Joint modeling of additive and non-additive (genetic line) effects in multi-environment trials

Theoretical and Applied Genetics

Volumn 114, Issue 8, 2007, Pages 1319-1332

  Oakey, Helena ^a   Verbyla, Arunas P ^a   Cullis, Brian R ^b   Wei, Xianming ^c   Pitchford, Wayne S ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b NSW DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

^c BSES LIMITED   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DATA ACQUISITION; GROWTH KINETICS; MEDICAL COMPUTING;

FAMILY DOMINANCE; GENETIC LINE; JOINT MODELING; MULTI-ENVIRONMENT TRIALS (MET); PARENTS;

GENETIC ENGINEERING;

ARTICLE; BIOLOGICAL MODEL; BREEDING; CROP; DOMINANT GENE; ENVIRONMENT; GENETICS; HYBRIDIZATION; INBREEDING; PEDIGREE; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL; SUGARCANE;

BREEDING; CROPS, AGRICULTURAL; ENVIRONMENT; GENES, DOMINANT; HYBRIDIZATION, GENETIC; INBREEDING; MODELS, GENETIC; MODELS, STATISTICAL; PEDIGREE; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SACCHARUM;

EID: 34248389703     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-007-0515-3     Document Type: Article

References (49)

1. Akaike H (1974) A new look at statistical model identification. IEEE Trans Autom Control AU-19:716-722
2. Bernardo R (1994) Prediction of maize single-cross performance using rflps and information from related hybrids. Crop Sci 34:20-25
3. Bernardo R (1996) Best linear unbiased prediction of maize single-cross performance. Crop Sci 36:50-56
4. de Boer IJM, Hoeschele I (1993) Genetic evaluation methods for populations with dominance and inbreeding. Theoret Appl Genet 86:245-258
5. BSES (1984) The Standard laboratory manual for Australian Sugar Mills, vol 1. Bureau of Sugar Experiment Stations, Indooroopilly, QLD, Australia, principles and practices edition
6. Cockerham CC (1954) An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 39:859-882
7. Cockerham CC (1983) Covariances of relatives from self-fertilization. Crop Sci 23:1177-1180
8. Cockerham CC, Weir BS (1984) Covariances of relatives stemming from a population undergoing mixed self and random mating. Biometrics 40:157-164
9. Cooper M, Hammer GL (2005) Preface to special issue: Complex traits and plant breeding-can we understand the complexities of gene-to-phenotype relationships and use such knowledge to enhance plant breeding outcomes? Aust J Agric Res 56:869-872
10. Cooper M, Podlich DW (1999) Genotype x environment interactions, selection response and heterosis. In: Coors JG, Pandey S (eds) Genetics and exploitation of heterosis in crops, chap 8, pp 81-92
11. Cooper M, Brennan P, Sheppard J (1996) A strategy for yield improvement of wheat which accomodates large genotype by environment interactions. In: Cooper M, Hammer GL (eds) Plant adaption and crop improvement, pp 487-512
12. Costa e Silva J, Borralho NMG, Potts BM (2004) Additive and non-additive genetic parameters from clonally replicated and seedling progenies of Eucalyptus globulus. Theoret Appl Genet 108:1113-1119
13. Crossa J, Burgueno J, Cornelius PL, McLaren G, Trethowan R, Krishnamachari A (2006) Modelling genotype X environment interaction using additive genetic covariances of relatives for predicting breeding values of wheat genotypes. Crop Sci 46:1722-1733
14. Cullis BR, Lill W, Fisher J, Read B, Gleeson A (1989) A new procedure for the analysis of early generation variety trials. Appl Stat 38:361-375
15. Cullis B, Gogel B, Verbyla A, Thompson R (1998) Spatial analysis of Multi-Environment early generation trials. Biometrics 54:1-18
16. Cullis B, Smith A, Coombes N (2006) On the design of early generation variety trials with correlated data. J Agric Biol Environ Stat 11:381-393
17. Davik J, Honne B (2005) Genetic variance and breeding values for resistance to wind-borne disease [Sphaeotheca Macularis (wallr. ex fr.)] in strawberry (Fragaria x ananassa duch.) estimated by exploring mixed models and spatial models and pedigree information. Theoret Appl Genet 111:256-264
18. Durel CE, Laurens F, Fouillet A, Lespinasse Y (1998) Utilization of pedigree information to estimate genetic parameters from large unbalanced data sets in apple. Theoret Appl Genet 96:1077-1085
