Mapping density response in maize: A direct approach for testing genotype and treatment interactions

Genetics

Volumn 173, Issue 1, 2006, Pages 331-348

  Gonzalo, Martin ^a   Vyn, Tony J ^a   Holland, James B ^b   McIntyre, Lauren M ^c,d  

^a PURDUE UNIVERSITY   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF FLORIDA   (United States)

^d UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE MAPPING; GENOTYPE; MAIZE; MEDICAL RESEARCH; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; STRESS;

CHROMOSOME MAPPING; GENETICS, POPULATION; GENOTYPE; HYBRIDIZATION, GENETIC; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHENOTYPE; ZEA MAYS;

CYRESTIS THYODAMAS; ZEA MAYS;

EID: 33744488041     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.045757     Document Type: Article

References (80)

1. BARTLETT, M., 1937 Properties of sufficiency and statistical tests. Proc. R. Soc. Lond. Ser. A 160: 268-282.
2. BARTON, C., and E. CRAMER, 1989 Hypothesis testing in multivariate linear models with randomly missing data. Commun. Stat. Sim. 18: 875-895.
3. BEAVIS, W., O. SMITH, D. GRANT and R. FINCHER, 1994 Identification of quantitative trait loci using small sample of top-crossed and F4 progeny from maize. Crop Sci. 34(4): 882-896.
4. BENJAMINI, Y., and Y. HOCHBERG, 1995 Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57(1): 289-300.
5. BERTIN, P., and A. GALLAIS, 2001 Genetic variation for nitrogen use efficiency in a set of recombinant inbred lines II - qtl detection and coincidences. Maydica 46(1): 53-68.
6. BETRAN, F., D. BECK, M. BANZIGER and G. EDMEADES, 2003 Secondary traits in parental inbreds and hybrids under stress and non-stress environments in tropical maize. Field Crops Res. 83(1): 51-65.
7. BOLANOS, J., and G. EDMEADES, 1996 The importance of the anthesis-silking interval in breeding for drought tolerance in tropical maize. Field Crops Res. 48(1): 65-80.
8. BORRAS, L., G. MADDONNI and M. OTEGUI, 2003 Leaf senescence in maize hybrids: plant population, row spacing and kernel set effects. Field Crops Res. 82(1): 13-26.
9. BOZDOGAN, H., 1987 Model selection and Akaike's Information Criterion (AIC): the general theory and its analytical extensions. Psychometrika 52(3): 345-370.
10. BRUNNER, S., K. FENGLER, M. MORGANTE, S. TINGEY and A. RAFALSKI, 2005 Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17(2): 343-360.
11. CARSON, M., C. STUBER and M. SENIOR, 2004 Identification and mapping of quantitative trait loci conditioning resistance to southern leaf blight of maize caused by Cochliobolus heterostrophus race O. Phytopathology 94(8): 862-867.
12. CATELLIER, D., and K. MULLER, 2000 Test for Gaussian repeated measures with missing data in small samples. Stat. Med. 19: 1101-1114.
13. CHAPMAN, S., and G. EDMEADES, 1999 Selection improves drought tolerance in tropical maize populations: II. Direct and correlated responses among secondary traits. Crop Sci. 39(5): 1315-1324.
14. COFFMAN, C., R. DOERGE, K. SIMONSEN, K. NICHOLS, C. DUARTE et al., 2005 Model selection in binary trait locus mapping. Genetics 170: 1281-1297.
15. CORANDER, J., and M. SILLANPAA, 2002 An unified approach to joint modeling of multiple quantitative and qualitative traits in gene mapping. J. Theor. Biol. 218: 435-446.
16. DERIEUX, M., M. DARRIGRAND, A. GALLAIS, Y. BARRIERE, D. BLOC et al., 1987 Evaluation of the genetic gain in grain maize during the last 30 years in France. Agronomie 7(1): 1-11.
17. DUVICK, D., 1992 Genetic contributions to advances in yield of United States maize. Maydica 37(1): 69-79.
18. EYHERABIDE, G., A. DAMILANO and J. COLAZO, 1994 Genetic gain for grain yield of maize in Argentina. Maydica 39(3): 207-211.
