Received: 8 January, 2008. Accepted: 17 February, 2008. Invited Review International Journal of Plant Breeding ©2008 Global Science Books Marker-assisted Gene Pyramiding for Inbred Line Development: Basic Principles and Practical Guidelines Guoyou Ye 1* • Kevin F. Smith 2 1 Bundoora Centre, Biosciences Division, The Department of Primary Industries Victoria, and Molecular Plant Breeding Cooperative Research Centre, 1 Park Drive, Bundoora Vic 3086, Australia 2 Hamilton Centre, Biosciences Division, The Department of Primary Industries, Mount Napier Road, Hamilton, Vic 3300, Australia Corresponding author: * guoyou.ye@dpi.vic.gov.au ABSTRACT Gene pyramiding, which aims to assemble multiple desirable genes into a single genotype, is a commonly used method in breeding for self-pollinated crops. Traditionally, the main use of gene pyramiding is to improve an existing elite cultivar through introgression of a few genes of large effects from other sources, since the presence of the target genes has to be monitored by phenotyping, which is only effective for major genes. Depending on the trait and inheritance of the targeted genes, gene pyramiding may require much labour, time and material resources. The development of modern plant molecular techniques and quantitative genetics in the last two decades has dramatically widened the applicability of gene pyramiding. It provides enhanced knowledge of the genetics of the breeding traits and of the relative genomic location of functionally related as well as neutral markers associated with the genes responsible for the traits. It facilitates the identification of genes with large effect for traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program. Marker-based selection reduces/eliminates extensive phenotyping, provides more effective options to control linkage drag, makes the pyramiding of genes with very similar phenotypic effects possible, and reduces the breeding duration. Marker- based gene pyramiding is now the method of choice for inbred line development targeted at improving traits controlled by major genes. In this review, we focus on aspects of designing an efficient marker-based gene pyramiding strategy for inbred line development. The basic principles of gene pyramiding, the process and useful guidelines for designing an efficient strategy, and the integration of gene discovery and pyramiding are discussed in this paper, while the successful use of gene pyramiding in practical breeding is summarised in a companion paper. _____________________________________________________________________________________________________________ Keywords: functional markers, introgression lines, marker-assisted selection, molecular markers, quantitative trait loci CONTENTS INTRODUCTION.......................................................................................................................................................................................... 1 GENERAL PRINCIPLES OF MARKER-ASSISTED GENE PYRAMIDING............................................................................................. 2 Basic assumptions and characteristics ....................................................................................................................................................... 2 Frequencies of genotypes in a segregating population............................................................................................................................... 2 Minimal population size for the recovery of desirable genotype ............................................................................................................... 3 PROCESS OF DESIGNING A GENE PYRAMIDING STRATEGY ........................................................................................................... 3 Designing the Fixation Scheme ................................................................................................................................................................. 3 Designing the Cross Scheme ..................................................................................................................................................................... 4 GUIDELINES FOR DESIGNING AN EFFICIENT GENE PYRAMIDING STARTEGY ........................................................................... 4 Guidelines for designing a gene pyramiding crossing scheme .................................................................................................................. 4 Methods for enhancing the efficiency of the fixation step ......................................................................................................................... 5 MAIN FACTORS AFFECTING GENE PYRAMIDING .............................................................................................................................. 6 Characteristics of the target traits/genes .................................................................................................................................................... 6 Reproductive characteristics ...................................................................................................................................................................... 6 A breeder’s capability to identify the ‘desired’ genotypes ......................................................................................................................... 6 Operating capital ....................................................................................................................................................................................... 6 INTEGRATING GENE DISCOVERY, VALIDATION AND PYRAMIDING.............................................................................................. 7 Advanced backcross QTL analysis (AB-QTL) .......................................................................................................................................... 7 Introgression lines (ILs)............................................................................................................................................................................. 7 Functional markers .................................................................................................................................................................................... 7 PROSPECTS.................................................................................................................................................................................................. 9 ACKNOWLEDGEMENTS ........................................................................................................................................................................... 9 REFERENCES............................................................................................................................................................................................... 9 _____________________________________________________________________________________________________________ INTRODUCTION Gene pyramiding is defined as a method aimed at assemb- ling multiple desirable genes from multiple parents into a single genotype. The end product of a gene pyramiding program is a genotype with all of the target genes. Gene- rally speaking, the objectives of gene pyramiding include: 1) enhancing trait performance by combining two or more complementary genes, 2) remedying deficits by introgres- sing genes from other sources, 3) increasing the durability ®