Construction of a genetic map based on high-throughput SNP genotyping and genetic mapping of a TuMV resistance locus in Brassica rapa

Molecular Genetics and Genomics

Volumn 289, Issue 2, 2014, Pages 149-160

  Chung, Hee ^a   Jeong, Young Min ^a   Mun, Jeong Hwan ^b   Lee, Soo Seong ^c   Chung, Won Hyong ^d   Yu, Hee Ju ^a  

^a The Catholic University of Korea   (South Korea)

^b Myong Ji University   (South Korea)

^c BioBreeding Institute   (South Korea)

^d Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

Brassica rapa; Breeding; Doubled haploid population; Genetic map; TuMV resistance locus

Indexed keywords

AGRONOMY; ARTICLE; BRASSICA RAPA; BRASSICACEAE; CHIIFU GENE; CHROMOSOME ARM; CULTIVAR; DOUBLED HAPLOID LINE; GENE; GENE LOCUS; GENE MAPPING; GENE SEGREGATION; GENE SEQUENCE; GENETIC MARKER; GENOME ANALYSIS; GENOTYPE; HORTICULTURE; INDEL MUTATION; MICROSPORE CULTURE; NONHUMAN; PLANT BREEDING; PLANT VIRUS; PRIORITY JOURNAL; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; TURNIP MOSAIC VIRUS; VIRUS RESISTANCE;

BRASSICA RAPA; BRASSICACEAE; TURNIP MOSAIC VIRUS;

BRASSICA RAPA; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENES, PLANT; GENETIC LINKAGE; GENETIC LOCI; GENETIC MARKERS; GENOME, PLANT; GENOTYPE; PLANT DISEASES; POLYMORPHISM, SINGLE NUCLEOTIDE; POTYVIRUS;

EID: 84898058826     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-013-0798-9     Document Type: Article

References (44)

1. Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet 119:507-517
2. Chen H, He H, Zou Y, Chen W, Yu R, Liu X, Yang Y, Gao YM, Xu JL, Fan LM, Li Y, Li ZK, Deng XW (2011) Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.). Theor Appl Genet 123:869-879
3. Cole AB, Király L, Lane LC, Wiggins BE, Ross K, Schoelz JE (2004) Temporal expression of PR-1 and enhanced mature plant resistance to virus infection is controlled by a single dominant gene in a new Nicotiana hybrid. Mol Plant Microbe Interact 17:976-985
4. Duprat A, Caranta C, Revers F, Menand B, Browning KS, Robaglia C (2002) The Arabidopsis eukaryotic initiation factor (iso)4E is dispensable for plant growth but required for susceptibility to potyviruses. Plant J 32:927-934
5. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Sun W, Wang H, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallee C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Yakub I, Birren BW, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archeveque P, Bellemare G, Saeki K, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861
6. Fujiwara A, Inukai T, Kim BM, Masuta C (2011) Combinations of a host resistance gene and the CI gene of turnip mosaic virus differentially regulate symptom expression in Brassica rapa cultivars. Arch Virol 156:1575-1581
7. Gallois JL, Charron C, Sanchez F, Pagny G, Houvenaghel MC, Moretti A, Ponz F, Revers F, Caranta C, German-Retana S (2010) Single amino acid changes in the turnip mosaic virus viral genome-linked protein (VPg) confer virulence towards Arabidopsis thaliana mutants knocked out for eukaryotic initiation factors eIF(iso)4E and eIF(iso)4G. J Gen Virol 91:288-293
8. Green SK, Deng TC (1985) Turnip mosaic virus strains in cruciferous hosts in Taiwan. Plant Dis 69:28-31
9. He XF, Fang YY, Feng L, Guo HS (2008) Characterization of conserved and novel microRNAs and their targets, including a TuMV-induced TIR-NBS-LRR class R gene-derived novel miRNA in Brassica. FEBS Lett 582:2445-2452
10. Hughes SL, Hunter PJ, Sharpe AG, Kearsey MJ, Lydiate DJ, Walsh JA (2003) Genetic mapping of the novel Turnip mosaic virus resistance gene TuRB03 in Brassica napus. Theor Appl Genet 107:1169-1173
11. Hyten DL, Song Q, Choi IY, Yoon MS, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND, Cregan PB (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 116:945-952
12. Jenner CE, Walsh JA (1996) Pathotypic variation in turnip mosaic virus with special reference to European isolates. Plant Pathol 45:848-856
13. Jenner CE, Wang X, Ponz F, Walsh JA (2002) A fitness cost for Turnip mosaic virus to overcome host resistance. Virus Res 86:1-6
14. Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, Drabek J, Lopez R, Price HJ (2005) Evolution of genome size in Brassicaceae. Ann Bot 95:229-235
15. Kaneko YH, Inukai T, Suehiro N, Natsuaki T, Masuta C (2004) Fine genetic mapping of the TuNI locus causing systemic veinal necrosis by turnip mosaic virus infection in Arabidopsis thaliana. Theor Appl Genet 110:33-40
16. Kang BC, Yeam I, Jahn MM (2005) Genetics of plant virus resistance. Annu Rev Phytopathol 43:581-621
17. Kim JS, Chung TY, King GJ, Jin M, Yang TJ, Jin YM, Kim HI, Park BS (2006) A sequence-tagged linkage map of Brassica rapa. Genetics 174:29-39
18. Kim H, Choi SR, Bae J, Hong CP, Lee SY, Hossain MJ, Van Nguyen D, Jin M, Park BS, Bang JW, Bancroft I, Lim YP (2009) Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genomics 10:432
19. Kim J, Kang W-H, Yang H-B, Park S, YuH J, Jang C-S, Kang B-C (2013) Identification of a broad-spectrum recessive gene in Brassica rapa and molecular analysis of the eIF4E gene family to develop molecular markers. Mol Breeding 32:385-398
20. Kosambi D (1944) The estimation of map distances from recombination values. Ann Eugen 12:172-175
21. Lellis AD, Kasschau KD, Whitham SA, Carrington JC (2002) Loss-of-susceptibility mutants of Arabidopsis thaliana reveal an essential role for eIF(iso)4E during potyvirus infection. Curr Biol 12:1046-1051
22. Liu XP, Lu WC, Liu BX, Li SY, Li JL, Zhao ZY, Wang HJ, Wang CH (1990a) A study on TuMV strain differentiation on cruciferous vegetables from ten regions of China: identification results with Green's methods. Virologica Sinica 1:82-87
23. Liu XP, Lu WC, Liu YK, Li JL (1990b) A study on TuMV strain differentiation of cruciferous vegetables from ten provinces in China: new host differentiator screening and strain classification. Chin Sci Bull 35:1734-1739
24. Liu B, Wang Y, Zhai W, Deng J, Wang H, Cui Y, Cheng F, Wang X, Wu J (2013) Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theor Appl Genet 126:231-239
25. Mun J-H, Yu H-J, Park S, Park BS (2009) Genome-wide identification of NBS-encoding resistance genes in Brassica rapa. Mol Genet Genomics 282:617-631
26. Park S, Yu H-J, Mun J-H, Lee SC (2010) Genome-wide discovery of DNA polymorphism in Brassica rapa. Mol Genet Genomics 283:135-145
27. Provvidenti R (1980) Evaluation of Chinese cabbage cultivars from Japan and the People's Republic of China for resistance to turnip mosaic virus and cauliflower mosaic virus. J Amer Soc Hort Sci 105:571-573
28. Qian W, Zhang S, Li F, Zhang H, Wu J, Wang X, Walsh JA, Sun R (2013) Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chinese cabbage (Brassica rapa L.). Theor Appl Genet 126:179-188
29. Ramchiary N, Lim YP (2011) Genetics of Brassica rapa L. In: Schmidt R, Bancroft I (eds) Genetics and genomics of the Brassicaceae. Springer, New York
30. Ramchiary N, Nguyen VD, Li X, Hong CP, Dhandapani V, Choi SR, Yu G, Piao ZY, Lim YP (2011) Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives. DNA Res 18:305-320
31. Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656-18661
32. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Misener S, Krawetz S (eds) Bioinformatics methods and protocols. Humana Press, p 365-386
33. Ruffel S, Dussault MH, Palloix A, Moury B, Bendahmane A, Robaglia C, Caranta C (2002) A natural recessive resistance gene against potato virus Y in pepper corresponds to the eukaryotic initiation factor 4E (eIF4E). Plant J 32:1067-1075
34. Rusholme RL, Higgins EE, Walsh JA, Lydiate DJ (2007) Genetic control of broad-spectrum resistance to turnip mosaic virus in Brassica rapa (Chinese cabbage). J Gen Virol 88:3177-3186
35. Seo MS, Jin M, Lee SS, Kwon SJ, Mun J-H, Park BS, Visser RG, Bonnema G, Sohn SH (2013) Mapping quantitative trait loci for tissue culture response in VCS3M-DH population of Brassica rapa. Plant Cell Rep 32:1251-1261
36. Suh SK, Green SK, Park HG (1995) Genetics of resistance to five strains of turnip mosaic virus in Chinese cabbage. Euphytica 81:71-77
37. The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035-1039
38. U N (1935) Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot 7:389-452
39. ® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands
40. Walsh JA, Sharpe AG, Jenner CE, Lydiate DJ (1999) Characterisation of resistance to turnip mosaic virus in oilseed rape (Brassica napus) and genetic mapping of TuRB01. Theor Appl Genet 99:1149-1154
41. Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD, Crouch J (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS ONE 4:e8451
42. Yoshii M, Nishikiori M, Tomita K, Yoshioka N, Kozuka R, Naito S, Ishikawa M (2004) The Arabidopsis cucumovirus multiplication 1 and 2 loci encode translation initiation factors 4E and 4G. J Virol 78:6102-6111
43. Zhang FL, Wang M, Liu XC, Zhao XY, Yang JP (2008) Quantitative trait loci analysis for resistance against turnip mosaic virus based on a doubled-haploid population in Chinese cabbage. Plant Breeding 127:82-86
44. Zhang X, Cal AJ, Borevitz JO (2011) Genetic architecture of regulatory variation in Arabidopsis thaliana. Genome Res 21:725-733