19. FROVA, C., P. KRAJEWSKI, N. DI FONZO, M. VILLA and M. SARI-GORLA, 1999 Genetic analysis of drought tolerence in maize by molecular markers. I. Yield components. Theor. Appl. Genet. 99(1-2): 280-288.
20. FU, H., and H. DOONER, 2002 Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. USA 99(14): 9573-9578.
21. GILBERT, H., and P. LE ROY, 2003 Comparison of three multitrait methods for QTL detection. Genet. Sel. Evol. 35(3): 281-304.
22. GILMOUR, A., B. CULLIS, S. WELLHAM and R. THOMPSON, 1999 ASREML Reference Manual. NSW Agriculture Biometric Bulletin No. 3, NSW Agriculture, Orange, New South Wales, Australia.
23. HALEY, C., and S. KNOTT, 1992 A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324.
24. HENDERSON, C. R., 1984 Applications of Linear Models in Animal Breeding. University of Guelph, Guelph, ON, Canada.
25. HIREL, B., P. BERTIN, I. QUILLERE, W. BOURDONCLE, C. ATTAGNANT et al., 2001 Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in maize. Plant Physiol. 125(3): 1258-1270.
26. HOLLAND, J., 2004 Implementation of molecular markers for quantitative traits in breeding programs - challenges and opportunities, in New Directions for a Diverse Planet: Proceedings for the 4th International Crop Science Congress, edited by T. FISCHER, N. TURNER, J. ANGUS, L. MCINTYRE, M. ROBERTSON, A. BORRELL and D. LLOYD. Crop Science Society, Brisbane, Australia (http://www.cropscience.org.au/icsc2004/symposia/3/4/203_hollandjb.htm).
27. HOSTERT, B., 2002 Quantitative trait locus mapping using near-isogenic lines of maize. M.S. Thesis, North Carolina State University, Raleigh, NC.
28. HUND, A., Y. FRACHEBOUD, A. SOLDATI, E. FRASCAROLI, S. SALVI et al., 2004 QTL controlling root and shoot traits of maize seedlings under cold stress. Appl. Microbiol. Biotechnol. 65(3):618-629.
29. JIANG, C., and Z. ZENG, 1995 Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127.
30. KAEPPLER, S., J. PARKE, S. MUELLER, L. SENIOR, C. STUBER et al., 2000 Variation among maize inbred lines and detection of quantitative trait loci for growth at low phosphorus and responsiveness to arbuscular mycorrhizal fungi. Crop Sci. 40(2): 358-364.
31. KNOTT, S., and C. HALEY, 2000 Multitrait least squares for quantitative trait loci detection. Genetics 156: 899-911.
32. KOROL, A., Y. RONIN and V. KIRZHNER, 1995 Interval mapping of quantitative trait loci employing correlated trait complexes. Genetics 140: 273-284.
33. LANDI, P., S. CONTI, F. GHERARDI, M. SANGUINETI and R. TUBEROSA, 1995 Genetic analysis of leaf ABA concentration and of agronomic traits in maize hybrids grown under different water regimes. Maydica 40(2): 179-186.
34. LANGE, C., and J. WHITTAKER, 2001 Mapping quantitative trait loci using generalized estimating equations. Genetics 159: 1325-1337.
35. LAWLESS, J., 1982 Statistical Models and Methods for Lifetime Data. Wiley, New York.
36. LI, X., X. LIU, M. LI and S. ZHANG, 2003 Identification of quantitative trait loci for anthesis-silking interval and yield components under drought stress in maize. Acta Bot. Sin. 45(7): 852-857.
37. LUND, M., P. SORENSEN, B. GULDBRANDTSEN and D. SORENSEN, 2003 Multitrait fine mapping of quantitative trait loci using combined linkage disequilibria and linkage analysis. Genetics 163: 405-410.
38. MA, C., G. CASELLA and R. WU, 2002 Functional mapping of quantitative trait loci underlying the character process: a theoretical framework. Genetics 161: 1751-1762.
39. MADDONNI, G., M. OTEGUI and A. CIRILO, 2001 Plant population density, row spacing and hybrid effects on maize canopy architecture and light attenuation. Field Crops Res. 71(3): 183-193.
40. MCCULLOCH, C., and S. SEARLE, 2001 Generalized, Linear, and Mixed Models. Wiley, New York.
