Abstract This paper summarizes results from a decade of collaborative research using advanced backcross (AB) populations to a) identify quan- titative trait loci (QTL) associated with improved performance in rice and to b) clone genes underlying key QTLs of interest. We demonstrate that AB-QTL analysis is capable of (1) success- fully uncovering positive alleles in wild germ- S. R. McCouch (&) Æ M. Sweeney Æ H. Jiang Æ M. Thomson Æ E. Septiningsih Æ J. Edwards Æ P. Moncada Æ J. Xiao Æ A. Garris Department of Plant Breeding & Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853, USA e-mail: srm4@cornell.edu J. Li Pioneer Hybrid International, Johnston, Iowa 50131, USA Present Address: M. Thomson Æ E. Septiningsih International Rice Research Institute, Los Ban ˜ os, Laguna, Philippines Present Address: J. Edwards University of Arizona, Tucson, AZ, USA Present Address: P. Moncada Cenicafe, Apartado aereo 2427, Manizales, Caldas, Colombia Present Address: J. Xiao Monsanto Corp, St. Louis, MO, USA Present Address: A. Garris USDA/ARS, Geneva, NY, USA Present Address: T. Tai University of California, Davis, CA, USA C. Martinez Æ J. Tohme CIAT, Cali, Colombia M. Sugiono ICABIOGRAD, 16111 Bogor, Indonesia A. McClung USDA-ARS, DBNRRC & Beaumont Rice Research Unit, Beaumont, TX 77713, USA L. P. Yuan China National Hybrid Rice Research & Development Center, Changsha, Hunan 41025, P.R. China S.-N. Ahn Dept of Agronomy, College of Agriculture, Chungnam National University, Daejeon, Republic of Korea Euphytica (2007) 154:317–339 DOI 10.1007/s10681-006-9210-8 123 Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa Susan R. McCouch Æ Megan Sweeney Æ Jiming Li Æ Hui Jiang Æ Michael Thomson Æ Endang Septiningsih Æ Jeremy Edwards Æ Pilar Moncada Æ Jinhua Xiao Æ Amanda Garris Æ Tom Tai Æ Cesar Martinez Æ Joe Tohme Æ M. Sugiono Æ Anna McClung Æ Long Ping Yuan Æ Sang-Nag Ahn Received: 23 February 2006 / Accepted: 9 June 2006 / Published online: 17 October 2006 Ó Springer Science+Business Media B.V. 2006