https://doi.org/10.1016/j.plaphy.2014.11.017
  25. Park SC, Kim YH, Kim SH, Jeong YJ, Kim CY, Lee JS, Bae JY, Ahn MJ, Jeong JC, Lee HS, Kwak SS (2015b) Overexpression of the IbMYB1 gene in an orange-fleshed sweetpotato cultivar produces a dual-pigmented transgenic sweetpotato with improved antioxidant activity. Physiol Plantarum 153:525-537 https://doi.org/10.1111/ppl.12281
  26. Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189-195 https://doi.org/10.1038/nature10158
  27. Roullier C, Benoit L, McKey DB, Lebot V (2013) Historical collections reveal patterns of diffusion of sweetpotato in Oceania obscured by modern plant movements and recombination. Proc Natl Acad Sci USA 110:2205-2210 https://doi.org/10.1073/pnas.1211049110
  28. Roullier C, Duputie A, Wennekes P, Benoit L, Fernandez Bringas VM, Rossel G, Tay D, McKey D, Lebot V (2013) Disentangling the origins of cultivated sweetpotato (Ipomoea batatas (L.) Lam.). PLoS One 8:e62707 https://doi.org/10.1371/journal.pone.0062707
  29. Schafleitner R, Tincopa LR, Palomino O, Rossel G, Robles RF, Alagon R, Rivera C, Quispe C, Rojas L, Pacheco JA, Solis J, Cerna D, Kim JY, Hou J, Simon R (2010) A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genomics 11:604 https://doi.org/10.1186/1471-2164-11-604
  30. Tao X, Gu YH, Wang HY, Zheng W, Li X, Zhao CW, Zhang YZ (2012) Digital gene expression analysis based on integrated de novo transcriptome assembly of sweetpotato [Ipomoea batatas (L.) Lam]. PLoS One 7:36234 https://doi.org/10.1371/journal.pone.0036234
  31. TRAS (2015) Sweetpotato genomic sequencing. TRAS Newsletter 1:3
  32. Ukoskit K and Thompson PG (1997) Autopolyploidy versus allopolyploidy and low-density randomly amplified polymorphic DNA linkage maps of sweetpotato. J Amer Soc Hort Sci 122:22-828
  33. Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 11:26 https://doi.org/10.1186/1471-2164-11-26
  34. Wang Z, Li J, Luo Z, Huang L, Chen X, Fang B, Li Y, Chen J, Zhang X (2011) Characterization and development of ESTderived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC Plant Biol 11:139 https://doi.org/10.1186/1471-2229-11-139
  35. Xie F, Burklew CE, Yang Y, Liu M, Xiao P, Zhang B, Qiu D (2012) De novo sequencing and a comprehensive analysis of purple sweetpotato (Impomoea batatas L.) transcriptome. Planta 236:101-113 https://doi.org/10.1007/s00425-012-1591-4
  36. Yan L, Lai X, Li X, Wei C, Tan X, Zhang Y (2015) Analyses of the complete genome and gene expression of chloroplast of sweetpotato [Ipomoea batata]. PLoS One 10:e0124083 https://doi.org/10.1371/journal.pone.0124083
  37. Zhao N, Yu X, Jie Q, Li H, Li Hua, Hu J, Zhai H, He S, Liu Q (2013) A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweetpotato. Mol Breeding 32:807-820 https://doi.org/10.1007/s11032-013-9908-y
  38. Ziska LH, Runion GB, Tomecek M, Prior SA, Torbet HA, Sicher R (2009) An evaluation of cassava, sweetpotato and field corn as potential carbohydrtae sources for bioethanol production in Alabama and Maryland. Biomass Bioenerg 33:1503-1508 https://doi.org/10.1016/j.biombioe.2009.07.014

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