Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize

Genetics

Volumn 174, Issue 3, 2006, Pages 1671-1683

  Fu, Yan ^a,d   Wen, Tsui Jung ^a   Ronin, Yefim I ^b   Chen, Hsin D ^a   Guo, Ling ^a   Mester, David I ^b   Yang, Yongjie ^a   Lee, Michael ^a   Korol, Abraham B ^b   Ashlock, Daniel A ^c   Schnable, Patrick S ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF HAIFA   (Israel)

^c UNIVERSITY OF GUELPH   (Canada)

^d DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE FREQUENCY; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC MARKER; GENETIC POLYMORPHISM; GENOMICS; GENOTYPE; INBRED STRAIN; MAIZE; MARKER GENE; MOLECULAR CLONING; NONHUMAN; PLANT GENETICS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS;

ALLELES; BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CROSSES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE FREQUENCY; GENES, PLANT; GENETIC MARKERS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT LOCI; RECOMBINATION, GENETIC; ZEA MAYS;

ZEA MAYS;

EID: 33751319169     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.060376     Document Type: Article

References (42)

1. ANDERSON, L. K., G. G. DOYLE, B. BRIGHAM, J. CARTER, K. D. HOOKER et al., 2003 High-resolution crossover maps for each bivalent of Zea mays using recombination nodules. Genetics 165: 849-865.
2. BARRETT, J. C., B. FRY, J. MALLER and M. J. DALY, 2005 Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
3. BHATTRAMAKKI, D., M. DOLAN, M. HANAFEY, R. WINELAND, D. VASKE et al., 2002 Insertion-deletion polymorphisms in 3′ regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol. Biol. 48: 539-547.
4. BRENDEL, V., L. XING and W. ZHU, 2004 Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20: 1157-1169.
5. BRUNNER, S., K. FENGLER, M. MORGANTE, S. TINGEY and A. RAFALSKI, 2005 Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17: 343-360.
6. CASA, A. M., C. BROUWER, A. NAGEL, L. WANG, Q. ZHANG et al., 2000 Inaugural article: the MITE family heartbreaker (Hbr): molecular markers in maize. Proc. Natl. Acad. Sci. USA 97: 10083-10089.
7. CASA, A. M., A. NAGEL and S. R. WESSLER, 2004 MITE display. Methods Mol. Biol. 260: 175-188.
8. CATO, S. A., R. C. GARDNER, J. KENT and T. E. RICHARDSON, 2001 A rapid PCR-based method for genetically mapping ESTs. Theor. Appl. Genet. 102: 296-306.
9. CHARDON, F., B. VIRLON, L. MOREAU, M. FALQUE, J. JOETS et al., 2004 Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168: 2169-2185.
10. CHOI, H. K., D. KIM, T. UHM, E. LIMPENS, H. LIM et al., 2004 A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166: 1463-1502.
11. COE, E., K. CONE, M. MCMULLEN, S. S. CHEN, G. DAVIS et al., 2002 Access to the maize genome: an integrated physical and genetic map. Plant Physiol. 128: 9-12.
12. CONE, K. C., M. D. MCMULLEN, I. V. BI, G. L. DAVIS, Y. S. YIM et al., 2002 Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol. 130: 1598-1605.
13. DIETRICH, C. R., F. CUI, M. L. PACKILA, J. LI, D. A. ASHLOCK et al., 2002 Maize Mu transposons are targeted to the 5′ untranslated region of the gl8 gene and sequences flanking Mu target-site duplications exhibit nonrandom nucleotide composition throughout the genome. Genetics 160: 697-716.
14. EMRICH, S. J., S. ALURU, Y. FU, T. J. WEN, M. NARAYANAN et al., 2004 A strategy for assembling the maize (Zea mays L.) genome. Bioinformatics 20: 140-147.
15. FALQUE, M., 2005 IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains. Bioinformatics 21: 3441-3442.
16. FALQUE, M., L. DECOUSSET, D. DERVINS, A. M. JACOB, J. JOETS et al., 2005 Linkage mapping of 1454 new maize candidate gene loci. Genetics 170: 1957-1966.
17. FU, H., and H. K. DOONER, 2002 Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. USA 99: 9573-9578.
