Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]

Abstract

Background Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail millet is nearly blank. Results In this study, we performed high-throughput sequencing of young spikelets from four foxtail millet varieties in different yield levels at booting stage. As a result, a total of 12,378 novel lncRNAs were identified, and 70 were commonly significantly differentially expressed in comparisons between high-yield varieties and conventional varieties, suggesting that they involved in yield formation and regulation in foxtail millet. Functional analysis revealed that among the 70 significantly differentially expressed lncRNAs, 67 could transcriptionally modulate target genes in cis and in trans. Moreover, 18 lncRNAs related to grain yield in foxtail millet were predicted to function as miRNA target mimics and regulate gene expression by competing for the interaction between miRNAs and their target mRNAs. Conclusion Our results will provide materials for elucidation of the molecular mechanisms of lncRNAs participate in yield regulation, and will contribute to high yield foxtail millet breeding.

Molecular genetics and phenotypic assessment of foxtail millet (Setaria italica (L.) P. Beauv.) landraces revealed remarkable variability of morpho-physiological, yield, and yield‐related traits

“…Its production and research have been neglected, perhaps partly due to its poor yield ( Sagar et al, 2020 ). Therefore, improving millet yield and resilience to stress is an urgent issue ( Zhao et al, 2020 ). Foxtail millet productivity and production in the semi-arid region of Rayalaseema, India, faces immense challenges of drought and heat stress.…”

Long Non-Coding RNAs: Discoveries, Mechanisms, and Research Strategies in Seeds

“…Although the phenotype and expression of genes controlling grain size and weight are altered in RNA interference plants, the accurate regulation mechanisms remain to be further studied. One reasonable speculation derived from studies of Setaria italica and chickpea is that lncRNAs related to grain yield act as miRNA target mimics and regulate expression of targets by competing for the interaction between miRNAs and their target mRNAs [36,37] (Figure 1). In fact, a few years ago, researchers demonstrated that the role of a rice lncRNA acts as an endogenous miRNA target mimic (eTM), in which osa-eTM160 attenuated the repression of osa-miR160 on osa-ARF18 mRNAs during early anther developmental stages, thereby affecting rice seed set and seed size [38].…”

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

“…Further, it has been shown that the unsaturated fatty acids are responsible for forming volatiles, thus leading to an unpleasant aroma during germination in foxtail millet ( Li et al, 2021b ). A recent study identified 18 long non-coding RNAs (lncRNAs) in relation to grain yield and predicted them to function as miRNA target mimics ( Zhao et al, 2020 ). The nutritional quality of foxtail millet was analyzed in response to elevated CO 2 levels and found that e CO 2 significantly enhanced the accumulation of K, Mn, Zn, and starch and promoted P accumulation.…”