Abstract
BackgroundIt is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level.ResultsInstead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627.ConclusionsThese results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0788-2) contains supplementary material, which is available to authorized users.
Highlights
It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.)
It was revealed that O. sativa L. ssp. japonica had been first domesticated from a specific population of O. rufipogon around the middle area of the Pearl river in southern China, and that O. sativa L. ssp. indica had been subsequently developed from crosses between japonica and local wild rice as the initial cultivars spread into Southeast and South Asia [6]
To overcome the limit of the structural variation (SV) detection, the Dongxiang wild rice (DXWR) transcriptome was sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication
Summary
It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. It is well accepted that cultivated rice was domesticated from common wild rice Japonica had been first domesticated from a specific population of O. rufipogon around the middle area of the Pearl river in southern China, and that O. sativa L. ssp. Zhang et al BMC Plant Biology (2016) 16:103 genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. During the past three decades, DXWR has been well investigated as a precious genetic resource for cultivated rice improvement or fundamental research on genetic diversity [8, 9], heterosis [10], cytoplasmic male sterility [11], fertility restoration [12], biomass [13], high yield [14,15,16], and resistance to biotic and abiotic stress [17,18,19,20,21]
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