QTL Analysis Using SNP Markers Developed by Next-Generation Sequencing for Identification of Candidate Genes Controlling 4-Methylthio-3-Butenyl Glucosinolate Contents in Roots of Radish, Raphanus sativus L

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Zou, Zhongwei ^a   Ishida, Masahiko ^b   Li, Feng ^a,c   Kakizaki, Tomohiro ^b   Suzuki, Sho ^a   Kitashiba, Hiroyasu ^a   Nishio, Takeshi ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b NARO Institute of Vegetable and Tea Science   (Japan)

^c INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BCAT4 GENE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC MARKER; GENOME ANALYSIS; MAM3 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPIC VARIATION; PLANT GENE; PLANT GENOME; PLANT ROOT; PMDH1 GENE; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; RADISH; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

2-ISOPROPYLMALATE SYNTHASE; ARABIDOPSIS; BASE SEQUENCE; BRASSICA RAPA; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GLUCOSINOLATES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MALATE DEHYDROGENASE; MOLECULAR SEQUENCE DATA; MULTIPLEX POLYMERASE CHAIN REACTION; PLANT PROTEINS; PLANT ROOTS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RAPHANUS; SYNTENY; TRANSAMINASES;

ARABIDOPSIS THALIANA; BRASSICA RAPA; RAPHANUS SATIVUS;

EID: 84872140551     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0053541     Document Type: Article

References (47)

