Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.) Zhi-Kang Li 1,2, *, Bin-Ying Fu 1,2 , Yong-Ming Gao 1,2 , Jian-Long Xu 1,2 , J. Ali 2 , H.R. Lafitte 2 , Yun-Zhu Jiang 2 , J. Domingo Rey 2 , C.H.M. Vijayakumar 2 R. Maghirang 2 , Tian-Qing Zheng 1,2 and Ling-Hua Zhu 1 1 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun St., 100081, Beijing, China (*author for correspondence; e-mail z.li@cgiar.org or zhkli@yahoo.com.cn); 2 International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines Received 11 November 2004; accepted in revised form 7 June 2005 Key words: abiotic stress tolerances, genetic networks, linkage disequilibrium, QTLs Abstract Tremendous efforts have been taken worldwide to develop genome-wide genetic stocks for rice functional genomic (FG) research since the rice genome was completely sequenced. To facilitate FG research of complex polygenic phenotypes in rice, we report the development of over 20 000 introgression lines (ILs) in three elite rice genetic backgrounds for a wide range of complex traits, including resistances/tolerances to many biotic and abiotic stresses, morpho-agronomic traits, physiological traits, etc., by selective introgression. ILs within each genetic background are phenotypically similar to their recurrent parent but each carries one or a few traits introgressed from a known donor. Together, these ILs contain a significant portion of loci affecting the selected complex phenotypes at which allelic diversity exists in the primary gene pool of rice. A forward genetics strategy was proposed and demonstrated with examples on how to use these ILs for large-scale FG research. Complementary to the genome-wide insertional mutants, these ILs opens a new way for highly efficient discovery, candidate gene identification and cloning of important QTLs for specific phenotypes based on convergent evidence from QTL position, expression profiling, functional and molecular diversity analyses of candidate genes, highlights the importance of genetic networks underlying complex phenotypes in rice that may ultimately lead to more complete understanding of the genetic and molecular bases of quantitative trait variation in rice. Introduction Since the recent completion of genome sequencing both indica and japonica rice (Yu et al., 2002; Goff et al., 2002), rice functional genomic research (FG) has entered a golden era. Although the complete DNA sequences of the two rice genomes have greatly enhanced our ability to understand individual rice genes and their biological roles, it remains a tremendous challenge facing all plant scientists to determine functions of individual rice genes and their relationships. Different from classical molecular biology studies that focus on characterizing functions of single genes, FG research has two unique characteristics in gene discovery and function assignment: the large scale and dependence on information management. In the first place, FG allows simultaneous studies of large groups of related genes affecting single or related phenotypes, making it possible to dissect gene networks and biochemical pathways underlying complex phenotypes at the molecular Plant Molecular Biology (2005) 59:33–52 Ó Springer 2005 DOI 10.1007/s11103-005-8519-3