Phylogeny of rice genomes with emphasis on origins of allotetraploid species

Abstract

The rice genus, Oryza, which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germ plasm. By generating and comparing two nuclear gene (Adh1 and Adh2) trees and a chloroplast gene (matK) tree of all rice species, phylogenetic relationships among the rice genomes were inferred. Origins of the allotetraploid species, which constitute more than one-third of rice species diversity, were reconstructed based on the Adh gene phylogenies. Genome types of the maternal parents of allotetraploid species were determined based on the matK gene tree. The phylogenetic reconstruction largely supports the previous recognition of rice genomes. It further revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome. Three species of the CCDD genome may have originated through a single hybridization event, and their maternal parent had the CC genome. The BBCC genome species had different origins, and their maternal parents had either a BB or CC genome. An additional genome type, HHKK, was recognized for Oryza schlechteri and Porteresia coarctata, suggesting that P. coarctata is an Oryza species. The AA genome lineage, which contains cultivated rice, is a recently diverged and rapidly radiated lineage within the rice genus.

A map of rice genome variation reveals the origin of cultivated rice

“…1. The genus Oryza consists of 23 species 23,24 , and the wild rice O. rufipogon is believed to be the immediate progenitor of the cultivated rice O. sativa ( Supplementary Fig. 2 and Supplementary Table 1).…”

The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species

“…Based on recent phylogenetic data, Ge et al (1999) proposed that Porteresia coarctata should be included in the genus as the 24th Oryza species. Cultivated rice is classified as an AA genome diploid and has six wild AA genome relatives.…”

“…The remaining 15 wild species are classified into nine other genome types that include both diploid and tetraploid species. Figure 1 shows a proposed phylogenetic tree of the genus Oryza as described by Ge et al (1999) based on the analysis of two nuclear and one chloroplast gene. The wild rice species offer a largely untapped resource of agriculturally important genes that have the potential to solve many of the problems in rice production that we face today such as yield, drought and salt tolerance and disease and insect resistance.…”

Cytogenetic comparisons between A and G genomes in Oryza using genomic in situ hybridization

“…The genus Oryza is composed of two cultivated and more than 20 wild species, and 10 genome sets have been identified including the diploids and tetraploids [1][2][3]. Wild rice species are extremely valuable gene resources for the genetic improvement of cultivated rice and for the study of genomics [4].…”

“…A variety of beneficial traits, such as disease and pest resistances, and tolerances to drought and shade stress, have been found in O. meyeriana [18,21]. Efforts have been devoted to understanding the genomic composition [2] and genetic variation [3,19,20] of O. meyeriana. However, the cytological features of O. meyeriana and the genomic relationship between A and G genomes have not been thoroughly investigated.…”