In rice, TWISTEDLEAF (TL), is transcribed from the opposite strand of the R2R3 MYB transcription factor gene locus (OsMYB60). Silencing TL via RNA interference reportedly results in abnormal leaves (Liu et al., 2018) (Figure 2A). In terms of disease resistance-related lncRNAs, an RNA sequencing-based analysis of rice leaves infected with Xanthomonas oryzae pv. oryzae (Xoo) revealed the interactions between 39 jasmonate (JA)-related protein-coding genes and 73 lncRNAs. The overexpression of ALEX1 enhances the resistance to Xoo and activates JA signaling (Yu et al., 2020) (Figure 2B). Research on anther and ovary meiosis in autotetraploid rice showed lncRNA57811 overexpression significantly decreases fertility and the seed setting rate, which reflects the critical roles of lncRNAs affecting polyploid rice pollen development (Li X. et al., 2020) (Figure 2C). In addition, MSTRG.28732.3, which is a lncRNA associated with drought resistance, interacts with miR171 to modulate the chlorophyll biosynthesis pathway, thereby influencing drought resistance through Os02g0662700, Os02g0663100, and Os06g0105350 in rice (Yang et al., 2022) (Figure 2D).

In maize, lncRNAs contribute to several growth and developmental processes. For example, Pi-deficiency-induced long-noncoding RNA1 (PILNCR1), which was identified following an analysis of strand-specific RNA libraries, can inhibit ZmmiR399-guided cleavage of ZmPHO2, ultimately affecting the ability of maize to tolerate low-Pi conditions (Du et al., 2018) (Figure 2E). The CRISPR/Cas9-based editing of the lncRNA GARR2 in the GARR2KO line leads to increases in bud height, second leaf sheath length, and endogenous GA3 levels. Additionally, according to RNA pull-down assays, GARR2 can influence the abundance of its target (ZmUPL1) during the gibberellin (GA) response (Li W. et al., 2022) (Figure 2F). Furthermore, sugarcane mosaic virus (SCMV)-responsive lncRNA–miRNA–mRNA networks have been established. The lncRNA10865-miR166j-3p-HDZ25/HDZ69 and lncRNA14234-miR394a-5p-SPL11 modules played roles in maize resistance to SCMV infection. Among them, after lncRNA10865 and lncRNA14234 were silenced, SCMV symptoms were aggravated and alleviated, respectively (Gao et al., 2023) (Figure 2G).

In a previous study on the mechanism mediating the cold resistance of winter wheat, lncR9A was revealed to function as a competing endogenous RNA (ceRNA) that regulates the cooperative interaction between tae-miR398 and TaCSD1 under cold conditions (Lu et al., 2020) (Figure 2H). An investigation on wheat grain fat biosynthesis detected a lncRNA that serves as a ceRNA modulating lipid accumulation through TaPDAT. More specifically, on the basis of a GFP reporter assay, lnc663 can sequester miR1128 through complementary interactions to up-regulate TaPDAT expression in tobacco (Madhawan et al., 2023) (Figure 2I). In addition, lncRNAs may also regulate abscisic acid/GA signaling to affect seed germination. The overexpression of miR9678 delays wheat seed germination by decreasing the bioactive GA content. Interestingly, miR9678 targeted the lncRNA WSGAR (Guo et al., 2018) (Figure 2J).

In summary, lncRNAs modulate the growth, development, and biotic and abiotic stress responses of major grain crops, including rice, maize, and wheat. While these biological processes may affect grain crop yields, the molecular mechanisms underlying lncRNA functions in grain crops must be more precisely deciphered to improve grain crop production.

Soybean is one of the main oil crops. In the study of soybean salt response stress, the interaction between Gmax_MSTRG.35921.1 and miR166i was verified by LAMP assay followed by RT-PCR, which indicated the potential regulatory role of lncRNA under salinity stress (Li C. et al., 2022) (Figure 3A). In addition, overexpressing lncRNA77580 in soybean could increase the drought tolerance and seed yield by increasing the number of seeds per plant (Chen X. et al., 2023) (Figure 3B). The lncRNA43234-miRNA10420-XM_014775781.1 network related to lipid synthesis was screened out by full-length transcriptome sequencing for Wild type (WT) soybean “JN18” (Jishendou 2006) and low linolenic acid mutant “MT72”. Overexpression of lncRNA43234 resulted in increased protein content and decreased oleic acid content in Arabidopsis thaliana seeds (Ma et al., 2021; Zhang A. et al., 2023) (Figure 3C).

