Abstract
BackgroundRice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. However, the quantity and quality of these unexplored resources remain unclear. Recent accumulation of the genomic information of both cultivated and wild rice species allows for their comparison at the molecular level. Here, we compared the genome sequence of Oryza sativa ssp. japonica with sets of bacterial artificial chromosome end sequences (BESs) from two wild rice species, O. rufipogon and O. nivara, and an African rice species, O. glaberrima.ResultsWe found that about four to five percent of the BESs of the two wild rice species and about seven percent of the African rice could not be mapped to the japonica genome, suggesting that a substantial number of genes have been lost in the japonica rice lineage; however, their close relatives still possess their counterpart genes. We estimated that during evolution, O. sativa has lost at least one thousand genes that are still preserved in the genomes of the other species. In addition, our BLASTX searches against the non-redundant protein sequence database showed that disease resistance-related proteins were significantly overrepresented in the close relative-specific genomic portions. In total, 235 unmapped BESs of the three relatives matched 83 non-redundant proteins that contained a disease resistance protein domain, most of which corresponded to an NBS-LRR domain.ConclusionWe found that the O. sativa lineage appears to have recently experienced massive gene losses following divergence from its wild ancestor. Our results imply that the domestication process accelerated large-scale genomic deletions in the lineage of Asian cultivated rice and that the close relatives of cultivated rice have the potential to restore the lost traits.
Highlights
Rice is one of the most important food crops in the world
A previous report revealed that Oj and O. sativa ssp. indica (Oi) were derived independently from O. rufipogon (Or) and O. nivara (On), respectively [20], the phylogenetic tree shows that the two Asian cultivated subspecies form the sister group of the wild rice species
Our results indicate that the phylogenetic relationships among Asian rice species cannot be uniquely determined by molecular sequence data, possibly because of incomplete speciation, variable gene histories due to the sorting of ancestral polymorphisms [25], or both
Summary
Rice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. Because crop yields have suffered serious losses due to various plant diseases, disease resistance has been one of the most important challenges in ensuring stable food supplies. A further threat may be posed by global climate change [5], which may affect crop yields in various ways, such as increasing the risk of plant diseases or causing direct damage at specific developmental stages (e.g., flowering time)
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