Construction of the first genetic linkage map of Japanese gentian (Gentianaceae)

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Nakatsuka, Takashi ^a   Yamada, Eri ^a   Saito, Misa ^a   Hikage, Takashi ^b   Ushiku, Yuka ^a   Nishihara, Masahiro ^a  

^a IWATE BIOTECHNOLOGY RESEARCH CENTER   (Japan)

^b Hachimantai City Floricultural Research and Development Center   (Japan)

Author keywords

AFLP; Functional marker; Genetic linkage map; iPBS; Japanese gentian; marker; RAPD; REMAP; SSR

Indexed keywords

MOLECULAR MARKER; PLANT DNA;

AGRONOMIC TRAIT; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BACKCROSSING; BINDING SITE; COLD TOLERANCE; DOUBLED HAPLOID LINE; FLOWER COLOR; FLOWERING; GENE CONTROL; GENETIC LINKAGE; GENETIC SELECTION; GENTIAN; GENTIANACEAE; HAPLOIDY; INTER SIMPLE SEQUENCE REPEAT; LINKAGE ANALYSIS; LONG TERMINAL REPEAT; MARKER ASSISTED BREEDING; MORPHOLOGICAL TRAIT; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PLANT BREEDING; PLANT STEM; PROGENY; PYROSEQUENCING; RAMET; RANDOM AMPLIFIED POLYMORPHIC DNA; RETROPOSON; RETROTRANSPOSON MICROSATTLITE AMPLIFIED POLYMORPHISM; SEQUENCE ANALYSIS;

CHROMOSOME MAPPING; GENETIC LOCI; GENETIC MARKERS; GENTIANACEAE; INBREEDING; MICROSATELLITE REPEATS; PIGMENTATION; PLANT STEMS; RETROELEMENTS;

GENTIANA; GENTIANA SCABRA; GENTIANA TRIFLORA; GENTIANACEAE;

EID: 84870066979     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-672     Document Type: Article

References (52)

