Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice

• Main Authors: Huang He, Yan-Fei Zhou, Yu-Wei Yang, Zhi Zhang, Meng-Qi Lei, Yan-Zhao Feng, Yu-Chan Zhang, Yue-Qin Chen, Jian-Ping Lian, Yang Yu
• Format: Article
• Language: English
• Published: MDPI AG 2021-04-01
• Series: International Journal of Molecular Sciences
• Subjects: agronomic traits; conservation; crop domestication; cultivated rice; lncRNAs; wild rice
• Online Access: https://www.mdpi.com/1422-0067/22/9/4742

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 <i>Oryza sativa</i> ssp. <i>japonica</i> and <i>O. sativa</i> ssp. <i>indica</i>, and their wild progenitor <i>O. </i><i>rufipogon</i>. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i>O. </i><i>rufipogon</i>, 2091 lncRNAs in <i>japonica</i> rice, and 2365 lncRNAs in <i>indica</i> 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.