Marker-based estimation of the coefficient of coancestry in hybrid breeding programmes

Theoretical and Applied Genetics

Volumn 118, Issue 6, 2009, Pages 1181-1192

  Maenhout, S ^a   De Baets, B ^b   Haesaert, G ^a  

^a UNIVERSITY COLLEGE GHENT   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE APPROACHES; CO ANCESTRIES; ESTIMATION PROCEDURES; HARDY-WEINBERG EQUILIBRIUMS; HYBRID BREEDINGS; INBRED LINES; LINEAR MIXED MODELS; MAIZE BREEDINGS; MATRIXES; MOLECULAR MARKERS; PEDIGREE ANALYSIS; POPULATION GENETICS; REFERENCE SETS; ROOT MEAN SQUARED ERRORS; VALUE ESTIMATIONS; VARIANCE STRUCTURES;

BIT ERROR RATE; CHROMOSOMES; COVARIANCE MATRIX; MAXIMUM LIKELIHOOD ESTIMATION; MODEL STRUCTURES; PARAMETER ESTIMATION;

FORESTRY;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BREEDING; COMPUTER SIMULATION; GENETIC MARKER; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; INBREEDING; MAIZE; MATHEMATICS; METHODOLOGY; POPULATION GENETICS;

ALGORITHMS; BREEDING; COMPUTER SIMULATION; GENETIC MARKERS; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; INBREEDING; MATHEMATICS; MODELS, GENETIC; SELECTION (GENETICS); ZEA MAYS;

ZEA MAYS;

EID: 64249167993     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-009-0972-y     Document Type: Article

References (46)

