Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
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Current status and prospects of kiwifruit (Actinidia chinensis) genomics

참다래 유전체 연구 동향

  • Kim, Seong-Cheol (Namhae Sub-Station, National Institute of Horticultural and Herbal Science, RDA) ;
  • Kim, Ho Bang (Life Sciences Research Institute, Biomedic Co., Ltd.) ;
  • Joa, Jae-Ho (Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, RDA) ;
  • Song, Kwan Jeong (Faculty of Bioscience and Industry, SARI, Jeju National University)
  • 김성철 (농촌진흥청 국립원예특작과학원 남해출장소) ;
  • 김호방 ((주)바이오메딕 생명과학연구소) ;
  • 좌재호 (농촌진흥청 국립원예특작과학원 온난화대응농업연구소) ;
  • 송관정 (제주대학교 생물산업학부 원예환경전공)
  • Received : 2015.12.23
  • Accepted : 2015.12.30
  • Published : 2015.12.31
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Abstract

Kiwifruit is a new fruit crop that was commercialized in the late 1970s. Recently, its cultivation and consumption have increased rapidly worldwide. Kiwifruit is a dioecious, deciduous, and climbing plant having fruit with hairs and various flesh colors and a variation in ploidy level; however, the industry consists of very simple cultivars or genotypes. The need for efficient cultivar improvement together with the evolutional and biological perspectives based on unique plant characteristics, have recently encouraged genome analysis and bioinformatics application. The draft genome sequence and chloroplast genome sequence of kiwifruit were released in 2013 and 2015, respectively; and gene annotation has been in progress. Recently, transcriptome analysis has shifted from previous ESTs analysis to the RNA-seq platform for intensive exploration of controlled genetic expression and gene discovery involved in fruit ascorbic acid biosynthesis, flesh coloration, maturation, and vine bacterial canker tolerance. For improving conventional breeding efficiency, molecular marker development and genetic linkage map construction have advanced from basic approaches using RFLP, RAPD, and AFLP to the development of NGS-based SSR and SNP markers linked to agronomically important traits and the construction of highly saturated linkage maps. However, genome and transcriptome studies have been limited in Korea. In the near future, kiwifruit genome and transcriptome studies are expected to translate to the practical application of molecular breeding.

키위는 세계적으로 1970년대 이후 상업화되어 최근 재배가 급속히 확대되고 있는 신종 과수이며, 국내에서도 재배와 소비량이 급격히 증가하고 있다. 키위는 자웅이주 낙엽성 덩굴 식물로 과피에 털이 있고 과육색이 다양한 특성을 가지고 있으며 배수성도 다양하나, 산업적인 품종 구성은 매우 단순하다. 독특한 식물적 특성에 기인한 진화 및 생물학적 관점은 물론 다양한 품종의 효율적 개발의 요구에 따라 최근 유전체 해석 및 활용 연구가 활발히 진행되고 있다. 키위 유전체 draft 서열과 엽록체 서열이 Illumina HiSeq 기반으로 각각 2013년과 2015년에 해독 되었으며 gene annotation 연구가 계속적으로 진행되고 있다. 과거 ESTs 기반의 전사체 분석에서 최근 RNA-seq 기반의 전사체 분석으로 전환되어 과일의 아스코르브산 생합성, 과육색 발현 및 성숙, 그리고 나무의 궤양병 저항성 관련 유전적 발현조절과 유전자 발굴 연구가 중점적으로 진행되고 있다. 전통육종의 효율을 증대하기 위한 분자표지 개발 및 유전자지도 작성에 있어서는 이전의 RFLP, RAPD, AFLP 기반의 연구에서 벗어나 NGS 기반의 유전체 및 전사체 정보의 해독에 의한 SSR 및 SNP 기반의 농업적으로 중요한 형질연관 분자마커 개발 및 고밀도 유전자지도 작성이 연구되고 있다. 그러나 국내 연구는 아직 제한적인 수준에서 진행되고 있다. 향후 키위 유전체 및 전사체 분석 연구는 가까운 장래에 실질적으로 분자육종에 적용될 것으로 전망된다.

