Abstract
Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice Oryza sativa ssp. japonica and O. sativa ssp. indica, and their wild progenitor O. rufipogon. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in O. rufipogon, 2091 lncRNAs in japonica rice, and 2365 lncRNAs in indica rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
Highlights
The Oryza genus is an ideal model for studying mechanistic insights into crop domestication
A number of long noncoding RNAs (lncRNAs) expressed in wild rice were revealed to be shorter in length and have fewer exon numbers when compared with lncRNAs from cultivated rice
To show vivid changes of the agronomic traits during rice domestication, we investigated the panicle architectures, seed-setting rate, and grain shape of three Oryza species: O. rufipogon collected from Hainan province, O. sativa ssp. japonica Nipponbare, and O. sativa ssp. indica 93-11
Summary
The Oryza genus is an ideal model for studying mechanistic insights into crop domestication. The Asian cultivated rice Oryza sativa is one of the most important staple crops worldwide and was domesticated from its wild progenitor Oryza rufipogon ~10,000 years ago [1]. As cultivating high-yield rice varieties is the core objective in ancient breeding, a number of morphological and physiological changes appeared during the domestication process, especially the yield-related traits including panicle complexity and grain size [1,2,3,4]. A similar divergence of domestication-related traits was observed between the African rice O. glaberrima and its wild ancestor O barthii [8]. Previous studies have reported that the two Asian rice varieties, O. sativa ssp. Pan-genome analysis of the whole set of coding genes among 66 rice accessions revealed extensive genomic variation in cultivated and wild rice
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