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PUBLICATIONS Book Singh RK, R Singh, G Ye, A Selvi, and GP Rao 2009.

Molecular Breeding in Crops: Principle, Method and Application. Studium Press, LLC, Texas, USA. Book Chapters 5. Ye G, KF Smith, and M Van Ginkel 2011. Designing markerassisted inbred line development strategies using computer simulation. Plant Breeding Reviews 34: 297-348 4. Ye G, and KF Smith 2010. Marker-assisted gene pyramiding for cultivar development. Plant Breeding Reviews 33: 219-256 3. Ye G, FC Ogbonnaya, and M Van Ginkel 2009. The use of markerassisted recurrent backcrossing in cultivar development. In Singh RK, R Singh, G Ye, A Selvi, and GP Rao (Eds). Molecular Breeding in Crops: Principle, Method and Application Pp 295319. Studium Press, LLC, Texas, USA. 2. Ye G, KF Smith 2009. Marker-assisted gene pyramiding. In Singh RK, R Singh, G Ye, A Selvi, and GP Rao (Eds). Molecular Plant Breeding: Principle, Method and Application. Pp 321-342.. Studium Press, LLC, Texas, USA 1. Ye G , and M. Van Ginkel 2009. Formulating marker-assisted selection strategies using computer simulation. In Singh RK, R Singh, G Ye, A Selvi, and GP Rao (Eds). Molecular Breeding in Crops: Principle, Method and Application . Pp 421-444. Studium Press, LLC, Texas, USA. Referred Journal Papers 34. Wei D, K Cui K. J Pan, J Xiang, L Nie, J Huang, and G Ye 2011. QTL mapping for nitrogen-use efficiency and nitrogendeficiency tolerance traits in rice. Plant and Soil (Accepted). 33. Liu G, Zhu H, Zhang G, Li L, and G Ye* 2011. Dynamic analysis of tiller number QTLs in rice (Oryza sativa L.) with single segment substitution lines. Theoretical and Applied Genetics (Accepted). 32. Wei D, K Cui K. J Pan, G Ye, J Xiang, L Nie, and J Huang 2011. Genetic dissection of grain nitrogen use efficiency and grain yield and their relationship in rice. Field Crops Research 124: 340346 31. Ye G, S Liang and JM Wan 2010. Mapping protein content in rice using single segment chromosome substitution lines. Theoretical and Applied Genetics 121: 741-750.

30. Li W, T Zhang, M. Dieters, and G Ye* 2009. The effects of component trait selection on genetic gain of lint yield in upland cotton breeding program investigated using simulation. SABRAO Journal of Breeding and Genetics 41: 83-100. 29. Kaur S, NOI Cogan, G. Ye, RC Baillie, ML Hand, AE Ling, AK McGearey, J. Kaur, CJ Hopkins, M. Todorovic, M. Mountford, D. Edwards, J. Batley, W. Burton, P. Salisbury, N. Gororo, S. Marcroft, G. Kearney, KF Smith, JW Forster, and GC Spangenberg 2009.Genetic map construction and QTL mapping of disease resistance to blackleg (Leptosphaeria maculans) in cultivars of Australian canola (Brassica napus L.). Theoretical and Applied Genetics. 120: 71-83 28. Wang Y, G Ye , N Luan, J Xiao, Y Chen, and DH Chen 2009. Boll size affects the insecticidal protein content in Bacillus thuringiensis (Bt) cotton. Field Crops Research 110: 106-110. 27. Liu SM, G Ye, KF Smith, and S Richards 2009. Segregation and transmission of scab reactions in pear breeding progenies under orchard diseased conditions. Scientica Horticulturae 120: 222-229. 26. Ogbonnaya FC, M Imtiaz M, G Ye, PR Hearnden, E Hernandez, RF Eastwood, and M Van Ginkel 2008. Genetic and QTL analyses of seed dormancy and preharvest sprouting resistance in the wheat germplasm CN10955. Theoretical and Applied Genetics 116: 891-902. 25. Zhang Y, Q Zhang, ZH He, Y Zhang, RJ Pea, and G Ye 2008. Solvent retention capacities as indirect selection criteria for sugar snap cookie quality in Chinese soft wheat genotypes. Australian Journal of Agricultural Research 59: 911-917 24. Ye G, and KF Smith 2008. Marker-assisted gene pyramiding for inbred line development: Basic principles and practical guidelines (Invited Review). International Journal of Plant Breeding 2: 1- 10. 23. Ye G, and KF Smith 2008. Marker-assisted gene pyramiding for inbred line development: Practical applications (Invited Review). International Journal of Plant Breeding 2: 11-22. 22. Li H, G Ye, and J Wang 2007. A Modified Algorithm for improvement of Composite Interval Mapping (CIM). Genetics 175: 361-374. 21. Ogbonnaya FC, G Ye, R Trethowan, F Dreccer, J Shepperd, and M van Ginkel 2007 Yield of synthetic backcross-derived lines in rainfed environments of Australia. Euphytica 157: 321-336. 20. Zhang X, L Zhang, G Ye, Y Wang, Y Chen, and DH Chen 2007. The impact of introducing the Bacillus thuringiensis gene into

