A high-density genetic map with array-based markers facilitates structural and quantitative trait locus analyses of the common wheat genome

DNA Research

Volumn 21, Issue 5, 2014, Pages 555-567

  Julio Cesar Masaru, Iehisa ^a   Ryoko, Ohno ^a   Tatsuro, Kimura ^b   Hiroyuki, Enoki ^b   Satoru, Nishimura ^b   Yuki, Okamoto ^a   Shuhei, Nasuda ^c   Shigeo, Takumi ^a  

^a KOBE UNIVERSITY   (Japan)

^b TOYOTA MOTOR CORPORATION   (Japan)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

Array based genotyping; Chromosomal synteny; High density genetic map; Next generation sequencing; QTL analysis

Indexed keywords

GENOMIC DNA; GENETIC MARKER;

ARTICLE; COMPUTER MODEL; GENE FREQUENCY; GENE MAPPING; GENE STRUCTURE; GENETIC LINKAGE; GENOME; GENOTYPE; HIGH THROUGHPUT SEQUENCING; NEXT GENERATION SEQUENCING; NONHUMAN; PLANT GENETICS; QUANTITATIVE TRAIT LOCUS; RETROPOSON; SIMPLE SEQUENCE REPEAT; TRANSPOSON; TRITICUM AESTIVUM; CHROMOSOME MAP; COMPUTER SIMULATION; DNA MICROARRAY; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; HORDEUM; PLANT GENOME; WHEAT;

CHROMOSOME MAPPING; COMPUTER SIMULATION; GENETIC LINKAGE; GENETIC MARKERS; GENOME, PLANT; HORDEUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT LOCI; TRITICUM;

EID: 84920918098     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsu020     Document Type: Article

References (44)

