Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

BMC Plant Biology

Volumn 12, Issue , 2012, Pages

  Trick, Martin ^a   Adamski, Nikolai M ^a   Mugford, Sarah G ^a   Jiang, Cong Cong ^a   Febrer, Melanie ^b   Uauy, Cristobal ^a,c  

^a NORWICH RESEARCH PARK   (United Kingdom)

^b EARLHAM INSTITUTE   (United Kingdom)

^c NATIONAL INSTITUTE OF AGRICULTURAL BOTANY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRITICUM AESTIVUM;

PLANT DNA;

ARTICLE; BIOLOGY; CHROMOSOME MAP; DNA SEQUENCE; GENE LIBRARY; GENETICS; METHODOLOGY; MOLECULAR GENETICS; PLANT GENOME; POLYPLOIDY; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTENY; WHEAT;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DNA, PLANT; GENE LIBRARY; GENOME, PLANT; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYPLOIDY; SEQUENCE ANALYSIS, DNA; SYNTENY; TRITICUM;

EID: 84856121095     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-12-14     Document Type: Article

References (51)

1. FAO statistical yearbook 2005-2006. WEB., http://www.fao.org/es/ess/yearbook/
2. Angiosperm DNA C-values database. , http://www.rbgkew.org.uk/cval/homepage.html
3. Flavell RB, Bennett MD, Smith JB, Smith DB. Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 1974, 12(4):257-269. 10.1007/BF00485947, 4441361.
4. Joppa LR, Du C, Hart GE, Hareland GA. Mapping gene(s) for grain protein in tetraploid wheat (Triticum turgidum L.) using a population of recombinant inbred chromosome lines. Crop Science 1997, 37(5):1586-1589.
5. Olmos S, Distelfeld A, Chicaiza O, Schlatter AR, Fahima T, Echenique V, Dubcovsky J. Precise mapping of a locus affecting grain protein content in durum wheat. Theor Appl Genet 2003, 107(7):1243-1251. 10.1007/s00122-003-1377-y, 12923624.
6. The International Brachypodium Initiative Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463(7282):763-768. 10.1038/nature08747, 20148030, The International Brachypodium Initiative.
7. Yu J, Hu S, Wang J, Wong G, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92. 10.1126/science.1068037, 11935017.
8. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al. The Sorghum bicolor genome and the diversification of grasses. Nature 2009, 457(7229):551-556. 10.1038/nature07723, 19189423.
9. Distelfeld A, Uauy C, Olmos S, Schlatter A, Dubcovsky J, Fahima T. Microcolinearity between a 2-cM region encompassing the grain protein content locus Gpc-6B1 on wheat chromosome 6B and a 350-kb region on rice chromosome 2. Funct Integr Genomics 2004, 4(1):59-66. 10.1007/s10142-003-0097-3, 14752608.
10. Bossolini E, Krattinger S, Keller B. Development of simple sequence repeat markers specific for the Lr34 resistance region of wheat using sequence information from rice and Aegilops tauschi. Theor Appl Genet 2006, 113(6):1049-1062. 10.1007/s00122-006-0364-5, 16896711.
11. Distelfeld A, Uauy C, Fahima T, Dubcovsky J. Physical map of the wheat high-grain protein content gene Gpc-B1 and development of a high-throughput molecular marker. New Phytol 2006, 169(4):753-763. 10.1111/j.1469-8137.2005.01627.x, 16441756.
12. Spielmeyer W, Singh RP, McFadden H, Wellings C, Huerta-Espino J, Kong X, Appels R, Lagudah E. Fine scale genetic and physical mapping using interstitial deletion mutants Lr34/Yr18: a disease resistance locus effective against multiple pathogens in wheat. Theor Appl Genet 2008, 116(4):481-490. 10.1007/s00122-007-0684-0, 18074114.
13. Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J. Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum). Theor Appl Genet 2003, 107(5):931-939. 10.1007/s00122-003-1331-z, 12830387.
14. Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J. A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 2006, 314(5803):1298-1301. 10.1126/science.1133649, 17124321.
15. Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B. A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 2009, 323(5919):1360-1363. 10.1126/science.1166453, 19229000.
16. Krattinger S, Wicker T, Keller B. Map-Based cloning of genes in Triticeae (Wheat and Barley). Genetics and Genomics of the Triticeae 2009, 337-357. New York: Springer, Muehlbauer GJ, Feuillet C.
17. Schneeberger K, Weigel D. Fast-forward genetics enabled by new sequencing technologies. Trends Plant Sci 2011, 16(5):282-288. 10.1016/j.tplants.2011.02.006, 21439889.
18. Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jorgensen J-E, Weigel D, Andersen SU. SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods 2009, 6(8):550-551. 10.1038/nmeth0809-550, 19644454.
19. Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, Bonetta D, Zhang J, Fung P, Gong Y, Wang PW, et al. Next-generation mapping of Arabidopsis genes. Plant J 2011, 67(4):715-725. 10.1111/j.1365-313X.2011.04619.x, 21518053.
20. Mokry M, Nijman I, Van Dijken A, Benjamins R, Heidstra R, Scheres B, Cuppen E. Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach. BMC Genomics 2011, 12(1):256. 10.1186/1471-2164-12-256, 3114748, 21599977.