1. Holst B, Williamson GA, (2004) A critical review of the bioavailability of glucosinolates and related compounds. Nat Prod Rep 21: 425-447.
2. Fashey JW, Zalcmann AT, Talalay P, (2001) The chemical diversity and distribution of glucosinolates and isothiocyanates among plants. Phytochemistry 56: 5-51.
3. Mithen RF, Dekker M, Verkerk R, Rabot S, Johnsom IT, (2000) The nutritional significance, biosynthesis and bioavailability of glucosinolates in human foods. J Sci Food Agric 80: 967-984.
4. Ramchiary N, Bisht NC, Gupta V, Mukhopadhyay A, Arumugam N, et al. (2007) QTL analysis reveals context-dependent loci for seed glucosinolate trait in the oilseed Brassica juncea: Importance of recurrent selection backcross scheme for the identification of 'true' QTL. Theor Appl Genet 116: 77-85.
5. Bisht NC, Gupta V, Ramchiary N, Sodhi YS, Mukhopadhyay A, et al. (2009) Fine mapping of loci involved with glucosinolate biosynthesis in oilseed mustard (Brassica juncea) using genomic information from allied species. Theor Appl Genet 118: 413-421.
6. Lou P, Zhao J, He H, Hanhart C, Del Carpio DP, et al. (2008) Quantitative trait loci for glucosinolate accumulation in Brassica rapa leaves. New Phytol 179: 1017-1032.
7. Wang H, Wu J, Sun SL, Liu B, Cheng F,et al. 2011, Glucosinolate biosynthetic genes in Brassica rapa. Gene 487: 135-142.
8. Zang YX, Kim HU, Kim JA, Lim MH, Jin M, et al. (2009) Genome-wide identification of glucosinolate synthesis genes in Brassica rapa. FEBS J 276: 3559-3574.
9. Gigolashvili T, Yatusevich R, Rollwitz I, Humphry M, Gershenzon J, et al. (2009) The plastidic bile acid transporter 5 is required for the biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana. Plant Cell 21: 1813-1829.
10. Sawada Y, Kuwahara A, Nagano M, Narisawa T, Sakata A, et al. (2009) Omics-based approaches to methionine side-chain elongation in Arabidopsis: characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase. Plant Cell Physiol 50: 1181-1190.
11. Kroymann J, Textor S, Tokuhisa JG, Falk KL, Bartram S, et al. (2001) A gene controlling variation in Arabidopsis glucosinolate composition is part of the methionine chain elongation pathway. Plant Physiol 127: 1077-1088.
12. Field B, Cardon G, Traka M, Botterman J, Vancanneyt G, et al. (2004) Glucosinolate and amino acid biosynthesis in Arabidopsis. Plant Physiol 135: 828-839.
13. Textor S, Kraker JW, Hause B, Gershenzon J, Tokuhisa JG, (2007) MAM3 catalyzes the formation of all aliphatic glucosinolate chain lengths in Arabidopsis. Plant Physiol 144: 60-71.
14. Brader G, Mikkelsen M, Halkier B, Tapio Palva E, (2006) Altering glucosinolate profiles modulates disease resistance in plants. Plant J 46: 758-767.
15. Grubb CD, Abel S, (2006) Glucosinolate metabolism and its control. Trends Plant Sci 11: 89-100.
16. Wittstock U, Halkier B, (2002) Glucosinolate research in the Arabidopsis era. Trends Plant Sci 7: 263-270.
17. Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, et al. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci 104: 6478-6483.
18. He Y, Mawhiney TP, Preuss ML, Schroeder AC, Chen B, et al. (2009) A redox-active isopropylmalate dehydrogenase functions in the biosynthesis of glucosinolates and leucine in Arabidopsis. Plant J 60: 679-690.
19. Bett KE, Lydiate DJ, (2003) Genetic analysis and genome mapping in Raphanus. Genome 46: 423-30.
20. Kamei A, Tsuro M, Kubo N, Hayashi T, Wang N, et al. (2010) QTL mapping of clubroot resistance in radish (Raphanus sativus L.). Theor Appl Genet 120: 1021-7.
21. Tsuro M, Suwabe K, Kubo N, Matsumoto S, Hirai M, (2005) Construction of a molecular linkage map of radish (Raphanus sativus L.), based on AFLP and Brassica-SSR markers. Breed Sci 55: 107-11.
22. Budahn H, Peterka H, Mousa MA, Ding Y, Zhang S, et al. (2009) Molecular mapping in oil radish (Raphanus sativus L.) and QTL analysis of resistance against beet cyst nematode (Heterodera schachtii). Theor Appl Genet 118: 775-82.
23. Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, et al. (2011) An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res 18: 221-232.
24. Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, et al. (2011) Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.). DNA Res 18: 401-411.
25. Tsuro M, Suwabe K, Kubo N, Matsumoto S, Hirai M, (2005) Construction of a molecular linkage map of radish (Raphanus sativus L.), based on AFLP and Brassica-SSR markers. Breed Sci 55: 107-11.
26. Carlson DG, Daxenbichler ME, VanEtten CH, (1985) Glucosinolate in radish cultivars. J Amer Soc Hort Sci 110: 634-638.
27. Ishida M, Nagata M, Ohara T, Kakizaki T, Hatakeyama K, et al. (2012) Small variation of glucosinolate composition in Japanese cultivars of radish (Raphanus sativus L.) accommodates simple quantitative analysis for breeding of glucosinolate component. Breed Sci 62: 63-70.
28. Ishii G, Saijo R, (1987) Effect of season, soil type, sulfate level, mulching and plant density on isothiocyanates content in radish root juice (Raphanus sativus L.). J Japan Soc Hort Sci 56: 313-320.
29. Ishida M, Kakizaki T, Ohara T, Morimitsu Y, (2011) Development of a simple and rapid extraction method of glucosinolates from radish roots. Breed Sci 61: 208-211.
30. Bjerg B, Sorensen H (1987) Quantitative analysis of glucosinolates and HPLC of intact glucosinolates, In: Wathelet J-P (ed) Glucosinolates in Rapeseeds: Analytical Aspects, Martinus Nijhoff Publishers, Dordrecht, Netherlands. 125-150.
31. Kaplinski L, Andreson R, Puurand T, Remm M, (2005) MultiPLX: automatic grouping and evaluation of PCR primers. Bioinformatics 21: 1701-2.
32. Doyle JJ, Doyle JL, (1990) Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
33. Shiokai S, Kitashiba H, Nishio T, (2010) Prediction of the optimum hybridization conditions of dot-blot-SNP analysis using estimated melting temperature of oligonucleotide probes. Plant Cell Rep 29: 829-34.
34. Shiokai S, Shirasawa K, Sato Y, Nishio T, (2010) Improvement of the dot-blot-SNP technique for efficient and cost-effective genotyping. Mol Breed 25: 179-85.
35. Van Ooijen JW (2006) JoinMap 4.0, Software for the calculation of genetic linkage maps in experimental populations. Kyazma, B.V.: Wageningen, The Netherlands.
36. Wang S, Basten CJ, Zeng ZB (2007) Windows QTL Cartographer 2.5, Department of Satistics. North Carolina State University, Ralegih, NC.
37. Braütigam A, Gowik U, (2010) What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biology 12: 831-841.
38. Trick M, Long Y, Meng JL, Bancroft I, (2009) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnology J 7: 334-346.
39. Halkier BA, Gershenzon J, (2006) Biology and biochemistry of glucosinolate, Ann Rev Plant Biol. 31: 303-333.
40. Wang XW, Wang HZ, Wang J, Sun RF, Wu J, et al. (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43: 1035-1040.
41. Schuster J, Knill J, Reichelt M, Gershenzon J, Binder S, (2006) BRANCHED-CHAIN AMINOTRANSFERASE4 is part of the chain elongation pathway in the biosynthesis of methionine-derived glucosinolates in Arabidopsis. Plant Cell 18: 2664-2679.
42. Ida ES, Fernando GF, Halkier BA, (2010) Biosynthesis of glucosinolates - gene discovery and beyond. Trends Plant Sci 15: 283-190.
43. Hansen CH, Wittstock U, Olsen CE, Hick AJ, Pickett JA, et al. (2001) Cytochrome p450 CYP79F1 from Arabidopsis catalyzes the conversion of dihomomethionine and trihomomethionine to the corresponding aldoximes in the biosynthesis of aliphatic glucosinolates. J. Biol. Chem 276: 11078-11085.
44. Chen SX, Glawischnig E, Jørgensen K, Naur P, Jørgensen B, et al. (2003) CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis. Plant J 33: 923-937.
45. Hemm MR, Ruegger MO, Chapple C, (2003) The Arabidopsis ref2 mutant is defective in the gene encoding CYP83A1 and shows both phenylpropanoid and glucosinolate phenotypes. Plant Cell 15: 179-194.
46. Naur P, Petersen BL, Mikkelsen MD, Bak S, Rasmussen H, et al. (2003) CYP83A1 and CYP83B1, two nonredundant cytochrome P450 enzymes metabolizing oximes in the biosynthesis of glucosinolates in Arabidopsis. Plant Physiol 133: 63-72.
47. Kroymann J, Donnerhacke S, Schnabelrauch D, Mitchell-Olds T, (2003) Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proc. Natl. Acad. Sci 100: 14587-14592.