Brassica napus L., which is one of three types of oilseed rape, has the highest grain yield among all oilseed rape varieties. The seed oil content decreases by 3.1%–3.9% following the overexpression of MSTRG.22563, but increases by approximately 2% if MSTRG.86004 is overexpressed (Li Y. et al., 2023) (Figure 3D). However, clubroot disease causes significant Brassica yield losses. A total of 464 differentially expressed lncRNAs were identified in the roots of resistant plants challenged with Plasmodiophora brassicae, with most of the genes targeted by these lncRNAs associated with plant–pathogen interactions and hormone signaling pathways (Summanwar et al., 2021). Furthermore, the positive effects of lncRNAs on B. napus drought tolerance have been elucidated. Certain lncRNAs affecting plant hormone signaling and defense mechanisms are co-expressed with protein-coding genes (Tan et al., 2020).

In 2019, a weighted correlation network analysis established a co-expression network comprising 4,713 lncRNAs, which enabled the identification of lncRNAs associated with the growth and development of various peanut tissues (Zhao et al., 2019). Concurrently, seeds from two peanut recombinant inbred lines (RIL8) with differing seed sizes were subjected to strand-specific whole transcriptome sequencing at 15 and 35 days after flowering (DAF). An examination of differentially expressed genes and qPCR data revealed the importance of 11 lncRNAs and their cis-acting target genes for peanut seed development (Ma et al., 2020). Furthermore, 10 lncRNAs functioned as ceRNAs involved in oxidation–reduction processes and other metabolic pathways during a root-knot nematode infection of peanut (Xu et al., 2022).

The findings of previous studies indicate lncRNAs modulate the oil content and quality of oil crops (e.g., soybean and rapeseed). Clarifying the gene regulatory network governing lipid metabolism is crucial for enhancing oil crop yield and quality. A thorough examination of the key lncRNAs associated with oil metabolism will provide relevant insights into the molecular mechanisms underlying lipid metabolism in oil crops.

The main sugar crops include sugarcane (Saccharum officinarum L.) and sugar beet (Beta vulgaris). In a study exploring sugarcane tiller development, 310 conserved lncRNAs were screened on the basis of a PacBio Iso-Seq analysis of leaf and tiller bud samples (Yan et al., 2021). Previous studies had shown that miR408 is important for the interaction between sugarcane and microorganisms. A long intergenic noncoding RNA (lincRNA) with significant complementarity to miR408 was predicted to act as miRNA bait, with inhibitory effects on the regulation of canonical miR408 targets (Thiebaut et al., 2017). Other studies showed that miRNAs influence sugarcane growth and development, stress resistance, and other processes (Li A. M. et al., 2023; Gao et al., 2022). The research conducted to date on sugarcane lncRNAs has primarily relied on predictions, which will need to be experimentally verified. In particular, the regulatory effects of lncRNAs on sweetness-related genes should be characterized.

Changes in gene expression during sugar beet responses to salt stress have been elucidated via whole transcriptome RNA-seq and degradome sequencing analyses, which identified 61 differentially expressed lncRNAs in roots and 55 target genes (Li J. et al., 2020). In another study, sugar beet responses to drought stress were examined, resulting in the detection of 386 differentially expressed lncRNAs; the expression of the most significantly up-regulated lncRNA increased more than 6,000-fold, whereas the expression of the most significantly down-regulated lncRNA decreased more than 18,000-fold (Zou et al., 2023). In sugar beet, the gene (Bv8_189980_mizi.t1) targeted by the lncRNA MSTRG.26204.1 encodes a B3 domain-containing transcriptional repressor (VAL1-like), suggesting this gene may be associated with vernalization. Hence, lncRNAs may be involved in the sugar beet vernalization process (Liang et al., 2022).

Although there is evidence indicating lncRNAs affect the drought resistance as well as the growth and development of sugar crops, their contribution to sugar biosynthesis and the underlying molecular mechanism remain unclear. Exploring the effects of lncRNAs on plant sugar biosynthesis pathways may provide insights relevant to regulating key sugar crop traits.

