Polyploidy and Crop Improvement

All crop plants are polyploid and some genomes have been duplicated more recently than others. Advancements in cytogenetic and molecular tools, including high-density genetic mapping, fl orescent in situ hybridization, and genome and EST sequencing, have enabled new insights into genome composition and the history of genome duplications in crop plants. We review this evidence and discuss the relevance of genome duplication to crop improvement. Polyploidy provides genome buffering, increased allelic diversity and heterozygosity, and permits novel phenotypic variation to be generated. Polyploid formation is often accompanied with loss of duplicated chromatin, changes in gene expression, novel epistatic interactions, and endosperm effects. All of these factors need be considered in a genome-wide context for optimizing marker assisted selection and crop plant improvement. Abbreviations: Ks, synonymous sites; FLC, FLOWERING LOCUS C. One of the most spectacular advances of the genomics era has been a renewed appreciation of the pervasiveness and importance of genome doubling in plant evolution. Although the prevalence of polyploidy in plants has classically been recognized from comparative analyses of chromosome numbers (Stebbins, 1950; Grant, 1981) and other biosystematic approaches (e.g., Masterson, 1994), it turns out that this mostly cytogenetically-based perspective greatly underestimated the role polyploidy has played in shaping modern plant genomes. With the advent of genome sequencing and the availability of extensive EST data sets and high-density, molecular marker-based maps, it became clear that all plant genomes harbor evidence of cyclical, recurrent episodes of genome doubling (Wendel, 2000; Bowers et al., 2003; Blanc and Wolfe, 2004; Paterson et al., 2004; Seoighe and Gehring, 2004; Cui et al., 2006). Th ese events have occurred at temporal scales ranging from ancient to contemporary, and are suspected to have fundamental signifi cance to plant adaptation and function. Given the importance of polyploidy in plants, it is not surprising that the subject has received considerable attention and has provided the focus for a number of reviews (Ramsey and Schemske, 1998; Osborn et al., 2003a; Soltis et al., 2004a; Wendel and Doyle, 2005; Adams and Wendel, 2005a; Adams and Wendel, 2005b; Durand and Hoberman, 2006; Chen and Ni, 2006). Th ese reviews provide excellent entries into the literature on modes, mechanisms and frequency of polyploid J.A. Udall, Dep. of Plant and Animal Sciences, Brigham Young Univ., Provo, UT; J.F. Wendel, Dep. of Ecology, Evolution, and Organismal Biology, Iowa State Univ., Ames, IA 50011. Received 25 July 2006. *Corresponding author ([email protected]). Published in Crop Sci 46(S1) (2006). Published 7 Sept. 2006. doi:10.2135/cropsci2006.07.0489tpg © Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA Ge ome The