Genomics approaches for the identification of genes determining important traits in sugarcane Rosanne E. Casu a,d, * , John M. Manners a,d , Graham D. Bonnett a,d , Phillip A. Jackson b,d , C. Lynne McIntyre a,d , Rob Dunne c , Scott C. Chapman a,d , Anne L. Rae a,d , Christopher P.L. Grof a,d a CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, Qld 4067, Australia b CSIRO Plant Industry, Davies Laboratory, Private Bag, Aitkenvale, Townsville, Qld 4818, Australia c CSIRO Mathematical and Information Sciences, Locked Bag 17, North Ryde, NSW 1670, Australia d Cooperative Research Centre for Sugar Industry Innovation through Biotechnology, Australia Abstract Sugarcane is a genetically complex polyploid grass, which makes the identification of associations between genes and traits difficult. Genomics science facilitates characterization of entire eukaryote genomes at the DNA sequence level, but for crop plants with complex genomes such as sugarcane, gene characterization is currently best achieved via expressed sequence tag (EST) analysis where sequence information is restricted to genes that are actually functioning in a particular tissue or situation. DNA microarrays allow simultaneous expression analysis of thousands of genes. Current work on EST and array analysis of gene expression in sugarcane is reviewed and insights on stem functions associated with maturation and sucrose accumulation are discussed. A strategy for associating gene expression with a trait is described in which individuals exhibiting particular traits are selected from segregating populations of sugarcane and their gene expression profiles compared. A preliminary experiment to test the feasibility and experimental design for this ‘genetical genomics’ strategy on a population segregating for sugar content is described. Given the complex genetics of sugarcane, this strategy and refinements of it, represent an attractive pathway to the identification of candidate genes that may control sugar accumulation and other traits in sugarcane. # 2005 Elsevier B.V. All rights reserved. Keywords: Sugarcane physiology; Sugar metabolism; EST sequencing; DNA markers; Microarrays; Genetical genomics 1. Introduction The physiology of a plant is determined by the interaction of its genome and its internal and external environment. Plant breeding manipulates the genome to develop new cultivars with desirable attributes. Genetic control of physiological ‘traits’ is tradition- ally studied by analysing the segregation of the trait of interest in conjunction with other phenotypic, biochemical and molecular markers in the progeny of crosses. In some diploid plants, such studies have led ultimately to the isolation of the DNA sequences of www.elsevier.com/locate/fcr Field Crops Research 92 (2005) 137–147 * Corresponding author. Tel.: +61 7 3214 2364; fax: +61 7 3214 2950. E-mail address: rosanne.casu@csiro.au (R.E. Casu). 0378-4290/$ – see front matter # 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.fcr.2005.01.029