1. Kohlein Gentians 1991, London: Christopher Helm, Kohlein.
2. Nishihara M, Nakatsuka T, Mizutani-Fukuchi M, Tanaka Y, Yamamura S. Gentians: From gene cloning to molecular breeding. Floricultural and Ornamental Biotechnology V 2008, 57-67. UK: Global Science Books.
3. Nekoduka S, Tanaka K, Harada Y, Sano T. Phylogenetic affinity of Mycochaetophora gentianae, the causal fungus of brown leaf spot on gentian (Gentiana triflora), to Pseudocercosporella-like hyphomycetes in Helotiales. Mycoscience 2010, 51:123-133.
4. Nekoduka S, Tanaka K, Sano T. Pathogenicity of Mycochaetophora gentianae, causal fungus of gentian brown leaf spot, as affected by host species, inoculum density, temperature, leaf wetness duration, and leaf position. J Gen Plant Pathol 2010, 76:370-376.
5. Mishiba K, Yamane K, Nakatsuka T, Nakano Y, Yamamura S, Abe J, Kawamura H, Takahata Y, Nishihara M. Genetic relationships in the genus Gentiana based on chloroplast DNA sequence data and nuclear DNA content. Breed Sci 2009, 59:119-127.
6. Arabidopsis-genome-initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815. Arabidopsis-genome-initiative.
7. Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2012, 480:520-524.
8. International-Rice-Genome-Sequencing-Project The map-based sequence of the rice genome. Nature 2005, 436:793-800. International-Rice-Genome-Sequencing-Project.
9. The-tomato-genome-consortium The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485:635-641. The-tomato-genome-consortium.
10. Nakatsuka T, Nishihara M, Mishiba K, Yamamura S. Temporal expression of flavonoid biosynthesis-related genes regulates flower pigmentation in gentian plants. Plant Science 2005, 168:1309-1318.
11. Nakatsuka T, Haruta KS, Pitaksutheepong C, Abe Y, Kakizaki Y, Yamamoto K, Shimada N, Yamamura S, Nishihara M. Identification and characterization of R2R3-MYB and bHLH transcription factors regulating anthocyanin biosynthesis in gentian flowers. Plant & cell physiology 2008, 49:1818-1829.
12. Imamura T, Nakatsuka T, Higuchi A, Nishihara M, Takahashi H. The gentian orthologs of the FT/TFL1 gene family control floral initiation in Gentiana. Plant & cell physiology 2011, 52:1031-1041.
13. Hikage T, Saitoh Y, Tanaka-Saito C, Hagami H, Satou F, Shimotai Y, Nakano Y, Takahashi M, Takahata Y, Tsutsumi K. Structure and allele-specific expression variation of novel alpha/beta hydrolase fold proteins in gentian plants. Mol Genet Genomics 2007, 278:95-104.
14. Hikage T, Kogusuri K, Tanaka-Saito C, Watanabe S, Chiba S, Kume K, Doi H, Saitoh Y, Takahata Y, Tsutsumi K. W14/15 esterase gene haplotype can be a genetic landmark of cultivars and species of the genus Gentiana L. Mol Gen Genomics 2011, 285:47-56.
15. Kakizaki Y, Nakatsuka T, Kawamura H, Abe J, Abe Y, Yamamura S, Nishihara M. Development of codominant DNA marker distinguishing pink from blue flowers in Gentiana scabra. Breed Res 2009, 11:9-14. (Japanese).
16. Nakatsuka T, Saito M, Sato-Ushiku Y, Yamada E, Nakasato T, Hoshi N, Fujiwara K, Hikage T, Nishihara M. Development of DNA markers that discriminate between white- and blue-flowers in Japanese gentian plants. Euphytica 2012, 184:335-344.
17. Shimada N, Nakatsuka T, Nakano Y, Kakizaki Y, Abe Y, Hikage T, Nishihara M. Identification of gentian cultivars using SCAR markers based on intron-length polymorphisms of flavonoid biosynthetic genes. Sci Hort 2009, 119:292-296.
18. Sato-Ushiku Y, Shimada N, Saito M, Yamada E, Hikage T, Nakatsuka T, Nishihara M. Development of simple sequence repeat markers for identification of Japanese gentian cultivars. J Japan Soc Hort Sci 2011, 80:475-485.
19. Ribaut JM, Hoisington D. Marker-assisted selection: new tools and strategies. Trends Plant Sci 1998, 3:236-239.
20. Jones N, Ougham H, Thomas H, Pasakinskiene I. Markers and mapping revisited: finding your gene. New Phytol 2009, 183:935-966.
21. Debener T, Mattiesch L:. Construction of a genetic linkage map for roses using RAPD and AFLP markers. Theor Appl Genet 1999, 99:891-899.
22. Yan Z, Denneboom C, Hattendorf A, Dolstra O, Debener T, Stam P, Visser PB. Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Theor Appl Genet 2005, 110:766-777.
23. Yagi M, Onozaki T, Taneya M, Watanabe H, Yoshimura T, Yoshinari T, Ochiai Y, Sibata M. Construction of genetic linkage map for the carnation by using RAPD and SSR marker and mapping quantitative trait loci (QTL) for resistance to bacterial wilt caused by Burkholderia caryophylli. J Japan Soc Hort Sci 2006, 75:166-172.
