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 rufipogon , which are considered as the ancestors of Asian cultivated rice ( sativa ), possess high genetic diversity serve a crucial resource for breeding novel cultivars rice. Although domestication related traits, such seed shattering plant architecture, have been intensively studied at phenotypic genomic levels, further investigation is needed to understand molecular basis differences between wild Drought stress one most severe abiotic stresses affecting growth production. Adaptation drought involves cascade genes regulatory factors that form complex networks. O. inhabits swampy areas with seasonally dry climate, an ideal material discover tolerance alleles. Long noncoding natural antisense transcripts (lncNATs), class long RNAs (lncRNAs), regulate corresponding sense play important role in development. However, contribution lncNATs response remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis Nipponbare ) two accessions (BJ89 BJ278) determine A total 1246 lncRNAs were identified, 1091 coding–noncoding NAT pairs, 50 expressed only Nipponbare, 77 BJ89 and/or BJ278. Of 240 differentially control conditions. Among these 12 detected 187 uniquely nivara. Furthermore, 10 pairs correlated enriched responsive GO terms; among these, nine found pair was shared Nipponbare. Conclusion We identified associated . These results will improve our understanding function accelerate breeding.