Keywords

References

  1. Avsar B, Aliabadi DE (2015) Putative microRNA analysis of the kiwifruit Actinidia chinensis through genomic data. International J Life Sci Biotechnol Pharma Res 4:96-99
  2. Collins BH, Horska A, Hotten PM, Riddoch C, Collins AR (2001) Kiwifruit protects against oxidative DNA damage in human cells and in vitro. Nutr Cancer 39:148-153 https://doi.org/10.1207/S15327914nc391_20
  3. Collins AR, Harrington V, Drew J, Melvin R (2003) Nutritional modulation of DNA repair in a human intervention study. Carcinogenesis 24:511-513 https://doi.org/10.1093/carcin/24.3.511
  4. Crowhurst RN, Lints R, Atkinson RG, Gardner RC (1990) Restriction-fragment-length-polymorphisms in the genus Actinidia (Actinidiaceae). Plant Syst Evol 172:193-203 https://doi.org/10.1007/BF00937806
  5. Crowhurst RN et al (2008) Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 9:351 https://doi.org/10.1186/1471-2164-9-351
  6. Cui Z, Huang H, Xiao X (2002) Actinidia in China. China Agri Sci Technol. Beijing
  7. Du D, Rawat N, Deng Z, Gmitter Jr FG (2015) Construction of citrus gene coexpression networks from microarray data using random matrix theory. Hortic Res 2:15026 https://doi.org/10.1038/hortres.2015.26
  8. Ferguson AR (1984) Kiwifruit: a botanical review. Hortic Rev 6:1-64
  9. Ferguson AR, Bollard EG (1990) Domestication of the kiwifruit, p. 165-246. In: IJ Warrington, GC Weston (eds.) Kiwifruit: science and management. Ray Richards Publisher in association with the New Zealand, Soc Hort Sci, Auckland
  10. Fraser LG, Harvey CF, Crowhurst RN, De Silva HN (2004) ESTderived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 108:1010-1016 https://doi.org/10.1007/s00122-003-1517-4
  11. Fraser LG, McNeilage MA, Tsang GK, Harvey CF, De Silva HN (2005) Cross-species amplification of microsatellite loci within the dioecious, polyploid genus Actinidia (Actinidiaceae). Theor Appl Genet 112:149-157 https://doi.org/10.1007/s00122-005-0117-x
  12. Fraser LG, Tsang GK, Datson PM, De Silva HN, Harvey CF, Gill GP, Crowhurst RN, McNeilage MA (2009) A gene-rich linkage map in the dioecious species Actinidia chinensis (kiwifruit) reveals putative X/Y sex-determining chromosomes. BMC Genomics 10:102 https://doi.org/10.1186/1471-2164-10-102
  13. Fredrique OS, Legave JM, Nicole MF, Hirsch AM (1994) Use of flow cytometry for rapid determination of ploidy level in the genus Actinidia. Sci Hort 57:303-313 https://doi.org/10.1016/S0304-4238(94)90113-9
  14. Gao J, Huang C, Ge C, Qu X, Gu Q, Xu X (2013) Analysis of differential gene expression during color-turning stages in yellow flesh kiwifruit (Actinidia chinensis) using DGE. J Fruit Sci 2013-03
  15. Gaj T, Gersbach CA, Barbas CF (2013) ZFN, TALEN, and CRISPR/Casbased methods for genome engineering. Trends Biotechnol 31:397-405 https://doi.org/10.1016/j.tibtech.2013.04.004
  16. Gill GP, Harvey CF, Gardner RC, Fraser LG (1998) Development of sex-linked PCR markers for gender identification in Actinidia. Theor Appl Genet 97:439-445 https://doi.org/10.1007/s001220050914
  17. Harvey CF, Gill GP, Fraser LG, McNeilage MA (1997) Sex determination in Actinidia. 1. Sex-linked markers and progeny sex ratio in diploid A. chinensis. Sex Plant Reprod 10:149-154 https://doi.org/10.1007/s004970050082
  18. Hill MG, Mauchline N, Jones MK, Sutherland PW (2011) The response of resistant kiwifruit (Actinidia chinensis) to armoured scale insect (Diaspididae) feeding. Arthropod-Plant Interact 5:149-161 https://doi.org/10.1007/s11829-011-9124-9