Cocoa, coffee, and tea are the main beverage crops worldwide. To date, there has been limited research on cocoa lncRNAs, but coffee and tea lncRNAs have been identified and functionally characterized. In Coffea canephora, 2,384 high-confidence lncRNAs were identified on the basis of a comprehensive genome-wide analysis (Lemos et al., 2020). A total of 10,564 lncRNAs were identified in another coffee species (Coffea arabica L.). Their involvement in important biological processes was predicted by a Gene Ontology (GO) analysis (Abdel-Salam et al., 2021). In tea (Camellia sinensis), lncRNAs are involved in disease resistance-related mechanisms. Additionally, in C. sinensis ‘Baiye No. 1’, differentially expressed lncRNAs participate in responses to periodic albinism through the GAMYB–miR159–lncRNA regulatory network (Xu et al., 2023). A recent study indicated MSTRG.20036, MSTRG.3843, MSTRG.26132, and MSTRG.56701 influence the development of tea leaf spot disease through cis-regulatory mechanisms (Huang et al., 2023). Another lncRNA (MSTRG.139242.1) may modulate the response to salt stress through Ca²⁺ ATPase 13 in the Ca²⁺ transport pathway (Wan et al., 2020). In response to daylight-induced withering, lncRNAs alter flavonoid and terpenoid metabolic pathways as well as JA/methyl jasmonate biosynthesis and signal transduction in oolong tea (C. sinensis) (Zhu et al., 2019). Thus, lncRNAs help regulate disease resistance mechanisms and salt stress responses in beverage crops. They also regulate the production of biologically active substances that influence the flavor profile and other characteristics of beverage crops.

Cotton seeds produce fiber. Some studies have shown that lncRNAs are involved in the disease resistance of cotton. For example, lncRNA2 and its target gene PG12 negatively regulate cotton resistance to verticillium wilt, while lncRNA7 and its target gene PMEI13 have the opposite effect (Zhang L. et al., 2022) (Figure 4A). Interestingly, lncRNAs are also involved in cotton responses to abiotic stress. More specifically, DAN1, which is a lincRNA associated with drought responses, can regulate AAAG motif-containing genes in the auxin response pathway (Tao et al., 2021) (Figure 4B). Another lincRNA, XH123, was revealed to control the cold stress response of cotton seedlings (Cao et al., 2021) (Figure 4C). The salt-responsive lncRNAs TRABA and lncRNA354 serve as upstream regulators that control the expression of the salt stress response-related genes GhBGLU24 and GhARF, respectively (Zhang X. et al., 2021; Cui et al., 2024) (Figure 4D). In cotton, MSTRG 2723.1 mediates the expression of key genes related to fatty acid metabolism, the MYB25-mediated pathway, and pectin metabolism to regulate fiber synthesis (Zou et al., 2022). In addition to cotton, hemp is another major fiber crop. In ramie (Boehmeria nivea L. Gaud), a MYB gene (BntWG10016451) is targeted by lncRNA00022274. The overexpression of this gene reportedly increases fiber production in A. thaliana (Fu et al., 2023). Considered together, the findings of earlier studies suggest lncRNAs play crucial roles in fiber crop responses to biotic and abiotic stresses, while also influencing fiber formation. These investigations have increased our understanding of how lncRNAs regulate plant fiber development.

Tomato (Solanum lycopersicum L.) is one of the most important vegetable crops. The silencing of lncRNA1459 reportedly decreases ethylene accumulation and carotenoid biosynthesis in tomato, with detrimental effects on fruit ripening (Li et al., 2018) (Figure 5A). During carotenoid biosynthesis, octahydro-lycopene synthase (PSY) catalyzes the formation of two GGPP molecules. Additionally, trans-splicing between SlPsy1 and the lncRNA ACoS-AS1 leads to the formation of yellow tomato fruit (Xiao et al., 2020) (Figure 5B). Overexpressing Solyc10g006360 decreases the formation of type I trichomes. An earlier study showed lncRNA000170, which is transcribed from the complementary strand of Solyc10g006360, may affect multicellular trichome formation by inducing target gene expression (Liao et al., 2020) (Figure 5C). In the study of tomato against Phytophthora infestans, overexpression of Sl-lncRNA47980 up-regulated the expression of SlGA2ox4, while overexpression of lncRNA39026 down-regulated the expression of miR168a and increases the expression of SlAGO1. In tomato, the overexpression of lncRNA23468 and lncRNA08489 significantly decreases the expression of miR482b and miR482e-3p, respectively, but the expression of target genes encoding NBS-LRR proteins increases significantly. These lncRNAs positively regulate the resistance of tomato plants to P. infestans. Conversely, Sl-lncRNA39896 negatively regulates tomato resistance to P. infestans; this lncRNA functions as an endogenous target mimic of Sl-miR166b that controls HDZ expression (Jiang et al., 2019; Hou et al., 2020; Su et al., 2023; Liu et al., 2022; Hong et al., 2022) (Figure 5D).