Diversity in the Oryza genus

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Abstract

The pan-tropical wild relatives of rice grow in a wide variety of habitats: forests, savanna, mountainsides, rivers and lakes. The completion of the sequencing of the rice nuclear and cytoplasmic genomes affords an opportunity to widen our understanding of the genomes of the genus Oryza. Research on the Oryza genus has begun to help to answer questions related to domestication, speciation, polyploidy and ecological adaptation that cannot be answered by studying rice alone. The wild relatives of rice have furnished genes for the hybrid rice revolution, and other genes from Oryza species with major impact on rice yields and sustainable rice production are likely to be found. Care is needed, however, when using wild relatives of rice in experiments and in interpreting the results of these experiments. Careful checking of species identity, maintenance of herbarium specimens and recording of genebank accession numbers of material used in experiments should be standard procedure when studying wild relatives of rice.

Introduction

The genus Oryza is small, including only about 23 species, but is remarkable in the diverse ecological adaptations of its species (Table 1). The Oryza genus has given rise to rice (Oryza sativa L.), a major source of nutrition for about two-thirds of mankind. Rice has been grown, perhaps uniquely, in sustainable high-output agroecosystems for thousands of years. In relation to genera containing other cereals, Oryza occupies a distinct phylogenetic position in a separate subfamily, the Ehrhartoideae [1].

The genus Oryza was named by Linnaeus in 1753. The haploid chromosome number of rice was determined by Kuwada in 1910, 46 years before the correct chromosome number of humans was known. It was not until the 1960s, however, that the characters that define the Oryza genus were clarified 2., 3.. The principle morphological characteristics of the genus include rudimentary sterile lemmas, bisexual spikelets, and narrow, linear, herbaceous leaves with scabrous margins.

The basic nomenclature of Oryza species has changed little since the 1960s (for review see [4••]). Tateoka [5] analyzed species across the whole genus on the basis of studies carried out in the world’s main herbaria and in the field in Asia and Africa. His work clarified the basic groups of species within the genus, and he called these groups species complexes (Table 1). Since the 1960s, four new Oryza species have been described, O. meridionalis, O. rhizomatis, O. indandamanica and O. neocaledonica. These are all closely related to previously known species (Table 1).

Germplasm collection of wild Oryza species was initiated in the late 1950s (as compiled in [6]). In the early 1970s, international efforts to collect landrace rice germplasm began in response to the spread of green revolution varieties [7]. Subsequently, these efforts broadened to collect more widely from the Oryza genepool [8]. In this paper, we review and discuss issues related to wild Oryza genetic resources. We also highlight particular Oryza species that reveal the current focus of research involving wild relatives of rice from conservation, phylogenetic and breeding perspectives.

Section snippets

The domestication syndrome and its degeneration in the O. sativa complex (AA genome)

In AA genome Oryza species, it appears that natural selection and artificial selection (i.e. selection by humans) have different genetic consequences. Asian cultivated rice evolved from the wild species O. rufipogon sensu lacto (an AA genome wild relative of rice that includes both annual and perennial ecotypes). The adaptation of O. rufipogon, particularly to different hydrological regimes, has resulted in distinct annual and perennial ecotypes. The genetic factors that are associated with

Species-focused research

The wild relatives of rice were initially used in breeding because of the need for new traits in the cultivated rice genepool [49]. However, the ability to introduce QTL from wild Oryza germplasm in wide crosses that could potentially improve quantitative traits, such as yield [50], and the desire to broaden the genetic base of rice cultivars [51] have recently resulted in the development of wide-hybridization programs in many countries. In the following sections, we describe two species for

Conclusions and future directions

The sequencing of the rice nuclear (in 2001–2002), chloroplast (in 1989) and mitochondrial (in 2002) genomes of rice has now been completed. The next decade will see the sequencing of other Oryza genomes. The recent approval of funding for the construction of a bacterial artificial chromosome (BAC) library for the genomes of Oryza is progress in this direction [69]. An early genome map using the CC-genome species O. officinalis initiated the study of comparative genomics in the genus Oryza [70]

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • of special interest

  • ••

    of outstanding interest

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