Factor analytic and reduced animal models for the investigation of additive genotype-by-environment interaction in outcrossing plant species with application to a Pinus radiata breeding programme

Theoretical and Applied Genetics

Volumn 127, Issue 10, 2014, Pages 2193-2210

  Cullis, Brian R ^a,b   Jefferson, Paul ^c   Thompson, Robin ^d   Smith, Alison B ^a  

^a UNIVERSITY OF WOLLONGONG   (Australia)

^b CSIRO   (Australia)

^c Radiata Pine Breeding Company   (New Zealand)

^d ROTHAMSTED RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALS; FORESTRY;

COMPUTATIONAL ISSUES; DEPLOYMENT STRATEGY; GENETIC CORRELATION; GENOTYPE BY ENVIRONMENTS; GENOTYPE-BY-ENVIRONMENT INTERACTION; LINEAR MIXED MODEL ANALYSIS; PEDIGREE INFORMATION; SOUTH-EASTERN AUSTRALIA;

ANALYTICAL MODELS;

ANIMALS; COMPUTATION; ENVIRONMENTS; MODELS; PLANTS; SPECIES IDENTIFICATION;

ANIMALIA; PINUS RADIATA; ZEA MAYS;

ANIMAL; AUSTRALIA; BIOLOGICAL MODEL; FACTORIAL ANALYSIS; GENETICS; GENOTYPE ENVIRONMENT INTERACTION; NEW ZEALAND; PINE; STATISTICAL MODEL;

ANIMALS; AUSTRALIA; FACTOR ANALYSIS, STATISTICAL; GENE-ENVIRONMENT INTERACTION; LINEAR MODELS; MODELS, GENETIC; NEW ZEALAND; PINUS;

EID: 84919780525     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-014-2373-0     Document Type: Article

References (26)

1. Apiolaza L (2012) Basic density of radiata pine in new zealand: genetic and environmental factors. Tree Genet Genomes 8:87–9
2. Bailey R (2008) Design of comparative experiments. Cambridge University Press, Cambridge
3. Baltunis B, Gapare W, Wu H (2010) Genetic parameters and genotype by environment interaction in radiata pine for growth and wood quality traits in australia. Silvae Genet 59:2–3
4. Beeck C, Cowling W, Smith A, Cullis B (2010) Analysis of yield and oil from a series of canola breeding trials. Part I: Fitting factor analytic models with pedigree information. Genome 53:992–1001
5. Burgueno J, Crossa J, Cotes J, Vincente F, Das B (2011) Prediction assessment of linear mixed models for multi-environment trials. Crop Sci 51:944–954
6. Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2009) ASReml-R reference manual, release 3. Technical report, Queensland Department of Primary Industries
7. Costa e Silva J, Potts B, Dutkowski G, (2006) Genotype by environment interaction for growth of eucalyptus globulus in Australia. Tree Genet Genomes 2:61–75
8. Cullis B, Smith A, Beeck C, Cowling W (2010) Analysis of yield and oil from a series of canola breeding trials. Part II: Exploring VxE using factor analysis. Genome 53:1002–1016
9. Core Team R (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
10. Gilmour AR, Thompson R, Cullis BR (1995) AI, an efficient algorithm for REML estimation in linear mixed models. Biometrics 51:1440–1450
11. Gilmour AR, Cullis BR, Welham SJ, Gogel BJ, Thompson R (2004) An efficient computing strategy for prediction in mixed linear models. Comput Stat Data Anal 44:571–586
12. Hardner C, Dieters M, Dale G, DeLacy I, Basford K (2010) Patterns of genotype-by-environment interaction in diameter at breast height at age 3 for eucalypt hybrid clones grown for reafforestation of lands affected by salinity. Tree Genet Genomes 6:833–851
13. Henderson CR (1950) Estimation of genetic parameters (abstract). Ann Math Stat 21:309–310
14. Kelly A, Smith A, Eccleston J, Cullis B (2007) The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials. Crop Sci 47:1063–1070
15. Kelly AM, Cullis BR, Gilmour AR, Eccleston JA, Thompson R (2009) Estimation in a multiplicative mixed model involving a genetic relationship matrix. Genet Select Evol 41:1286–1297
16. Kempton RA (1984) The use of biplots in interpreting variety by environment interactions. J Agric Sci Camb 103:123–135
17. Oakey H, Verbyla A, Cullis B, Pitchford W, Kuchel H (2006) Joint modelling of additive and non-additive genetic line effects in single field trials. Theor Appl Genet 113:809–819
18. Oakey H, Verbyla A, Cullis B, Wei X, Pitchford W (2007) Joint modelling of additive and non-additive (genetic line) effects in multi-environment trials. Theor Appl Genet 114:1319–1332
19. Quass RL, Pollack E (1980) Mixed model methodology for farm and ranch beef cattle testing programs. J Animal Sci 51:1277–1287
20. Raymond C (2011) Genotype by environment interactions for pinus radiata in new south wales, australia. Tree Genet Genomes 7:819–833
21. Schutz W, Cockerham CC (1966) The effect of field blocking on gain from selection. Biometrics 22:843–863
22. Smith A, Cullis BR, Thompson R (2001) Analyzing variety by environment data using multiplicative mixed models and adjustments for spatial field trend. Biometrics 57:1138–1147
23. Stefanova K, Smith A, Cullis B (2009) Enhanced diagnostics for the spatial analysis of field trials. J Agric Biol Environ Stat 14:1–19
24. Thompson R, Cullis B, Smith A, Gilmour A (2003) A sparse implementation of the average information algorithm for factor analytic and reduced rank variance models. Aust N Z J Stat 45:445–459
25. White I, Rainer PR, Knap Brotherstone S (2006) Variance components for survival of piglets at farrowing using a reduced animal model. Genet Select Evol 38:359–370
26. Zapata-Valenzuela J (2012) Use of analytical factor structure to increase heritability of clonal progeny tests of pinus taeda l. Chil J Agric Res 72:309–315