Rice Genetics IV - IRRI books - International Rice Research Institute

genomes occupy the basal positions relative to those of the BC and CD genomes (Fig.1), suggesting that the former had more ancient origins, which may have allowedmore extensive genomic rearrangement including possible deletions of somehomeologous loci. Southern blotting and more gene phylogenies can be employed tofurther test the hypothesis of gene deletion.Moreover, the study focused mainly on relationships among genome types anddid not involve interspecific relationships in depth. A well-resolved and strongly supportedphylogeny of Oryza at the species level is needed to provide a basis for aninformative and predictive classification, a better understanding of evolution and biogeography,and more effective use of wild rice germplasm.Evolution of genes and genomes in allotetraploid speciesAllopolyploidy is a widely documented mechanism of speciation in flowering plants(Masterson 1994). Previous cytogenetic studies have inferred genomic compositionsof the allotetraploid species and provided necessary background as well as intriguinghypotheses for further molecular phylogenetic analyses. The Adh phylogenies determinedthe origins of allotetraploid genomes of Oryza and suggested that these genomesoriginated at different times. The BC genome originated most recently, whilethe HJ and HK genomes are more ancient (Figs. 1, 3). Allotetraploid species withdifferent origins and ages in the Oryza genus serve as a good system for investigatinga variety of questions concerning the formation and evolution of polyploid species.As reviewed in recent literature (Soltis and Soltis 2000, Wendel 2000), the study ofpolyploidy represents an intriguing topic in plant evolutionary biology. We are particularlyinterested in the following questions in the rice genus.Gene silencing or deletion following polyploidization. It has been suggested thatcycles of polyploidization and diploidization have contributed to the species diversityof angiosperms (Wendel 2000). If this is true, gene silencing or deletion should occurat a large number of homeologous loci in older allopolyploids. For the Adh genes,both homeologous loci are retained in the recently originated BC and CD genomes.As mentioned above, however, multiple combinations of PCR primers failed to amplifyone of the homeologous loci of the Adh2 gene from the HJ genome and one ofthe homeologous loci of the Adh1 gene from the HK genome (Ge et al 1999). Thissuggests that one of the Adh homeologous loci has been deleted from the allotetraploidgenomes. It is thus of great interest to investigate whether gene silencing (e.g.,pseudogene formation) or gene deletion also occurs at other nuclear loci of the HJ andHK genomes.Adaptive evolution of duplicated genes in allotetraploid genomes. Although anallotetraploid genome tends to reduce its genetic redundance through gene silencingor deletion, it may also take advantage of genetic redundancy. Genome duplicationcould allow the relaxation of purifying selection on one of the homeologous loci andsubsequently the evolution of a new function of the locus (Soltis and Soltis 2000,Wendel 2000). If the new function is acquired through fixation of mutations in theprotein-coding region driven by positive selection, it can be detected by comparingthe ratio of nonsynonymous to synonymous substitutions (Ka/Ks) (Li 1997). Further,Phylogeny of the genus Oryza . . . 101