21. Trick M, Long Y, Meng J, Bancroft I. Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnology J 2009, 7(4):334-346.
22. Oliver R, Lazo G, Lutz J, Rubenfield M, Tinker N, Anderson J, Wisniewski-Morehead N, Adhikary D, Jellen E, Maughan PJ, et al. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics 2011, 12(1):77. 10.1186/1471-2164-12-77, 3041746, 21272354.
23. Trebbi D, Maccaferri M, De Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti M, Massi A, Van der-Vossen E, Tuberosa R. High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf). Theor Appl Genet 2011, 123(4):555-569. 10.1007/s00122-011-1607-7, 21611761.
24. Michelmore R, Paran I, Kesseli R. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 1991, 88(21):9828-9832. 10.1073/pnas.88.21.9828, 52814, 1682921.
25. Triticum aestivum: UniGene Build #57. , http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=4565
26. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
27. Dvorak J, Akhunov ED, Akhunov AR, Deal KR, Luo M-C. Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat. Mol Biol Evol 2006, 23(7):1386-1396. 10.1093/molbev/msl004, 16675504.
28. Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, Baker D, Long Y, Meng J, Wang X, et al. Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotech 2011, 29(8):762-766.
29. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
30. Chinese Spring sequence at cerealsDB. , http://www.cerealsdb.uk.net/
31. Rustenholz C, Hedley P, Morris J, Choulet F, Feuillet C, Waugh R, Paux E. Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources. BMC Genomics 2010, 11(1):714. 10.1186/1471-2164-11-714, 3019236, 21167071.
32. Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, et al. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 2011, 23(5):1706-1718. 10.1105/tpc.111.086629, 3123954, 21622801.
33. Massa AN, Wanjugi H, Deal KR, O'Brien K, You FM, Maiti R, Chan AP, Gu YQ, Luo MC, Anderson OD, et al. Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes. Molecular Biology and Evolution 2011, 28(9):2537-2547. 10.1093/molbev/msr080, 3163431, 21470968.
34. Mayer KFX, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, et al. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 2011, 23(4):1249-1263. 10.1105/tpc.110.082537, 3101540, 21467582.
35. Cantu D, Pearce S, Distelfeld A, Christiansen M, Uauy C, Akhunov E, Fahima T, Dubcovsky J. Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence. BMC Genomics 2011, 12(1):492. 10.1186/1471-2164-12-492, 3209470, 21981858.
36. Uauy C, Brevis JC, Dubcovsky J. The high grain protein content gene Gpc-B1 accelerates senescence and has pleiotropic effects on protein content in wheat. J Exp Bot 2006, 57(11):2785-2794. 10.1093/jxb/erl047, 16831844.
37. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, et al. Genome-wide in situ exon capture for selective resequencing. Nat Genet 2007, 39(12):1522-1527. 10.1038/ng.2007.42, 17982454.
38. Saintenac C, Jiang D, Akhunov ED. Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol 2011, 12:R88. 10.1186/gb-2011-12-9-r88, 21917144.
39. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10(1):57-63. 10.1038/nrg2484, 2949280, 19015660.
40. Lander ES, Waterman MS. Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 1988, 2(3):231-239. 10.1016/0888-7543(88)90007-9, 3294162.
41. Wendl M, Wilson R. Aspects of coverage in medical DNA sequencing. BMC Bioinformatics 2008, 9(1):239. 10.1186/1471-2105-9-239, 2430974, 18485222.
42. Allen AM, Barker GLA, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D'Amore R, McKenzie N, et al. Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnology J 2011, 9(9):1086-1099.
43. Peleg Z, Saranga Y, Suprunova T, Ronin Y, Röder M, Kilian A, Korol A, Fahima T. High-density genetic map of durum wheat × wild emmer wheat based on SSR and DArT markers. Theor Appl Genet 2008, 117(1):103-115. 10.1007/s00122-008-0756-9, 18437346.
44. Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, Barbazuk WB, Springer NM, Schnable PS. High-Throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics 2010, 184(1):19-26. 10.1534/genetics.109.107557, 2815916, 19884313.
45. Chao S, Zhang W, Akhunov E, Sherman J, Ma Y, Luo M-C, Dubcovsky J. Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars. Mol Breed 2009, 23(1):23-33.
46. Aegilops tauschii Genome Sequencing Project. , http://www.cshl.edu/genome/wheat
47. Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, et al. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology J 2011, 9(7):768-775.
48. International Wheat Genome Sequencing Consortium. , http://www.wheatgenome.org/
49. Howard T, Rejab NA, Griffiths S, Leigh F, Leverington-Waite M, Simmonds J, Uauy C, Trafford K. Identification of a major QTL controlling the content of B-type starch granules in Aegilops. J Exp Bot 2011, 62(6):2217-2228. 10.1093/jxb/erq423, 3060699, 21227932.
50. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
51. KBiosciences. , http://www.kbioscience.co.uk/