Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing

Theoretical and Applied Genetics

Volumn 128, Issue 2, 2015, Pages 259-272

  Mun, Jeong Hwan ^a   Chung, Hee ^b   Chung, Won Hyong ^c   Oh, Mijin ^d   Jeong, Young Min ^b   Kim, Namshin ^c   Ahn, Byung Ohg ^d   Park, Beom Seok ^d   Park, Suhyoung ^e   Lim, Ki Byung ^f   Hwang, Yoon Jung ^g   Yu, Hee Ju ^b  

^a Myong Ji University   (South Korea)

^b The Catholic University of Korea   (South Korea)

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

^d National Institute of Animal Science   (South Korea)

^e Rural Development Administration   (South Korea)

^f Kyungpook National University   (South Korea)

^g Sahmyook University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CROPS; GENES; GENETIC ENGINEERING; MAPPING; PLANTS (BOTANY); SCAFFOLDS; SEED;

ARABIDOPSIS THALIANA; COMPARATIVE ANALYSIS; GENOME SEQUENCING PROJECTS; GENOME STRUCTURES; GENOMIC RESOURCES; MAPPING POPULATIONS; PCR-BASED MARKERS; SEQUENCE ANALYSIS;

POPULATION STATISTICS;

GENETIC MARKER; PLANT DNA;

CHROMOSOME MAP; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENETIC MARKER; GENETICS; GENOTYPE; GENOTYPING TECHNIQUE; PLANT GENOME; RAPHANUS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, PLANT; GENETIC MARKERS; GENOME, PLANT; GENOTYPE; GENOTYPING TECHNIQUES; POLYMORPHISM, SINGLE NUCLEOTIDE; RAPHANUS; SEQUENCE ANALYSIS, DNA;

EID: 84925497211     PISSN: 00405752     EISSN: 14322242     Source Type: Journal    
DOI: 10.1007/s00122-014-2426-4     Document Type: Article

References (50)

