Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.)

Abstract

Background Long noncoding RNAs (lncRNAs) are emerging as important regulators in eukaryotes and play crucial roles in plant growth and development as well as stress response. However, current lncRNA studies were mainly performed at the individual level and those associated with spike architecture remain elusive in wheat. Results In this study, RNA-seq of 186 spike samples were used to identify the lncRNA landscape in wheat spike. A total of 35,913 lncRNAs as well as 1,619 lncRNA-mRNA pairs comprised of 443 lncRNAs and 464 mRNAs were obtained. The lncRNAs displayed rather low conservation among wheat and other gramineous species. Genetic diversity analysis based on population genomics showed that obvious genetic bottleneck effect occurred on these lncRNAs during wheat domestication. Regulatory network analysis revealed that 122 lncRNA could act as ceRNA to involve in endogenous competition. Association analysis of candidate lncRNA-mRNA pairs identified 170 lncRNAs and 167 target miRNAs significantly associated with spike-related traits, including lncRNA.127690.1/TraesCS2A02G518500.1 (PMEI) and lncRNA.104854.1/TraesCS6A02G050300.1 (ATG5) were related to heading date and spike length, respectively. Conclusions This study provided the first pan-lncRNA data of bread wheat spike, which will contribute to the future use of lncRNA for improving the spike or yield-related traits in wheat and beyond.