  19. Hill MG, Wurms KV, Davy MW, Gould E, Allan A, Mauchline NA, Luo Z, Chee AA, Stannard K, Storey RD, Rikkerrink EH (2015) Transcriptome analysis of kiwifruit (Actinidia chinensis) bark in response to armoured scale insect (Hemiberlesia lataniae) feeding. PLoS ONE 10:e0141664 https://doi.org/10.1371/journal.pone.0141664
  20. Hopping ME (1994) Flow cytometric analysis of Actinidia species. New Zealand J Bot 32:85-93 https://doi.org/10.1080/0028825X.1994.10410410
  21. Huang WG, Cipriani G, Morgante M, Testolin R (1998) Microsatellite DNA in Actinidia chinensis: isolation, characterisation, and homology in related species. Theor Appl Genet 97:1269-1278 https://doi.org/10.1007/s001220051019
  22. Huang HW, Li ZZ, Li JQ, Kubisiak TL, Layne DR (2002) Phylogenetic relationships in Actinidia as revealed by RAPD analysis. J American Soc Hort Sci 127:759-766
  23. Huang S et al (2013) Draft genome of the kiwifruit Actinidia chinensis. Nature Commun 4:2640 https://doi.org/10.1038/ncomms3640
  24. Huang H (2014) The genus Actinidia, a world monograph. Science Press, Beijing
  25. Kim SC, Jung YH, Kim M, Kim CH, Koh SC, Kang SH (2003) Genetic relationships of genus Actinidia based on random amplified polymorphic DNA analysis. Hort Environ Biotechnol 44:340-344
  26. Kim YJ, Kwak CI, Gu YY, Hwang IT, Chun JY (2004a) Annealing control primer system for identification of differentially expressed genes on agarose gels. BioTechniques 36:424-426, 428, 430 https://doi.org/10.2144/04363ST02
  27. Kim SC, Jung YH, Kim M, Koh SC, Song KJ, Kim HB (2004b) Characterization of a RAPD fragment unique to species with hairy fruit skin in the genus Actinidia. J Plant Biol 47:210-215 https://doi.org/10.1007/BF03030510
  28. Kim CH, Kim SC, Jan KC, Song EY, Kim M, Moon DY, Song KC, Lee JS, Suh HD, Song KJ (2007a) A new kiwifruit cultivar, 'Jecy Gold' with yellow flesh. Kor J Breed Sci 39:258-259
  29. Kim CH, Kim SC, Jang KC, Song EY, Ro NY, Moon DY, Lee JS, Seong KC (2007b) A new kiwifruit cultivar, 'Jecy Green'. Kor J Breed Sci 39:508-509
  30. Kim CH, Kim SC, Song EY, Ro NY, Kim M, Kang KH, Jang KC, Chun SJ (2009) A new kiwifruit, 'Jecy Sweet' with high soluble solids content. Kor J Hort Sci Technol 39:508-509
  31. Kim HB, Jun SS, Choe S, Cho JY, Choi SB, Kim SC (2010a) Identification of differentially expressed genes from male and female flowers of kiwifruit. African J Biotechnol 9:6684-6694
  32. Kim M, Kim SC, Song KJ, Kim HB, Kim IJ, Song EY, Chun SJ (2010b) Transformation of carotenoid biosynthetic genes using a micro-cross section method in kiwifruit (Actinidia deliciosa cv. Hayward). Plant Cell Rep 29:1339-1349 https://doi.org/10.1007/s00299-010-0920-y
  33. Kim DG, Jin YG. Jin JY, Kim SC, Han CH, Lee YJ (2011) Effects of the Actinidia chinensis on loperamide-induced constipation in rat. Kor J Plant Res 24:61-68 https://doi.org/10.7732/kjpr.2011.24.1.061
  34. Kim SC, Uhm YK, Ko S, Oh CJ, Kwack YB, Kim HL, Lee Y, An CS, Park PB, Kim HB (2015) KiwiPME1 encoding pectin methylesterase is specifically expressed in the pollen of a dioecious plant species, kiwifruit (Actinidia chinensis). Hort Environ Biotechnol 56:402-410 https://doi.org/10.1007/s13580-015-0145-7
  35. Korea Agricultural Marketing Information Service (KAMIS) (2014) Korea agricultural and marine product circulation information. http://www.kamis.co.kr/kamis/index.jsp
  36. Korkovelos AE, Mavromatis AG, Huang WG, Hagidimitriou M, Giakoundis A, Goulas CK (2008) Effectiveness of SSR molecular markers in evaluating the phylogenetic relationships among eight Actinidia species. Sci Hortic 116:305-310 https://doi.org/10.1016/j.scienta.2008.01.011
