New algorithm improves fine structure of the barley consensus SNP map

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Endelman, Jeffrey B ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; BARLEY; COMPUTER PROGRAM; CONTROLLED STUDY; DIRECTED ACYCLIC GRAPH; GENE LOCUS; GENE MAPPING; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC MARKER; GENETIC PROCEDURES; LINKAGE ANALYSIS; NONHUMAN; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURE ANALYSIS; TELOMERE; CHROMOSOME MAP; DNA SEQUENCE; GENETICS; HORDEUM; METHODOLOGY; MOLECULAR GENETICS; PLANT GENOME; VALIDATION STUDY;

HORDEUM;

PLANT DNA;

ALGORITHMS; CHROMOSOME MAPPING; DNA, PLANT; GENOME, PLANT; HORDEUM; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 81155157967     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-407     Document Type: Article

References (31)

1. Beavis WD, Grant D. A linkage map based on information from four F2 populations of maize (Zea mays L.). Theor Appl Genet 1991, 82:636-644.
2. Stam P. Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 1993, 3:739-744.
3. Somers DJ, Isaac P, Edwards K. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 2004, 109:1105-1114. 10.1007/s00122-004-1740-7, 15490101.
4. Mace ES, Rami J-F, Bouchet S, Klein PE, Klein RR, Kilian A, Wenzl P, Xia L, Halloran K, Jordan DR. A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers. BMC Plant Biol 2009, 9:13. 10.1186/1471-2229-9-13, 2671505, 19171067.
5. Danan S, Veyrieras J-B, Lefebvre V. Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC Plant Biol 2011, 11:16. 10.1186/1471-2229-11-16, 3037844, 21247437.
6. Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R. Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics 2005, 274:515-527. 10.1007/s00438-005-0046-z, 16244872.
7. Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 2006, 7:206. 10.1186/1471-2164-7-206, 1564146, 16904008.
8. Marcel TC, Varshney RK, Barbieri M, Jafary H, de Kock MJD, Graner A, Niks RE. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. Theor Appl Genet 2007, 114:487-500. 10.1007/s00122-006-0448-2, 17115126.
9. Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Grosse I, Graner A. A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet 2007, 114:823-839. 10.1007/s00122-006-0480-2, 17219208.
10. Varshney RK, Marcel TC, Ramsay L, Russell J, Röder MS, Stein N, Waugh R, Langridge P, Niks RE, Graner A. A high density barley microsatellite consensus map with 775 SSR loci. Theor Appl Genet 2007, 114:1091-1103. 10.1007/s00122-007-0503-7, 17345060.
11. Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szücs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 2009, 10:582. 10.1186/1471-2164-10-582, 2797026, 19961604.
12. Alsop BP, Farre A, Wenzl P, Wang JM, Zhou MX, Romagosa I, Kilian A, Steffenson BJ. Development of wild barley-derived DArT markers and their integration into a barley consensus map. Mol Breeding 2011, 27:77-92.
13. Jansen J, de Jong AG, van Ooijen JW. Constructing dense genetic linkage maps. Theor Appl Genet 2001, 102:1113-1122.
14. Wu Y, Close TJ, Lonardi S. Accurate construction of consensus genetic maps via integer linear programming. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011, 8:381-394. 10.1109/TCBB.2011.16, 20479505.
15. Yap IV, Schneider D, Kleinberg J, Matthews D, Cartinhour S, McCouch SR. A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps. Genetics 2003, 165:2235-2247. 1462874, 14704199.
16. MergeMap Online. , http://mergemap.org
17. Hamblin MT, Close TJ, Bhat PR, Chao S, Kling JG, Abraham KJ, Blake T, Brooks WS, Cooper B, Griffey CA, Hayes PM, Hole DJ, Horsley RD, Obert DE, Smith KP, Ullrich SE, Muehlbauer GJ, Jannink J-L. Population structure and linkage disequilibrium in U.S. barley germplasm: Implications for association mapping. Crop Sci 2010, 50:556-566.
18. Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ. Association mapping of spot blotch resistance in wild barley. Mol Breeding 2010, 26:243-256.
19. Cuesta-Marcos A, Szücs P, Close TJ, Filichkin T, Muehlbauer GJ, Smith KP, Hayes PM. Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: Implications for association mapping in germplasm arrays varying in size and structure. BMC Genomics 2010, 11:707. 10.1186/1471-2164-11-707, 3018479, 21159198.
20. Barley Coordinated Agricultural Project (CAP). , http://barleycap.org
21. Caldwell KS, Langridge P, Powell W. Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice. Plant Physiol 2004, 136:1-14.
22. R: A language and environment for statistical computing. , http://www.R-project.org/
23. R package DAGGER. , http://cran.r-project.org/web/packages/DAGGER/
24. Cormen TH, Leiserson CE, Rivest RL, Stein C. Introduction to Algorithms 2009, Cambridge: MIT Press, 3.
25. Graphviz dot. , http://graphviz.org
26. Boyd S, Vandenberghe L. Convex Optimization 2004, Cambridge: Cambridge University Press.
27. R package quadprod. , http://cran.r-project.org/web/packages/quadprog/
28. R package Rglpk. , http://cran.r-project.org/web/packages/Rglpk/
29. Liu BH. Statistical Genomics 1998, Boca Raton: CRC Press.
30. BLAST 2 Sequences. , http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi
31. Voorrips RE. MapChart: Software for the graphical presentation of linkage maps and QTLs. J Heredity 2002, 93:77-78.