Publications

Lin, J., V. Arief, Z. Jahufer, J. Osorno, P. McClean, D. Jarquin, and V. Hoyos-Villegas. 2023. Simulations of rate of genetic gain in dry bean breeding programs. Theoretical and Applied Genetics 136: 1-22.

Jahufer, M.Z.Z., S.K. Arojju, M.J. Faville, K. Ghamkhar, D. Luo, V. Arief, W.-H. Yang, M. Sun, I.H. Delacy, A.G. Griffiths, C. Eady, W. Clayton, A.V. Stewart, R.M. George, V. Hoyos-Villegas, K.E. Basford and B. Barret. 2021.Deterministic and stochastic modelling of impacts from genomic selection and phenomics on genetic gain for perennial ryegrass dry matter yield. Scientific Reports 11: 13265.

Ali, M., L. Zhang, I.H. DeLacy, V. Arief, M. Dieters, W.H. Pfeiffer, J. Wang and H. Li. 2020. Modeling and simulation of recurrent phenotypic and genomic selections in plant breeding under the presence of epistasis. The Crop Journal 8: 866-877.

Hoyos-Villegas, V., V. Arief, W.-H. Yang, M. Sun, I.H. DeLacy, B. Barrett, Z. Jahufer and K. Basford. 2018. QuLinePlus: Extending plant breeding strategy and genetic model simulation to cross-pollinated populations – case studies in forage breeding. Heredity 122: 684-695.   

Jahufer, M.Z.Z. and D. Luo. 2018. DeltaGen: A comprehensive decision support tool for plant breeders. Crop Science 58: 1118-1131.

Arief, V.N., I.H. DeLacy, M.J. Dieters and K.E. Basford. 2014. Application of marker-trait association profiles in simulating plant breeding strategies 15th Australasian Plant Breeding Conference. St Kilda, Victoria.

Li, H. and J. Wang. 2011. QuMARS, A QU-GENE application module that simulates marker assisted recurrent selection. Version 1.0. User’s Manual. 

Wang, J. 2011. Simulation modeling in crop breeding. Journal of the Indian Society of Agricultural Statistics 65: 225-235.

Wang, J., S.C. Chapman, D.G. Bonnett and G.J. Rebetzke. 2009. Simultaneous selection of major and minor genes: use of QTL to increase selection efficiency of coleoptile length of wheat (Triticum aestivum L.). Theoretical and Applied Genetics 119: 65-74. 

Wang, J., R.P. Singh, H.-J. Braun and W.H. Pfeiffer. 2009. Investigating the efficiency of the single backcrossing breeding strategy through computer simulation. Theoretical and Applied Genetics 118: 683-694.

Wang, J. and M. Dieters. 2008a. QuLine, A software that simulates breeding programs for developing inbred lines. Version 2.1. User’s Manual.

Wang, J. and M. Dieters. 2008b. QuHybrid, A QU-GENE application module that simulates breeding programs for developing hybrids. Version 1.0. User’s Manual.

Wang, J., S.C. Chapman, D.G. Bonnett, G.J. Rebetzke and J. Crouch. 2007. Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection. Crop Science 47: 582-588. 

Cooper, M., D.W. Podlich and L. Luo. 2007. Modeling QTL effects and MAS in plant breeding. In: R. K. Varshney and R. Tuberosa (Eds.). Genomics-Assisted Crop Improvement: Vol. 1: Genomics Approaches and Platforms. Springer Netherlands, Dordrecht. p. 57-95.

Wang, J., X. Wan, H. Li, W.H. Pfeiffer, J. Crouch and J. Wan. 2007. Application of identified QTL-marker associations in rice quality improvement through a design-breeding approach. Theoretical and Applied Genetics 115: 87-100.

Wang, J., M. van Ginkel, D. Podlich, G. Ye, R. Trethowan, W. Pfeiffer, I.H. DeLacy, M. Cooper and S. Rajaram. 2003. Comparison of two breeding strategies by computer simulation. Crop Science 43: 1764-1773.

Podlich, D.W. and M. Cooper. 1998. QU-GENE: a simulation platform for quantitative analysis of genetic models. Bioinformatics 14: 632-653.

Faux, A.-M., G. Gorjanc, R.C. Gaynor, M. Battagin, S.M. Edwards, D.L. Wilson, S.J. Hearne, S. Gonen and J.M. Hickey. 2016. AlphaSim: Software for Breeding Program Simulation. Plant Genome 9.

Lin, Z., N.O.I. Cogan, L.W. Pembleton, G.C. Spangenberg, J.W. Forster, B.J. Hayes and H.D. Daetwyler. 2016. Genetic gain and inbreeding from genomic selection in a simulated commercial breeding program for perennial Ryegrass. The Plant Genome 9.

Kauffman, S.A 1993. The origins of order: self-organization and selection in evolution. Oxford University Press, New York.