24. Yagi M, Kimura T, Yamamoto T, Isobe S, Tabata S, Onozaki T. QTL analysis for resistance to bacterial wilt (Burkholderia caryophylli) in carnation (Dianthus caryophyllus) using an SSR-based genetic linkage map. Mol Breeding 2012, 30:495-509.
25. Abe H, Nakano M, Nakatsuka A, Nakayama M, Koshioka M, Yamagishi M. Genetic analysis of floral anthocyanin pigmentation traits in Asiatic hybrid lily using molecular linkage maps. Theor Appl Genet 2002, 105:1175-1182.
26. Shokeen B, Choudhary S, Sethy NK, Bhatia S. Development of SSR and gene-targeted markers for construction of a framework linkage map of Catharanthus roseus. Ann Bot 2011, 108:321-336.
27. Grattapaglia D, Sederoff R. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: Mapping strategy and RAPD markers. Genetics 1994, 137:1121-1137.
28. Bert PF, Charmet G, Sourdille P, Hayward MD, Balfourier F. A high-density molecular map for ryegrass (Lolium perenne) using AFLP markers. Theor Appl Genet 1999, 99:445-452.
29. Jones S, Dupal P, Dumsday L, Hughes J, Forster W. An SSR-based genetic linkage map for perennial ryegrass ( Lolium perenne L.). Theor Appl Genet 2002, 105:577-584.
30. Doi H, Takahashi R, Hikage T, Takahata Y. Embryogenesis and doubled haploid production from anther culture in gentian (Gentiana triflora). Plant Cell Tissue Organ Cult 2011, 102:27-33.
31. Nakatsuka T, Nishihara M, Mishiba K, Hirano H, Yamamura S. Two different transposable elements inserted in flavonoid 3',5'-hydroxylase gene contribute to pink flower coloration in Gentiana scabra. Mol Gen Genomics 2006, 275:231-241.
32. Kalendar R, Antonius K, Smykal P, Schulman AH. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 2010, 121:1419-1430.
33. Remington DL, Whetten RW, Liu BH, O'Malley DM. Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor Appl Genet 1999, 98:1279-1292.
34. Yamagishi M, Abe H, Nakano M, Nakatsuka A. PCR-based molecular markers in Asiatic hybrid lily. Sci Hort 2002, 96:225-234.
35. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature reviews 2011, 12:499-510.
36. Santana Q, Coetzee M, Steenkamp E, Mlonyeni O, Hammond G, Wingfield M, Wingfield B. Microsatellite discovery by deep sequencing of enriched genomic libraries. Biotechniques 2009, 46:217-223.
37. Martin JF, Pech N, Meglecz E, Ferreira S, Costedoat C, Dubut V, Malausa T, Gilles A. Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX titanium pyrosequencing. BMC genomics 2010, 11:560.
38. Kalendar R, Schulman AH. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat Protoc 2006, 1:2478-2484.
39. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 1999, 98:704-711.
40. Nishihara M, Hikage T, Yamada E, Nakatsuka T. A single-base substitution suppresses flower color mutation caused by a novel miniature inverted-repeat transposable element in gentian. Mol Genet Genomics 2011, 286:371-382.
41. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 1995, 23:4407-4414.
42. Vuylsteke M, Peleman JD, van Eijk MJ. AFLP technology for DNA fingerprinting. Nat Protoc 2007, 2:1387-1398.
43. Ye GN, Hemmat M, Lodhi MA, Weeden NF, Reisch BI. Long primers for RAPD mapping and fingerprinting of grape and pear. Biotechniques 1995, 20:368-371.
44. Haanstra JP, Lauge R, Meijer-Dekens F, Bonnema G, de Wit PJ, Lindhout P. An integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum × L. pennellii F2 populations. Theor Appl Genet 1999, 99:254-271.
45. Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J, Fei Z, Staub JE, Zalapa JE, Cuevas HE, Dace G, et al. A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC plant biology 2011, 11:111.
46. Truco MJ, Antonise R, Lavelle D, Ochoa O, Kozik A, Witsenboer H, Fort SB, Jeuken MJ, Kesseli RV, Lindhout P, et al. A high-density, integrated genetic linkage map of lettuce (Lactuca spp.). Theor Appl Genet 2007, 115:735-746.
47. Dunemann F, Kahnau R, Stange I. Analysis of complex leaf and flower characters in Rhododendron using a molecular linkage map. Theor Appl Genet 1999, 98:1146-1155.
48. Andersen JR, Lubberstedt T. Functional markers in plants. Trends Plant Sci 2003, 8:554-560.
49. Nakatsuka T, Nishihara M, Mishiba K, Yamamura S. Two different mutations are involved in the formation of white-flowered gentian plants. Plant Science 2005, 169:949-958.
50. Fukuoka H, Nunome N, Minamiyama Y, Kono I, Namiki N, Kojima A. read2Marker: a data processing tool for microsatellite marker development from a large data set. Biotechniques 2005, 39:472-476.
51. Kawasaki S, Murakami Y. Genome analysis of Lotus japonicus. J Plant Res 2000, 113:497-506.
52. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.