41. MCLEAN, R., and W. SANDERS, 1988 Approximating degrees of freedom for standard errors in mixed linear models, pp. 50-59 in Proceedings of the Statistical Computing Section, edited by the AMERICAN STATISTICAL ASSOCIATION. New Orleans.
42. MICKELSON, S., C. STUBER, L. SENIOR and S. KAEPPLER, 2002 Quantitative trait loci controlling leaf and tassel traits in a B73 x Mo17 population of maize. Crop Sci. 42: 1902-1909.
43. MODARRES, A., R. HAMILTON, M. DIJAK, L. DWYER, D. STEWART et al., 1998 Plant population density effects on maize inbred lines grown in short-season environments. Crop Sci. 38(1): 104-108.
44. MORRIS, J. S., 2002 The BLUPs are not "best" when it comes to boot-strapping. Stat. Probab. Lett. 56: 425-430.
45. PEREZ-ENCISO, M., and I. MISZTAL, 2004 Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics 20(16): 2792-2798.
46. PHILLIPS, P., M. WHITLOCK and K. FOWLER, 2001 Inbreeding changes the shape of the genetic covariance matrix in Drosophila melanogaster. Genetics 158: 1137-1145.
47. PIEPHO, H., 1997 Analyzing genotype-environment data by mixed models with multiplicative terms. Biometrics 53: 761-766.
48. PIEPHO, H., 2005 Statisical tests for qtl and qtl-by-environment effects in segregating populations derived from line crosses. Theor. Appl. Genet. 110: 561-566.
49. REITER, R., J. COORS, M. SUSSMAN and W. GABELMAN, 1991 Genetic analysis of tolerance to low phosphorus stress in maize using restriction fragment length polymorphisms. Theor. Appl. Genet. 82(5): 561-568.
50. RIBAUT, J., D. HOISINGTON, J. DEUTSCH, C. JIANG and D. GONZALEZ-DE LEON, 1996 Identification of quantitative trait loci under drought conditions in tropical maize. 1. Flowering parameters and the anthesis-silking interval. Theor. Appl. Genet. 92(7): 905-914.
51. RIBAUT, J., C. JIANG, D. GONZALEZ-DE LEON, G. EDMEADES AND D. HOISINGTON, 1997 Identification of quantitative trait loci under drought conditions in tropical maize. 2. Yield components and marker-assisted selection strategies. Theor. Appl. Genet. 94(6-7): 887-896.
52. RIBAUT, J. M., M. BANZIGER, J. BETRAN, C. JIANG, G. EDMEADES et al., 2001 Use of molecular markers in plant breeding: drought tolerance improvement in tropical maize, pp. 85-99 in Quantitative Genetics, Genomics, and Plant Breeding, edited by M. KANG. CAB Publishing, Oxon, UK.
53. ROSIELLE, A. A., and J. HAMBLIN, 1981 Theoretical aspects of selection for yield in stress and non-stress environments. Crop Sci. 21(6): 943-946.
54. RUSSELL, W., 1991 Genetic improvement of maize yields. Adv. Agron. 46: 245-298.
55. SANGOI, L., M. GRACIETTI, C. RAMPAZZO and P. BIANCHETTI, 2002 Response of Brazilian maize hybrids from different eras to changes in plant density. Field Crops Res. 79(1): 39-51.
56. SANGUINETI, M., R. TUBEROSA, P. LANDI, S. SALVI, M. MACCAFERRI et al., 1999 QTL analysis of drought related traits and grain yield in relation to genetic variation for leaf abscisic acid concentration in field-grown maize. J. Exp. Bot. 50(337): 1289-1297.
57. SARI-GORLA, M., P. KRAJEWSKI, N. DI FONZO, M. VILLA and C. FROVA, 1999 Genetic analysis of drought tolerance in maize by molecular markers. II. Plant height and flowering. Theor. Appl. Genet. 99(1-2): 289-295.
58. SCHLUCHTER, M. D., and J. D. ELASHOFF, 1990 Small-sample adjustments to test with unbalanced repeated measures assuming several covariance structures. J. Stat. Comput. Sim. 37: 69-87.
59. SCHÖN, C. C., H. F. UTZ, S. GROH, B. TRUBERG, S. OPENSHAW et al., 2004 Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167: 485-498.
60. SEARLE, S., G. CASELLA and C. MCCULLOCH, 1992 Variance Components. John Wiley & Sons, New York.
61. SEATON, G., C. HALEY, S. KNOTT, M. KEARSEY and P. VISSCHER, 2002 QTL Express: mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics 18(2): 339-340.