cotton on boll nitrogen metabolism. Environmental and Experimental Botany 61: 175-180. 19. Zhang X, G Ye, L Zhang, Y Wang, Y Chen, and DH Chen 2007. Effect of gibberellic acid and zeatin on boll development in trans-Bacillus thuringiensis gene cotton. Field Crops Research 103: 5- 10. 18. He H, L Xu, X Peng, G Yang, C Zhu, Z Liu, and G Ye* 2007. Molecular tagging of the male fertility restorer gene for the 501-8S cytoplasmic male sterility in rapeseed (Brassica napus. L.). Australian Journal of Agricultural Research 58: 753758. 17. Ye G, D Moody, L Emebiri, and M van Ginkel 2007. Designing an optimal marker-based pedigree selection strategy for parent building in barley in the presence of repulsion linkage, using computer simulation. Australian Journal of Agricultural Research 58: 243-251. 16. He H, X Peng, H Gong, C Zhu, and G Ye* 2006. Fertility behaviour of rice (Oryza sativa) lines with dominant sterile gene and inheritance of male sterility and fertility restoration. Field Crops Research 98: 30 38. 15. He H, X Peng, H Gong, C Zhu, and G Ye* 2006. Characterisation of male sterility line of indica rice (Oryza sativa,Spp. Indica). Australian Journal of Agricultural Research 57: 457 464. 14. Zhang Y, ZH He, A Zhang, M van Ginkel, and G Ye 2006. Pattern analysis of grain yield performance of Chinese and CIMMYT spring wheat cultivars in Chinas spring wheat regions and CIMMYTs management environments. Euphytica 147: 409420. 13. Zhang Y, ZH He, A Zhang, M Ginkel, RJ Pea, and G Ye 2006. Pattern analysis on protein properties of Chinese and CIMMYT spring wheat cultivars grown in Chinas spring wheat regions and CIMMYTs managed environments. Australian Journal of Agricultural Research 57: 811-822. 12. Kuchel H, G Ye, R Fox, and S Jefferies 2005. Genetic and Economic Analysis of a Targeted Marker Assisted Wheat Breeding Strategy. Molecular Breeding 16: 67-78. 11. Zhang Y, Y Zhang, ZH He, and G Ye 2005. Milling quality and protein properties of autumn-sown Chinese wheats evaluated through multilocational trials. Euphytica 143: 209-222. 10. Chen DH, G Ye, C Yang, Y Chen, and Y Wu 2005. Effect of high temperature on the insecticidal properties of Bt Cotton. Environmental and Experimental Botany 53: 333-342.