18. FU, Y., S. J. EMRICH, L. GUO, T. J. WEN, D. A. ASHLOCK et al., 2005 Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proc. Natl. Acad. Sci. USA 102: 12282-12287.
19. GUPTA, P. K., S. RUSTGI and P. L. KULWAL, 2005 Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol. Biol. 57: 461-485.
20. HEDRICK, P. W., 1987 Gametic disequilibrium measures: proceed with caution. Genetics 117: 331-341.
21. JIANG, N., Z. BAO, X. ZHANG, S. R. EDDY and S. R. WESSLER, 2004 Pack-MULE transposable elements mediate gene evolution in plants. Nature 431: 569-573.
22. KANTETY, R. V., M. LA ROTA, D. E. MATTHEWS and M. E. SORRELLS, 2002 Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501-510.
23. KOSAMBI, D., 1944 The estimation of map distances from recombination values. Ann. Eugen. 12: 172-175.
24. LAI, J., Y. LI, J. MESSING and H. K. DOONER, 2005 Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. USA 102: 9068-9073.
25. LAL, S. K., M. J. GIROUX, V. BRENDEL, C. E. VALLEJOS and L. C. HANNAH, 2003 The maize genome contains a helitron insertion. Plant Cell 15: 381-391.
26. LEE, M., N. SHAROPOVA, W. D. BEAVIS, D. GRANT, M. KATT et al., 2002 Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population. Plant Mol. Biol. 48: 453-461.
27. LIU, Z. J., and J. F. CORDER, 2004 DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238: 1-37.
28. LU, H., J. ROMERO-SEVERSON and R. BERNARDO, 2002 Chromosomal regions associated with segregation distortion in maize. Theor. Appl. Genet. 105: 622-628.
29. MESTER, D., Y. RONIN, D. MINKOV, E. NEVO and A. KOROL, 2003 Constructing large-scale genetic maps using an evolutionary strategy algorithm. Genetics 165: 2269-2282.
30. MESTER, D. I., Y. I. RONIN, E. NEVO and A. B. KOROL, 2004 Fast and high precision algorithms for optimization in large-scale genomic problems. Comput. Biol. Chem. 28: 281-290.
31. MORGANTE, M., S. BRUNNER, G. PEA, K. FENGLER, A. ZUCCOLO et al., 2005 Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 37: 997-1002.
32. PHILLIPS, R. L., R. A. KLEESE and S. S. WANG, 1971 The nucleolus organizer region of maize: chromosomal site of DNA complementary to ribosomal RNA. Chromosoma 36: 79-88.
33. ROZEN, S., and H. SKALETSKY, 2000 Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386.
34. SALVI, S., R. TUBEROSA, E. CHIAPPARINO, M. MACCAFERRI, S. VEILLET et al., 2002 Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize. Plant Mol. Biol. 48: 601-613.
35. STOREY, J. D., and R. TIBSHIRANI, 2003 Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100: 9440-9445.
36. VLADUTU, C., J. MCLAUGHLIN and R. L. PHILLIPS, 1999 Fine mapping and characterization of linked quantitative trait loci involved in the transition of the maize apical meristem from vegetative to generative structures. Genetics 153: 993-1007.
37. VROH BI, I., M. D. MCMULLEN, H. SANCHEZ-VILLEDA, S. SCHROEDER, J. GARDINER et al., 2006 Single nucleotide polymorphisms and insertion-deletions for genetic markers and anchoring the maize fingerprint contig physical map. Crop Sci. 46: 12-21.
38. WILLIAMS, R. W., J. GU, S. QI and L. LU, 2001 The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biol. 2: RESEARCH0046.
39. WINKLER, C. R., N. M. JENSEN, M. COOPER, D. W. PODLICH and O. S. SMITH, 2003 On the determination of recombination rates in intermated recombinant inbred populations. Genetics 164: 741-745.
40. WU, J., H. MIZUNO, M. HAYASHI-TSUGANE, Y. ITO, Y. CHIDEN et al., 2003 Physical maps and recombination frequency of six rice chromosomes. Plant J. 36: 720-730.
41. YAO, H., L. GUO, Y. FU, L. A. BORSUK, T. J. WEN et al., 2005 Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol. Biol. 57: 445-460.
42. ZHANG, Q., J. ARBUCKLE and S. R. WESSLER, 2000 Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize. Proc. Natl. Acad. Sci. USA 97: 1160-1165.