62. SMITH, A., B. CULLIS and R. THOMPSON, 2001a Analyzing variety by environment data using multiplicative mixed models and adjustments for spatial field trend. Biometrics 57: 1138-1147.
63. SMITH, A., B. CULLIS and R. THOMPSON, 2001b Exploring variety-environment data using random effects ammi models with adjustments for spatial field trend: part 1: theory, pp. 323-335 in Quantitative Genetics, Genomics, and Plant Breeding, edited by M. KANG. CAB Publishing, Oxon, UK.
64. SMITH, B., 1995 The Emergence of Agriculture. Freeman, New York.
65. SORENSEN, P., M. LUND, B. GULDBRANDTSEN, J. JENSEN and D. SORENSEN, 2003 A comparison of bivariate and univariate QTL mapping in livestock populations. Genet. Sel. Evol. 35(6): 605-622.
66. STOREY, J., and R. TIBSHIRANI, 2003 Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100(16): 9440-9445.
67. STUBER, C., S. LINCOLN, D. WOLFF, T. HELENTJARIS and E. LANDER, 1992 Identification of genetic factors contributing to heterosis in a hybrid from 2 elite maize inbred lines using molecular markers. Genetics 132: 823-839.
68. TOLLENAAR, M., 1991 Physiological basis of genetic improvement of maize hybrids in Ontario from 1959 to 1988. Crop Sci. 31(1): 119-124.
69. TUBEROSA, R., and S. SALVI, 2004 Markers, genomics and post-genomics approaches - Will they assist in selecting for drought tolerance?, in New Directions for a Diverse Planet: Proceedings for the 4th International Crop Science Congress, edited by T. FISCHER, N. TURNER, J. ANGUS, L. MCINTYRE, M. ROBERTSON, A. BORRELL AND D. LLOYD. Crop Science Society, Brisbane, Australia (http://www.cropscience.org.au/icsc2004/symposia/3/6/1851_tuberosar.htm).
70. TUBEROSA, R., M. SANGUINETI, P. LANDI, S. SALVI, E. CASARINI et al., 1998 RFLP mapping of quantitative trait loci controlling abscisic acid concentration in leaves of drought-stressed maize (Zea mays L.). Theor. Appl. Genet. 97(5-6): 744-755.
71. TUBEROSA, R., S. SALVI, M. SANGUINETI, P. LANDI, M. MACCAFERRI et al., 2002a Mapping QTLs regulating morpho-physiological traits and yield: case studies, shortcomings and perspectives in drought-stressed maize. Ann. Bot. 89: 941-963.
72. TUBEROSA, R., M. SANGUINETI, P. LANDI, M. MICHELA GIULIANI, S. SALVI et al., 2002b Identification of QTLs for root characteristics in maize grown in hydroponics and analysis of their overlap with QTLs for grain yield in the field at two water regimes. Plant Mol. Biol. 48(5): 697-712.
73. VELDBOOM, L., and M. LEE, 1996 Genetic mapping of quantitative trait loci in maize in stress and nonstress environments: I. Grain yield and yield components. Crop Sci. 36(5): 1310-1319.
74. VERHOEVEN, K., K. SIMONSEN and L. MCINTYRE, 2005 Implementing false discovery rate control: increasing your power. Oikos 108: 643-647.
75. VERMERRIS, W., and L. MCINTYRE, 1999 Time to flowering in brown midrib mutants of maize: an alternative approach to the analysis of developmental traits. Heredity 83: 171-178.
76. VYN, T., and D. HOOKER, 2002 Assessment of multiple- and single-factor stress impacts on corn. Field Crops Res. 75(2-3): 123-137.
77. WHITTAKER, J., R. THOMPSON and P. VISSCHER, 1996 On the mapping of QTL by regression of phenotypes on marker type. Heredity 77: 23-32.
78. WOLFINGER, R., 1996 Heterogeneous variance-covariance structures for repeated measures. J. Agric. Biol. Environ. Stat. 1: 205-230.
79. ZHAO, W., C. MA, J. CHEVERUD and R. WU, 2004 A unifying statistical model for QTL mapping of genotype x sex interaction for developmental trajectories. Physiol. Genomics 19(2): 218-227.
80. ZUCKER, D., O. LIEBERMAN and O. MANOR, 2000 Improved small sample inference in the mixed linear model: Bartlett correction and adjusted likelihood. J. R. Stat. Soc. Ser. B 62(4): 827-838.