Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

Abstract

Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress

“…Consistent with previous studies (Li et al, 2014;Zhu et al, 2015), most of the novel lncRNAs identified in the present study were located in the intergenic regions (Figure 2B), indicating that the type of novel lncRNAs were long intergenic non-coding RNAs (lincRNAs). In addition, lncRNA had short transcript length as well as low exon number (Figures 2C, D), which is in line with previous results (Chen et al, 2021a;Xu et al, 2021).…”

“…Leaf soluble sugar content and peroxidase (POD) activity of sugar beet were determined according to the reports of DuBois et al (2002) and Patra and Mishra (1979), respectively. Salicylic acid (SA) content was measured by the method of Yalpani et al (1993). Leaves of sugar beet were ground into a fine powder within liquid nitrogen, and approximately 0.50 g samples were collected for subsequent experiments.…”