Rice Genetics IV - IRRI books - International Rice Research Institute

Molecular markers and evolutionary relationships of rice speciesConsiderable effort has been devoted to studying the relationships of rice genomesand species, although the phylogeny of Oryza has been less explored than that ofother major crop plants such as maize (Gaut et al 2000), soybean (Doyle et al 1996),and cotton (Wendel and Albert 1992).Morishima and Oka (1960) studied 42 morphological characters of 16 Oryza speciesby numerical taxonomic methods. They found that Roschevicz’s sectionSativa could be divided into two groups. One group was represented by O. sativa,with five species (A genome), and the other by O. officinalis, with seven species (C,BC, CD genomes) (Morishima and Oka 1960). Based on 15 morphological, ploidy,and habit characters and the distribution of Oryza species, Sharma (1986) reconstructeda phylogenetic tree of Oryza species and found that O. ridleyi, O. meyeriana, and O.schlechteri formed a clade at the basal position of this tree.Evolutionary relationships among the rice genomes and species were also investigatedby various methods, including protein (Sarkar and Raina 1992), isozyme (Second1985), and organelle and nuclear DNA restriction fragment length polymorphisms(RFLPs) (Dally and Second 1990, Second 1991, Wang et al 1992, Abe et al 1999).These studies provided only limited information on the phylogeny of the genus becauseof either incomplete sampling or the nature of the data. Wang et al (1992) conductedthe most comprehensive study on phylogenetic relationships of 21 Oryza species.The UPGMA (unweighted pair-group method, arithmetic average) dendrogram,generated by genetic distances estimated from 25 genomic RFLP clones, indicatedfour species complexes that corresponded to those of Vaughan (1989). In addition,Wang et al (1992) suggested that BBCC tetraploids (O. malampuzhaensis, O. punctata,and O. minuta) were likely to have independent origins and that CCDD tetraploidspossibly had an ancient origin with the closest living diploids containing the C and Egenomes. However, using phenetic methods and data other than DNA sequences,these studies often produced contradictory results and failed to reconstruct origins ofallotetraploid species with their parents indicated clearly.Recently, the PCR-based methods such as random amplified polymorphic DNA(RAPDs), amplified fragment length polymorphisms (AFLPs), and inter simple sequencerepeats (ISSRs) have been increasingly used for a variety of studies on populationgenetics and phylogenetic reconstruction at lower taxonomic levels (Wolfe andListon 1998). In addition to the application of these markers to the analysis of populationgenetics and germplasm management, they have also been used to detect geneticsimilarity and phylogenetic relationships among Oryza species (Ishii et al 1996,Aggarwal et al 1999, Joshi et al 2000). However, PCR-based analyses are sensitive tominor modifications in experimental protocols and to problems of homology assessment(Wolfe and Liston 1998), particularly when involving distinct species. Moreover,the dendrogram generated based on genetic distance may not accurately reflectthe phylogenetic relationships of the genomes and species. Therefore, there is a greatneed for a robust phylogenetic reconstruction of Oryza species based on molecularphylogenetic approaches and DNA sequence data.94 Song Ge et al