1. Kihara, H. 1944, Discovery of the DD-analyser, one of the ancestors of Triticum vulgare, Agric. Hortic, 19, 889-90 [in Japanese].
2. McFadden, E.S. and Sears, E.R. 1944, The artificial synthesis of Triticum spelta, Rec. Genet. Soc. Am., 13, 26-7.
3. Akbari, M., Wenzl, P., Caig, V, et al. 2006, Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome, Theor. Appl. Genet., 113, 1409-20.
4. Wenzl, P., Carling, J., Kudrna, D., et al. 2004, Diversity arrays technology (DArT) for whole-genome profiling of barley, Proc. Natl. Acad. Sci. USA, 101, 9915-20.
5. Sorrells, M.E., Gustafson, J.P., Somers, D., et al. 2011, Reconstruction of the Synthetic W7984 x Opata M85 wheat reference population, Genome, 54, 875-82.
6. Zhang, L.Y., Liu, D.C., Guo, X.L., et al. 2011, Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers, BMC Genetics, 12, 42.
7. Trebbi, D., Maccaferri, M., de Heer, P., et al. 2011, Highthroughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.), Theor. Appl. Genet, 123, 555-69.
8. Allen, A.M., Barker, G.L.A., Berry, ST., et al. 2011, Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L), Plant Biotechnol. J., 9, 1086-99.
9. Lai, K., Duran, C., Berkman, P.J., et al. 2012, Single nucleotide polymorphism discovery from wheat next-generation sequence data, Plant Biotechnol. J., 10, 743-9.
10. Cavanagh, C.R., Chao, S., Wang, S., et al. 2013, Genomewide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars, Proc. Natl. Acad. Sci. USA, 110, 8057-62.
11. Poland, J.A., Brown, P.J., Sorrells, M.E. and Jannink, J.L. 2012, Development of high-density genetic maps for barley and wheat usinganovel two-enzyme genotypingby-sequencing approach, PLoS ONE, 7, e32253.
12. Saintenac, C., Jiang, D., Wang, S. and Akhunov, E. 2013, Sequence-based mapping of the polyploid wheat genome, G3-Genes Genomes Genet., 3, 1105-14.
13. van Poecke, R.M.P., Maccaferri, M., Tang, J., et al. 2013, Sequence-based SNP genotyping in durum wheat, Plant Biotechnol. J., 11, 809-17.
14. Winfield, M.O., Wilkinson, P.A., Allen, A.M., et al. 2012, Targeted re-sequencing of the allohexaploid wheat exome, Plant Biotechnol. J., 10, 733-42.
15. Davey, J.W., Hohenlohe, P.A., Etter, P.D., Boone, J.Q., Catchen, J.M. and Blaxter, M.L. 2011, Genome-wide genetic marker discovery and genotyping using next-generation sequencing, Nat. Rev. Genet., 12, 499-510.
16. Kobayashi, F., Takumi, S. and Handa, H. 2010, Identification of quantitative trait loci for ABA responsive-ness at the seedling stage associated with ABA-regulated gene expression in common wheat, Theor. Appl. Genet., 121, 629-41.
17. Enoki, H., Nishimura, S. and Murakami, A. 2011, Method for designing probe in DNA microarray, and DNA microarray provided with probe designed thereby, International publication number: WO 2011/074510.
18. Enoki, H., Nishimura, S. and Murakami, A. 2012, Method for designing probe in DNA microarray, and DNA microarray provided with probe designed thereby, US patent application 20120190582A1.
19. Zerbino, D.R. and Birney, E. 2008, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res., 18, 821-9.
20. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25.
21. Beales, J., Turner, A., Griffiths, S., Snape, J.W. and Laurie, D.A. 2007, A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.), Theor. Appl. Genet., 115, 721-33.
22. Iwata, H. and Ninomiya, S. 2006, AntMap: constructing genetic linkage maps using an ant colony optimization algorithm, Breed. Sci., 56, 371-7.
23. Lorieux, M. 2012, MapDisto: fast and efficient computation of genetic linkage maps, Mol. Breed., 30, 1231-5.
24. Kosambi, D.D. 1944, The estimation of map distance from recombination values, Ann. Eugen., 12, 172-5.
25. Jia, J., Zhao, S., Kong, X., et al. 2013, Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation, Nature, 496, 91-5.
26. Ling, H.Q., Zhao, S., Liu, D., et al. 2013, Draft genome of the wheat A-genome progenitor Triticum urartu, Nature, 496, 87-90.
27. International Barley Genome Sequencing Consortium. 2012, A physical, genetic and functional sequence assembly of the barley genome, Nature, 491, 711-6.
28. Luo, M.C., Gu, Y.Q., You, F.M., et al. 2013, A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor, Proc. Natl. Acad. Sci. USA, 110, 7940-5.
29. Krzywinski, M., Schein, J., Birol, I., et al. 2009, Circos: an information aesthetic for comparative genomics, Genome Res., 19, 1639-45.
30. Broman, K.W., Wu, H., Sen, Ś. and Churchill, G.A. 2003, R/qtl: QTL mapping in experimental crosses, Bioinformatics, 19, 889-90.
31. Devos, K.M., Dubcovsky, J., Dvořák, J., Chinoy, C.N. and Gale, M.D. 1995, Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination, Theor. Appl. Genet., 91, 282-8.
32. Ma, J., Stiller, J., Berkman, P.J., et al. 2013, Sequence-based analysis of translocations and inversions in bread wheat (Triticum aestivum L.), PLoS ONE, 8, e79329.
33. Brenchley, R., Spannagl, M., Pfeifer, M., et al. 2012, Analysis of the bread wheat genome using whole-genome shotgun sequencing, Nature, 491, 705-10.
34. Sears, E.R. and Loegering, W.Q. 1961, A pollen-killing gene in wheat, Genetics, 46, 897.
35. Takumi, S., Motomura, Y., Iehisa, J.C.M. and Kobayashi, F. 2013, Segregation distortion caused by weak hybrid necrosis in recombinant inbred lines of common wheat, Genetica, 141, 463-70.
36. Chu, C.G., Faris, J.D., Friesen, T.L. and Xu, S.S. 2006, Molecular mapping of hybrid necrosis genes Ne1 and Ne2 in hexaploid wheat using microsatellite markers, Theor. Appl. Genet., 112, 1374-81.
37. Bikard, D., Patel, D., Le Metté, C., et al. 2009, Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana, Science, 323, 623-6.
38. Mizuta, Y., Harushima, Y. and Kurata, N. 2010, Ricepollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes, Proc. Natl. Acad. Sci. USA, 107, 20417-22.
39. Yang, J., Zhao, X., Cheng, K., et al. 2012, A killer-protector system regulates both hybrid sterility and segregation distortion, Science, 337, 1336-40.
40. Yu, H., Xie, W., Wang, J., et al. 2011, Gainsin QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers, PLoS ONE, 6, e17595.
41. Díaz, A., Zikhali, M., Turner, A.S., Isaac, P. and Laurie, D.A. 2012, Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum), PLoS ONE, 7, e33234.
42. Nguyen, A.T., Iehisa, J.C.M., Mizuno, N., Nitta, M., Nasuda, S. and Takumi, S. 2013, Differential contribution of two Ppd-1 homoeoalleles to early-flowering phenotype in Nepalese and Japanese varieties of common wheat, Breed. Sci., 63, 374-83.
43. Yan, L., Helguera, M., Kato, K., Fukuyama, S., Sherman, J. and Dubcovsky, J. 2004, Allelic variation at the VRN-1 promoter region in polyploid wheat, Theor. Appl. Genet., 109, 1677-86.
44. Evers, A.D., Cox, R.I., Shaheedullah, M.Z. and Withey, R.P. 1990, Predicting milling extraction rate by image analysis of wheat grains, Asp. Appl. Biol., 25, 417-26.