9. Chen DH, G Ye, C Yang, Y Chen, and Y Wu 2005. Effect of introducing Bacillus thuringigesis gene on nitrogen metabolism in Cotton. Field Crops Research 92: 1-9. 8. Zhang Y, ZH He, G. Ye, A Zhang, and M Van Ginkel 2004. Effect of environment and genotype on bread-making quality of springsown spring wheat cultivars in China. Euphytica 139: 75-83. 7. Wang J, M van Ginkel, R Trethowan, G. Ye, IH DeLacy, D Podlich, and M. Cooper 2004. Simulating the effects of dominance and epistasis on selection response in the CIMMYT Wheat Breeding Program using QuCim. Crop Science 44: 2006-2018. 6. Wang J, M. van Ginkel, D Podlich, G Ye, R Trethowan, W Pfeiffer, IH DeLacy, M Cooper, and Rajaram, 2003. Comparison of two breeding strategies by computer simulation. Crop Science 43: 1764-1773. 5. Ye G, DL McNeil, and GD Hill 2003. Inheritance of foliar resistance to Ascochyta Blight in Lentil (Lens culinaris Medik). New Zealand Journal of Crop and Horticultural Science 31: 7783. 4. Ye G, DL McNeil, and GD Hill 2002. Breeding for Ascochyta blight resistance in Lentil. Plant Breeding 121: 185-191. 3. Ye G, DL McNeil, and GD Hill 2002. Minor genes are involved in Ascochyta blight resistance in lentil. Journal of Genetics and Breeding 56: 21-28. 2. Ye G, DL McNeil, AJ Conner, and GD Hill 2002. Multiple shoot formation from lentil seeds. New Zealand Journal of Crop and Horticultural Science 30: 1-8. 1. Ye G, DL McNeil, AJ Conner, and GD Hill 2000. Improved protocol for the multiplication of lentil hybrids without genetic change by culturing single node explants. SABRAO Journal of Breeding & Genetics 32:13-21.
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Corresponding author

Referred Conference Papers Ye G, MJ Dieters, A Pudmenzky, K Micallef, and KE Basford 2004. Simulation of positive assortative mating for Inbred Line development using QU-GENE. 4th International Crop Science Congress: New Direction for A Diverse Planet. Brisbane, Australia. Ye, G, HA Eagles, and MJ Dieters 2004. Parental selection using known genes for inbred line development. Cereals 2004, Proceedings of 54th Australian Cereal Chemistry Conferences and 11th Wheat Breeders Assembly Pp. 245-248 Ye, G, and MJ Dieters 2004. Comparison of Modified Bulk/Pedigree and Bulk Methods using QU-GENE. Cereals 2004, Proceedings of

54th Australian Cereal Chemistry Conferences and 11th Wheat Breeders Assembly Pp. 202-205 Eagles HA, DB Moody, RF Eastwood, GJ Hollamby, GB Cornish, KA Cane, G Ye and PJ Martin 2004. Using data from plant breeding programs to estimate gene effects. Cereals 2004, Proceedings of 54th Australian Cereal Chemistry Conferences and 11th Wheat Breeders Assembly Pp 210-213 Ye G, DL McNeil, and GD Hill 2001. Genetic variation for minor genes conditioning Ascochyta blight resistance in lentils. 4th European Conference on Grain Legumes , Cracow. Pp. 240-241 Ye G, DL McNeil, and GD Hill 2001. Inheritance of resistance to Ascochyta blight in lentil. New Zealand Plant protection 54: 198201 Ye G, DL McNeil, and GD Hill 2000. Some methods for analysing multisite plant variety trials. I. Estimating genotype means at each site. Agronomy New Zealand 31: 13-24 Ye G, DL McNeil, and GD Hill 2000. Some methods for analysing multisite plant variety trials. II. Selection for yield and stability. Agronomy New Zealand 31: 25-33. Ye G, DL McNeil, and GD Hill 2000. Two major genes confer Ascochyta blight resistance in Lens orientalis. New Zealand Plant protection 53: 109-133. Ye G, DL McNeil, and GD Hill 2000. Lentil Ascochyta blight and breeding for its resistance. New Zealand Plant protection 53: 97-102. Ye G, X Shen, and MD Wilcox 1995. Breeding strategies for Paulownia in China. In X Shen (ed) Proceeding of Asia-pacific seminar on tree breeding. Chinese Forestry Publishing House. Posters Bartolome, VI, Mohammadi R, and G Ye 2012. Griffings Diallel Analysis Using R. The 12th SABRAO Congress on Plant Breeding. 13-16 January 2012, Chiang Mai, Thailand Gulles AA. VA Bartolome, RI Zhella, A Morantte, LA Nora, and G Ye. 2011. Using R-CropStat for basic experimental designs and analyses. Federation of Crop Science Societies of the Philippines (FCSSP) scientific conference. 2011. 9-14 May Legazpi City, Philippines. Ye G. 2009. What can computer simulation offer to MAS in rice breeding? International Rice Genetics Symposium. 17-23 November, 2009, Manila, Philippines Forster JW, NI Cogan , RC Baillie, ML Hand, G Ye, C Bandaranayake, GC Spangenberg, and KF Smith 2009. Gene-Associated SNP marker development and implementation for temperate