  37. Kruger J, Thomas CM, Golstein C, Dixon MS, Smoker M, Tang SK, Mulder L, Jones JDG (2002) A tomato cysteine protease required for Cf-2-dependent disease resistance and suppression of autonecrosis. Science 296:744-747 https://doi.org/10.1126/science.1069288
  38. Li HL (1952) A taxonomic review of the genus Actinidia. J Arnold Arvoretum (Harvard university) 33:1-6
  39. Li W, Liu Y, Zeng S, Xiao G, Wang G, Wang Y, Peng M, Huang H (2015) Gene Expression profiling of development and anthocyanin accumulation in kiwifruit (Actinidia chinensis) based on transcriptome sequencing. PLoS ONE 10:e0136439 https://doi.org/10.1371/journal.pone.0136439
  40. Li C, Zhang B (2016) MicroRNAs in control of plant development. J Cell Physiol 231:303-313 https://doi.org/10.1002/jcp.25125
  41. Liang CF (1984) Actinidia, p. 309-324. In: KM Feng (ed.) Flora reipublicae popularis sinicae. Science press, Beijing
  42. Man Y, Wang Y, Zhang L, Li Z, Qin R, Jiang Z, Sun X, Liu C (2011) Development of microsatellite markers in Actinidia arguta (Actinidiaceae) based on the NCBI data platform. American J Bot e310-e315
  43. Man YP, Wang YC, Jiang ZW, Gong JJ (2015) Transcriptomic analysis of pigmented inner pericarp of red-fleshed kiwifruit in response to high temperature. Acta Hortic 10.17660/ActaHortic.2015.1096.23
  44. Michelotti V, Lamontanara A, Buriani G, Cellini A, Donati I, Vanneste JL, Cattivelli L, Spinelli F, Orru L, Tacconi G (2015a) Unraveling the molecular interaction between Pseudomonas syringae pv. actinidiae (Psa) and the kiwifruit plant through RNAseq approach. Acta Hortic 10.17660/ActaHortic.2015.1095.10
  45. Michelotti V, Lamontanara A, Orru L, Cattivelli L, Tacconi G, Buriani G, Cellini A, Donati I, Spinelli F, Vanneste J (2015b) RNA-seq analysis of the molecular interaction between Pseudomonas syringae pv. actinidiae (Psa) and the kiwifruit. Acta Hortic 10.17660/ActaHortic.2015.1096.41
  46. Nieuwenhuizen NJ, Maddumage R, Tsang GK, Fraser LG, Cooney JM, De Silva HN, Green S, Richardson KA, Atkinson RG (2012) Mapping, complementation, and targets of the cysteine protease actinidin in kiwifruit. Plant Physiol 158:376-388 https://doi.org/10.1104/pp.111.187989
  47. Novo M, Romo S, Rey M, Prado MJ, Gonzalez MV (2010) Identification and sequence characterisation of molecular markers polymorphic between male kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) accessions exhibiting different flowering time. Euphytica 175:109-121 https://doi.org/10.1007/s10681-010-0192-1
  48. Pei C, Law YW (1948) Notes on Actinidia of Szechuan and Sikang. Bot Bull Acad Sinica 2:25-33
  49. Save R, Serrano L (1986) Some physiological and growth responses of kiwi fruit (Actinidia chinensis) to flooding. Physiol Plant 66:75-78 https://doi.org/10.1111/j.1399-3054.1986.tb01236.x
  50. Schmid R (1978) Reproductive anatomy of Actinidia chinensis (Actinidiaceae). Bot J Syst Pfl 100:149-195
  51. Scortichini M, Marcelletti S, Ferrante P, Petriccione M, Firrao G (2012) Pseudomonas syringae pv. actinidiae: a re-emerging, multi-faceted, pandemic pathogen. Mol Plant Pathol 13:631-640 https://doi.org/10.1111/j.1364-3703.2012.00788.x
  52. Shi T, Huang H, Barker MS (2010) Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Ann Bot 106:497-504 https://doi.org/10.1093/aob/mcq129
  53. Shirkot P, Sharma DR, Mohapatra T (2002) Molecular identification of sex in Actinidia deliciosa var. deliciosa by RAPD markers. Sci Hortic 94:33-39 https://doi.org/10.1016/S0304-4238(01)00357-0
  54. Testolin R, Cipriani G, Costa G (1995) Sex segregation ratio and gender expression in the genus Actinidia. Sex Plant Reprod 8:129-132