1. Al-Shehbaz I, Beilstein M, Kellogg E (2006) Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview. Plant Syst Evol 259:89–120
2. Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, Baker D, Long Y, Meng J, Wang X, Liu S, Trick M (2011) Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol 29:762–766
3. Bett K, Lydiate D (2003) Genetic analysis and genome mapping in Raphanus. Genome 46:423–430
4. Budahn H, Peterka H, Mousa M, Ding Y, Zhang S, Li J (2009) Molecular mapping in oil radish (Raphanus sativus L.) and QTL analysis of resistance against beet cyst nematode (Heterodera schachtii). Theor Appl Genet 118:775–782
5. Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid K, Weigel D (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956–963
6. Celton J-M, Christoffels A, Sargent D, Xu X, Rees D (2010) Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map. BMC Biol 8:155
7. Cheng F, Mandáková T, Wu J, Xie Q, Lysak M, Wang X (2013) Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa. Plant Cell 25:1541–1554
8. Chung H, Jeong Y-M, Mun J-H, Lee S-S, Chung W-H, Yu H-J (2014) Construction of a genetic map based on high throughput SNP genotyping and genetic mapping of a TuMV resistance locus in Brassica rapa. Mol Genet Genomics 289:149–160
9. Deschamps S, Llaca V, May G (2012) Genotyping-by-sequencing in plants. Biology 1:460–483
10. Edenberg H, Liu Y (2009) Laboratory methods for high-throughput genotyping. Cold Spring Harb Protoc 2009:pdb-top62
11. Elshire R, Glaubitz J, Sun Q, Poland J, Kawamoto K, Buckler E, Mitchell S (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379
12. Hall A, Fiebig A, Preuss D (2002) Beyond the Arabidopsis genome: opportunities for comparative genomics. Plant Physiol 129:1439–1447
13. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076
14. Huang S, Deng L, Guan M, Li J, Lu K, Wang H, Fu D, Mason A, Liu S, Hua W (2013) Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus. BMC Genomics 14:717
15. Hwang Y-J, Yu H-J, Mun J-H, Ryu K, Park B-S, Lim K-B (2012) Centromere repeat DNA originated from Brassica rapa is detected in the centromere region of Raphanus sativus chromosomes. Korean J Hortic Sci Technol 30:751–756
16. Jeong Y-M, Chung W-H, Chung H, Kim N, Park B-S, Lim K-B, Yu H-J, Mun J-H (2014) Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica. Theor Appl Genet 127:1975–1989
17. Johnston J, Pepper A, Hall A, Chen Z, Hodnett G, Drabek J, Lopez R, Price H (2005) Evolution of genome size in Brassicaceae. Ann Bot 95:229–253
18. Jones E, Sullivan H, Bhattramakki D, Smith J (2007) A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theor Appl Genet 115:361–371
19. Kamei A, Tsuro M, Kobo N, Hayashi T, Wang N, Fujimura T, Hirai M (2010) QTL mapping of clubroot resistance in radish (Raphanus sativus L.). Theor Appl Genet 120:1021–1027
20. Kiss G, Kereszt A, Kiss P, Endre G (1998) Colormapping: a non-mathematical procedure for genetic mapping. Acta Biol Hung 49:125–142
21. Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y, Tonosaki K, Shirasawa S, Fukushima A, Yokoi S, Takahata Y, Kakizaki T, Ishida M, Okamoto S, Sakamoto K, Shirasawa K, Tabata S, Nishio T (2014) Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res. doi:10.1093/dnares/dsu014
22. Kosambi D (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175
23. Lai K, Duran C, Berkman P, Lorenc M, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D (2012) Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol J 10:743–749
24. Lee S-S, Lee S-A, Yang J, Kim J (2011) Developing stable progenies of xBrassicoraphanus, an intergeneric allopolyploid between Brassica rapa and Raphanus sativus, through induced mutation using microspore culture. Theor Appl Genet 122:885–891
25. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler Transform. Bioinformatics 25:1754–1760
26. Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, Ito T, Fujii H, Kishitani S, Kitashiba H, Nishio T (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
27. Lim K, de Jong H, Yang T, Park J, Kwon S, Kim J, Lim M, Kim J, Jin M, Jin Y, Kim S, Lim Y, Bang J, Kim H, Park B (2005) Characterization of rDNA and tandem repeats in the heterochromatin of Brassica rapa. Mol Cell 19:436–444
28. Lysak M, Koch M, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15:516–525
29. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo M (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303
30. Mun J-H, Kim D-J, Choi H-K, Gish J, Debellé F, Mudge J, Denny R, Endré G, Saurat O, Dudez A, Kiss G, Roe B, Young N, Cook D (2006) Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps. Genetics 172:2541–2555
31. Mun J-H, Kwon SJ, Yang TJ, Seol YJ, Jin M, Kim JA, Lim MH, Kim JS, Lee SI, Baek S, Choi BS, Kim DS, Kim N, Yu HJ, Lim KB, Lim YP, Bancroft I, Hahn JH, Park BS (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10:R111
32. Nussbaumer T, Martis M, Roessner S, Pfeifer M, Bader K, Sharma S, Gundlach H, Spannagl M (2013) MIPS PlantsDB: a database framework for comparative plant genome research. Nucleic Acids Res 41:D1144–D1151
33. Ossowski S, Schneeberger K, Clark R, Lanz C, Warthmann N, Weigel D (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18:2024–2033
34. Park S, Yu HJ, Mun JH, Lee SC (2010) Genome-wide discovery of DNA polymorphism in Brassica rapa. Mol Genet Genomics 283:135–145
35. Prakash S, Bhat S, Quiros C, Kirti P, Chopra V (2009) Brassica and its close allies: cytogenetics and evolution. In: Jules J (ed) Plant Breed Reviews, vol 31. Wiley, London, pp 21–187
36. Rozen S, Skaletsky H (1999) Primer3 on the WWW for General Users and for Biologist Programmers. In: Misener S, Krawetz S (eds) Bioinformatics Methods and Protocols. Humana Press, Totowa, pp 365–386
37. Santosh K, Travis W, Sylvie C (2012) SNP Discovery through next-generation sequencing and its applications. Int J Plant Genomics 2012:ID 831460
38. Shen D, Sun H, Huang M, Zheng Y, Li X, Fei Z (2013) RadishBase: a database for genomics and genetics of radish. Plant Cell Physiol 54:e3
39. Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M, Kishida Y, Kohara M, Takahashi C, Tsuruoka H, Wada T, Sakai T, Isobe S (2011) An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res 18:221–232
40. Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M, Belzile F (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8:e54603
41. Song K, Osborn T, Williams P (1990) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 3. Genomic relationships in Brassica and related genera and the origin of B. oleracea and B. rapa (syn. campestris). Theor Appl Genet 79:497–506
42. Subbaiyan G, Waters D, Katiyar S, Sadananda A, Vaddadi S, Henry R (2012) Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotechnol J 10:623–634
43. Trick M, Adamski N, Mugford S, Jiang C-C, Febrer M, Uauy C (2012) Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploidy wheat. BMC Plant Biol 12:14
44. Tsuro M, Suwabe K, Kobo 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 55:107–111
45. Uitdewilligen J, Wolters A, D’hoop B, Borm T, Visser R, van Eck H (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE 8:e62355
46. ® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma B. V, Wageningen
47. Wang S, Wang X, He Q, Liu X, Xu W, Li L, Gao J, Wang F (2012) Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep 31:1437–1447
48. Xu X, Liu X, Ge S, Jensen J, Hu F, Li X, Dong Y, Gutenkunst R, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W (2011) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30:105–111
49. Yang Y, Tai P, Chen Y, Li W (2002) A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA. Mol Phylogenet Evol 23:268–275
50. Yu H-J, Park S-G, Oh M, Hwang H-J, Kim N, Chung H, Sohn S-H, Park B-S, Mun J-H (2011) The Brassica rapa tissue-specific EST database. Korean J Hortic Sci Technol 29:633–640