pasture grass improvement. Plant & Animal Genomes XVII Conference. January 10-14, 2009,Town & Country Convention Center, San Diego, CA Edwards D, A Ling, P Salisbury, W Burton, G Ye, M Vardy, S Kaur, J Kaur, G Spangenberg, J Batley 2007. Characterisation of molecular genetics markers and candidate resistance genes at a conserved blackleg resistance locus. Plant & Animal Genomes XV Conference. January 13-17, 2007 Town & Country Convention Center San Diego, CA. Li H, Z Li, G. Ye, and J Wang 2007. Inclusive composite interval mapping of quantitative trait genes. The 3rd International Conference of Quantitative Genetics, Zhejiang University, Hangzhou, China August 19 -24, 2007. Ye G, D Moody, L Eemebiri, and M Van Ginkel 2006. Design a Marker-based pedigree selection strategy for parent building in barley using computer Simulation. XIII EUCARPIA Biometrics in Plant Breeding Section Meeting 30 August - 1 September 2006, Zagreb, Croatia. Ogbonnaya FC, Ye G, Trethowan, R., Dreccer, F., Sheppard, J., van Ginkel, M. 2006. Yield of synthetic backcross-derived lines in rainfed environments of Australia. Pp. 12: Reynolds M.P. & Godinez D. (Eds): Extended Abstracts of the International Symposium on Wheat Yield Potential 'Challenges to International Wheat Breeding" March 20-24th, 2006 Cd. Obregon, Mexico. Delacy, IH, G Ye, RE Eiseman, J Sheppard, and P Banks 2004. QUGENE simulation of pyramiding multiple genes for disease and pest resistance in a breeding program. Seed the Future Conference, Canberra, Australia 21-24 September 2004. Wang J, M van Ginkel, R Trethowan, G Ye, D Podlich, IH DeLacy, and M Cooper 2003. QuCim, A software program that simulates inbred breeding programs, is exemplified by the role of pleiotrophy, Dominance, epistasis and linkage on selection. The Tenth International Wheat Genetics Symposium (TIWGS), Paestum, Italy, 1 - 6 September 2003. Wang J, M van Ginkel, G Ye, D Podlich, R Trethowan, W Pfeiffer, IH DeLacy, and M Cooper 2003. QuCim with applications: A software program that simulates inbred breeding programs. Arnel Hallauer International Symposium on Plant Breeding, Mexico City, 17-22 August, 2003 Wang J, M van Ginkel, G Ye, I DeLacy, R Trethowan and WH Pfeiffer. 2003. QuCim/QuLine Application 1: Comparison of two breeding methods. Poster for GRDC/CIMMYT/UQ Breeding Simulation and Germplasm Exchange Workshop, Brisbane, Australia. 28-30 July 2003.

Wang J, M van Ginkel, G Ye, I DeLacy, R Trethowan and WH Pfeiffer. 2003. QuCim/QuLine Application 3: Effects on selection of dominance, epistasis, pleiotropy and linkage. Poster for GRDC/CIMMYT/UQ Breeding Simulation and Germplasm Exchange Workshop, Brisbane, Australia. 28-30 July 2003. Wang J, M van Ginkel, G Ye, I DeLacy, R Trethowan and WH Pfeiffer. 2003. How does QuCim/QuLine simulate a breeding program? Poster for GRDC/CIMMYT/UQ Breeding Simulation and Germplasm Exchange Workshop, Brisbane, Australia. 28-30 July 2003. Wang J, M van Ginkel, G Ye, I DeLacy, R Trethowan and WH Pfeiffer. 2003. Defining the breeding methods in QuCim. Poster for GRDC/CIMMYT/UQ Breeding Simulation and Germplasm Exchange Workshop, Brisbane, Australia. 28-30 July 2003.