Transcriptome Screening of Long Noncoding RNAs and Their Target Protein-Coding Genes Unmasks a Dynamic Portrait of Seed Coat Coloration Associated with Anthocyanins in Tibetan Hulless Barley

Abstract

Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding genes (PCGs). Here, we conducted a comprehensive bioinformatics analysis to identify a total of 9414 long noncoding RNAs (lncRNAs) in the seed coats of purple and white hulless barley along a developmental gradient. Transcriptome-wide profiles of lncRNAs documented several properties, including GC content fluctuation, uneven length, a diverse range of exon numbers, and a wide variety of transcript classifications. We found that certain lncRNAs in hulless barley possess detectable sequence conservation with Hordeum vulgare and other monocots. Furthermore, both differentially expressed lncRNAs (DElncRNAs) and PCGs (DEPCGs) were concentrated in the later seed development stages. On the one hand, DElncRNAs could potentially cis-regulate DEPCGs associated with multiple metabolic pathways, including flavonoid and anthocyanin biosynthesis in the late milk and soft dough stages. On the other hand, there was an opportunity for trans-regulated lncRNAs in the color-forming module to affect seed coat color by upregulating PCGs in the anthocyanin pathway. In addition, the interweaving of hulless barley lncRNAs and diverse TFs may function in seed coat coloration. Notably, we depicted a dynamic portrait of the anthocyanin synthesis pathway containing hulless barley lncRNAs. Therefore, this work provides valuable gene resources and more insights into the molecular mechanisms underlying anthocyanin accumulation in hulless barley from the perspective of lncRNAs, which facilitate the development of molecular design breeding in crops.

Long Noncoding RNAs in Response to Hyperosmolarity Stress, but Not Salt Stress, Were Mainly Enriched in the Rice Roots

“…To comprehensively pinpoint lncRNAs involved in the processes induced by OsOSCA1.1, salt, and hyperosmolarity stress in rice, we conducted lncRNA identification based on 24 RNA-seq data sets [ 32 ]. It contained the seedling roots of ZH11 and ososca1.1 exposed to the solution (hyperosmolarity stress, salt stress, and control) and their corresponding shoots [ 17 ].…”

“…To make the transcript fit the lncRNA characteristics, we employed an established pipeline to identify lncRNAs in the rice shoots and roots ( Figure 1 a) [ 32 ]. The transcript models were mainly compared with PCG transcripts and classified.…”

“…In rice, various regulation functions of lncRNA, such as in panicle development and fertility, early endosperm development, blast disease resistance, and other aspects, have been validated [ 25 , 26 , 27 ]. The prerequisite for researching target lncRNAs is the identification and mining of lncRNAs, as has been performed in the published works about various plant groups [ 28 , 29 , 30 , 31 , 32 , 33 ]. For rice, results on root salt-responsive lncRNAs and leaf drought-related lncRNAs have been reported [ 34 , 35 ].…”

Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice

“…In fact, PPO has been suggested to be responsible for melanin production in rice (Fukuda et al ., 2012 ), sesame (Wei et al ., 2016 ), bitter gourd (Zhong et al ., 2022 ), persimmon (Qi et al ., 2020 ) and watermelon (Li et al ., 2019 ). The significance of lncRNA in diverse biological processes is crucial in plant kingdoms, which can modulate the expression of target genes through cis ‐ and trans ‐acting mechanisms; impact the structure and function of chromatin; and participate in RNA transcription, splicing and stabilization (Zheng et al ., 2023 ). Several studies have illustrated the significance of lncRNAs in plant development and colour formation process (Li et al ., 2023 ; Zheng et al ., 2023 ).…”

“…The significance of lncRNA in diverse biological processes is crucial in plant kingdoms, which can modulate the expression of target genes through cis ‐ and trans ‐acting mechanisms; impact the structure and function of chromatin; and participate in RNA transcription, splicing and stabilization (Zheng et al ., 2023 ). Several studies have illustrated the significance of lncRNAs in plant development and colour formation process (Li et al ., 2023 ; Zheng et al ., 2023 ). In this study, two Blp_lncRNAs were identified to be significantly co‐expressed with HvBlp , which may be involved in the stage‐ and tissue‐specific expression of HvBlp .…”