  55. Testolin R, Huang WG, Lain O, Messina R, Vecchione A, Cipriani G (2001) A kiwifruit (Actinidia spp.) linkage map based on microsatellites and integrated with AFLP markers. Theor Appl Genet 103:30-36 https://doi.org/10.1007/s00122-001-0555-z
  56. The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635-641 https://doi.org/10.1038/nature11119
  57. Van der Hoorn RAL (2008) Plant proteases: from phenotypes to molecular mechanisms. Annu Rev Plant Biol 59:191-223 https://doi.org/10.1146/annurev.arplant.59.032607.092835
  58. Voogd C, Wang T, Varkonyi-Gasic E (2015) Functional and expression analyses of kiwifruit SOC1-like genes suggest that they may not have a role in the transition to flowering but may affect the duration of dormancy. J Exp Bot 66:4699-4710 https://doi.org/10.1093/jxb/erv234
  59. Vissers MC, Carr AC, Pullar JM, Bozonet SM (2013) The bioavailability of vitamin C from kiwifruit. Adv Food Nutr Res 68:125-147 https://doi.org/10.1016/B978-0-12-394294-4.00007-9
  60. Wang T, Gleave AP (2012) Applications of Biotechnology in Kiwifruit (Actinidia). p. 3-30. In: EC Agbo (ed.) Innovations in Biotechnology, InTech, Shanghai
  61. Watanabe K, Takahashi B, Shirato K (1990) Chromosome numbers in kiwifruit (Actinidia deliciosa) and related species. J Japanese Soc Hort Sci 58:835-840 https://doi.org/10.2503/jjshs.58.835
  62. Wong DCJ, Sweetman C, Ford CM (2014) Annotation of gene function in citrus using gene expression information and co-expression networks. BMC Plant Biol 14:186 https://doi.org/10.1186/1471-2229-14-186
  63. Woo JW, Kim J, Kwon SI, Corvalan C, Cho SW, Kim H, Kim SG, Kim ST, Choe S, Kim JS (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat Biotechnol 33:1162-1164 https://doi.org/10.1038/nbt.3389
  64. Xiao XG, Zhang LS, Li SH, Wang B, Testolin R, Cipriani G (1999) First step in the search for AFLP markers linked to sex in Actinidia. Pro 4th Intl Symp 498:99-104
  65. Xu Q et al. (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59-66 https://doi.org/10.1038/ng.2472
  66. Yan G, Yao J, Ferguson AR, McNeilage MA, Seal AG, Murray B (1997) New reports of chromosome numbers in Actinidia (Actinidiaceae). New Zealand J Bot 35:181-186 https://doi.org/10.1080/0028825X.1997.10414154
  67. Yao X, Tang P, Li Z, Li D, Liu Y, Huang H (2015) The first complete chloroplast genome sequences in Actinidiaceae: genome structure and comparative analysis. PLoS ONE 10:e0129347 https://doi.org/10.1371/journal.pone.0129347
  68. Zhang RM (1981) Selected varieties of kiwifruit, p. 134-141. In: ZZ. Qu (ed.). Mihoutaode Zaipei he Liyong. Nongye Chubanshe, Beijing
  69. Zhang JY, Huang SN, Mo ZH, Xuan JP, Jia XD, Wang G, Guo ZR (2015a) De novo transcriptome sequencing and comparative analysis of differentially expressed genes in kiwifruit under waterlogging stress. Mol Breed 35:208 https://doi.org/10.1007/s11032-015-0408-0
  70. Zhang Q, Liu C, Liu Y, VanBuren R, Yao X, Zhong C, Huang H (2015b) High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers. DNA Res 22:367-375 https://doi.org/10.1093/dnares/dsv019
  71. Zhang X, Huang C, Zhong M, Chen C, Lang B, Qu X, Xu X (2015c) Analysis of expression of the related genes with carotenoids synthesis in yellow flesh kiwifruit (Actinidia chinensis) based on RNA-seq. J Fruit Sci 2015-3
  72. Zhou J, Liu YF, Huang HW (2011) Characterization of 15 novel single nucleotide polymorphisms (SNPs) in the Actinidia chinensis species complex (Actinidiaceae). American J Bot 98:E100-E102 https://doi.org/10.3732/ajb.1000442

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