19. Dutkowski GW, Costa e Silva J, Gilmour AR, Lopez GA (2002) Spatial analysis methods for forest genetic trials. Can J For Res 32:2201-2214
20. Edwards JW, Lamkey KR (2002) Quantitative genetics of inbreeding in a synthetic maize population. Crop Sci 42:1094-1104
21. Falconer DS, Mackay T (1996) Introduction to quantitative genetics, 4th edn. Longman Group Ltd, London
22. Gilmour AR, Gogel B, Cullis BR, Thompson R (2006) ASReml, user Guide. Release 2.0. Hemel Hempstead. VSN International Ltd, UK
23. Gilmour AR, Cullis B, Verbyla AP (1997) Accounting for natural and extraneous variation in the analysis of field experiments. J Agric Biol Environ Stat 2:269-293
24. Griffing B (1956) Concept of general and specific combining ability in relation to diallel crossing systems. Aust J Biol Sci 9:463-493
25. Harris DL (1964) Genotypic covariances between inbred relatives. Genetics 50:1319-1348
26. Henderson CR (1950) Estimation of genetic parameters (abstract). The Ann Math Stat 21:309-310
27. Henderson CR (1976) A simple method for computing the inverse of a numerator relationship matrix used in the prediction of breeding values. Biometrics 32:69-83
28. Henderson CR (1984) Applications of linear models in animal breeding. University of Guelph, Guelph
29. Hoeschele I, VanRaden PM (1991) Rapid inversion of dominance relationship matrices for noninbred populations by including sire by dam subclass effects. J Diary Sci 74:557-569
30. Jannoo N, Grivet L, David L, Glaszmann J-C (2004) Differential chromosome pairing affinities at meiosis in polyploid sugarcane revealed by molecular markers. Heredity 93:460-467
31. John J, Ruggiero K, Williams E (2002) ALPHA(n)-designs. Aust N Z J Stat 44:457-465
32. Kelly AM, Smith AB, Eccleston JA, Cullis BR (2007) The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials. Crop Sci (in press)
33. Lo LL, Fernando RL, Cantet RJC, Grossman M (1995) Theory for modelling means and covariances in a two-breed population with dominance inheritance. Theoret Appl Genet 90:49-62
34. Lu PX, Huber DA, White TL (1999) Potential biases of incomplete linear models in heritability estimation and breeding value prediction. Can J For Res 29:724-736
35. Meuwissen THE, Luo Z (1992) Computing inbreeding coefficients in large populations. Genet Select Evol 24:305-313
36. Oakey H, Verbyla A, Pitchford W, Cullis B, Kuchel H (2006) Joint modelling of additive and non-additive genetic line effects in single field trials. Theoret Appl Genet 113:809-819
37. Panter DM, Allen FL (1995) Using best linear unbiased predictions to enhance breeding for yield in soybean: I. choosing parents. Crop Sci 35:397-405
38. Patterson HD, Thompson R (1971) Recovery of inter-block information when block sizes are unequal. Biometrika 58:545-554
39. Patterson HD, Silvey V, Talbot M, Weatherup STC (1977) Variability of yields of cereal varieties in U.K. trials. J Agric Sci Camb 89:238-245
40. Podlich DW, Cooper M, Basford KE (1999) Computer simulation of a selection strategy to accommoodate genotype-environment interactions in a wheat recurrent selection programme. Plant Breed 118:17-28
41. Quaas RL (1976) Computing the diagonal elements and inverse of a large numerator relationship matrix. Biometrics 32:949-953
42. R Development Core Team (2005) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
43. Smith A, Cullis B, Thompson R (2001) Analyzing variety by environmental data using multiplicative mixed models and adjustments for spatial field trend. Biometrics 57:1138-1147
44. Smith AB, Cullis BR, Thompson R (2005) The analysis of crop cultivar breeding and evaluation trials: an overview of current mixed model approaches. J Agric Sci 143:1-14
45. Stuber CW, Cockerham CC (1966) Gene effects and variances in hybrid populations. Genetics 54:1279-1286
46. Verbyla AP, Oakey H (2006) The variance-covariance matrix for relatives undergoing mendelian sampling and inbreeding (submitted)
47. van der Werf JHJ, de Boer IJM (1989) Influence of non-additive effects on estimation of genetic parematers in diarly cattle. J Diary Sci 72:2606-2614
48. Whitaker D, Williams ER, John JA (2006) Cycdesign 3.0: A package for the computer generation of experimental designs. CycSoftware Ltd, Hamilton, New Zealand
49. Wright S (1922) Coefficients of inbreeding and relationship. Am Nat 56:330-338