1. AD Anderson BS Weir 2007 A maximum-likelihood method for the estimation of pairwise relatedness in structured populations Genetics 176 421 440
2. DJ Balding 2003 Likelihood-based inference for genetic correlation coefficients Theor Popul Biol 63 221 230
3. R Bernardo 1993 Estimation of coefficient of coancestry using molecular markers in maize Theor Appl Genet 85 1055 1062
4. R Bernardo 1994 Prediction of maize single-cross performance using RFLPs and information from related hybrids Crop Sci 34 20 25
5. R Bernardo 1995 Genetic models for predicting maize single-cross performance in unbalanced yield trial data Crop Sci 35 141 147
6. R Bernardo 1996 Best linear unbiased prediction of the performance of crosses between untested maize inbreds Crop Sci 36 50 56
7. R Bernardo 1996 Best linear unbiased prediction of maize single-cross performance Crop Sci 36 872 876
8. AM Casa G Pressoir PJ Brown SE Mitchell WL Rooney MR Tuinstra CD Franks S Kresovich 2008 Community resources and strategies for association mapping in sorghum Crop Sci 48 30 40
9. TS Cox YT Kiang MB Gorman DM Rodgers 1985 Relationship between coefficient of parentage and genetic similarity indices in soybean Crop Sci 25 529 532
10. L Emik C Terrill 1949 Systematic procedures for calculating inbreeding coefficients J Hered 40 51 55
11. Gilmour A, Gogel B, Cullis B, Welham S, Thompson R (2002) ASREML User Guide Release 1.0. VSN International Ltd
12. JC Gower 1971 A general coefficient of similariy and some of its properties Biometrics 27 857 874
13. JF Hayes WG Hill 1981 Modification of estimates of parameters in the construction of genetic selection indices ('Bending') Biometrics 37 483 493
14. Henshall JM, Meyer K (2002) PDMATRIX-Programs to make matrices positive definite. In: Proceedings of the 7th world congress on genetics applied to livestock production, vol 33. Communication No. 28-12, pp 753-754
15. Hepler AB (2005) Improving forensic identification using Bayesian networks and relatedness estimation. Dissertation, North Carolina State University, Raleigh, NC
16. JC Ho S Kresovich KR Lamkey 2005 Extent and distribution of genetic variation in U.S. Maize: historically important lines and their open-pollinated dent and flint progenitors Crop Sci 45 1891 1900
17. Jacquard A (1974) The genetic structure of populations. Springer, New York
18. JL Jannink MCAM Bink RC Jansen 2001 Using complex plant pedigrees to map valuable genes Trend Plant Sci 6 337 342
19. H Jorjani L Klei U Emanuelson 2003 A simple method for weighted bending of genetic (co)variance matrices J Dairy Sci 86 677 679
20. JA Labate KR Lamkey SE Mitchell S Kresovich H Sullivan SC Smith 2003 Molecular and historical aspects of corn belt dent diversity Crop Sci 43 80 91
21. CC Li DE Weeks A Chakravarti 1993 Similarity of DNA fingerprints due to chance and relatedness Hum Hered 43 45 52
22. BA Loiselle VL Sork J Nason C Graham 1995 Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae) Am J Bot 82 1420 1425
23. M Lynch 1988 Estimation of relatedness by DNA fingerprinting Mol Biol Evol 5 584 599
24. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates, Inc, Sunderland
25. M Lynch K Ritland 1999 Estimation of pairwise relatedness with molecular markers Genetics 152 1753 1766
26. S Maenhout B De Baets G Haesaert E Van Bockstaele 2007 Support vector machine regression for the prediction of maize hybrid performance Theor Appl Genet 115 1003 1013
27. S Maenhout B De Baets G Haesaert E Van Bockstaele 2008 Marker-based screening of maize inbred lines using support vector machine regression Euphytica 161 123 131
28. Meza JC, Oliva RA, Hough PD, Williams PJ (2007) OPT++: an object-oriented toolkit for nonlinear optimization. ACM (TOMS) 33(2), article 12
29. BG Milligan 2002 Maximum-likelihood estimation of relatedness Genetics 163 1153 1167
30. JA Nelder R Mead 1965 A simplex method for function minimization Comput J 7 4 308 313
31. DM Panter FL Allen 1995 Using best linear unbiased predictions to enhance breeding for yield in soybean. 1. Choosing parents Crop Sci 35 397 405
32. DM Panter FL Allen 1995 Using best linear unbiased predictions to enhance breeding for yield in soybean. 2. Selection of superior crosses from a limited number of yield trials Crop Sci 35 405 410
33. HP Piepho J Möhring AE Melchinger A Büchse 2008 BLUP for phenotypic selection in plant breeding and variety testing Euphytica 161 209 228
34. DC Queller KF Goodnight 1989 Estimating relatedness using genetic markers Evolution 43 258 275
35. K Ritland 1996 Estimators for pairwise relatedness and individual inbreeding coefficients Genet Res 67 175 185
36. AC Sørensen R Pong-Wong JJ Windig JA Woolliams 2002 Precision of methods for calculating identity-by-descent matrices using multiple markers Genet Sel Evol 34 557 579
37. B Stich AE Melchinger M Frisch HP Maurer M Heckenberger JC Reif 2005 Linkage disequilibrium in European elite maize germplasm investigated with SSRs Theor Appl Genet 111 723 730
38. B Stich AE Melchinger HP Piepho S Hamrit W Schipprack HP Maurer JC Reif 2007 Potential causes of linkage disequilibrium in a European maize breeding program investigated with computer simulations Theor Appl Genet 115 529 536
39. C Stuber C Cockerham 1966 Gene effects and variances in hybrid populations Genetics 54 1279 1286
40. EA Thompson 1975 The estimation of pairwise relationships Ann Hum Genet 39 173 188
41. T Van de Casteele P Galbusera E Matthysen 2001 A comparison of microsatellite-based pairwise relatedness estimators Mol Ecol 10 1539 1549
42. J Wang 2002 An estimator for pairwise relatedness using molecular markers Genetics 160 1203 1215
43. S Wright 1943 Isolation by distance Genetics 28 114 138
44. S Wright 1951 The genetical structure of populations Ann Eugen 15 323 354
45. JM Yu G Pressoir WH Briggs IV Bi M Yamasaki JF Doebley MD McMullen BS Gaut DM Nielsen JB Holland S Kresovich ES Buckler 2006 A unified mixed-model method for association mapping that accounts for multiple levels of relatedness Nat Genet 38 203 208
46. Z Zhang RJ Todhunter ES Buckler LD Van Vleck 2007 Technical note: use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood. J Anim Sci 85 881 885