Optimal population value selection: A population-based selection strategy for genomic selection

...................................................................................................................... v CHAPTER I GENERAL INTRODUCTION ............................................................... 1 CHAPTER II LITERATURE REVIEW ....................................................................... 4 CHAPTER III SELECTION ON OPTIMAL POPULATION VALUE INCREASES GENETIC GAIN RELATIVE TO EXISTING GENOMIC SELECTION METHODS ................................................. 10 Abstract ......................................................................................................................... 10 Introduction ................................................................................................................... 11 Selection Methods ......................................................................................................... 12 Genomic selection ..................................................................................................... 13 Weighted genomic selection ..................................................................................... 13 Optimal haploid value selection ................................................................................ 14 Optimal population value selection .......................................................................... 14 Simulation ..................................................................................................................... 17 In silico breeding process model ............................................................................... 17 Data ........................................................................................................................... 20 Experimental setup .................................................................................................... 22 Data analysis ............................................................................................................. 23 Results ........................................................................................................................... 24 Selection method comparison ................................................................................... 24 Trends in OPV selection methods ............................................................................. 28 Discussion ..................................................................................................................... 32 Selection method comparison ................................................................................... 32 Trends in OPV selection methods ............................................................................. 35 Impact on total maize production ............................................................................. 36 Validity of results ...................................................................................................... 37 Conclusion .................................................................................................................... 38 CHAPTER IV GENERAL CONCLUSIONS AND FUTURE WORK ...................... 39 REFERENCES ................................................................................................................ 43 APPENDIX A PSEUDO-CODE FOR THE IMPLEMENTATION OF THE BASIC BREEDING PROCESS .......................................................... 48