**7.1. lncRNA in plant fertility**

The participation of lncRNAs in producing the male sterile lines in *O. sativa* is an important example of plant fertility. These male sterile lines are necessary for the hybridization and


point mutation of C to G in osa-sm R5864w, resulting in the loss of function, leads to the pro-

Role of Next-Generation RNA-Seq Data in Discovery and Characterization of Long Non-Coding…

http://dx.doi.org/10.5772/intechopen.72773

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Plant lncRNAs are known to increase the complexity of transcriptome and proteome by participating in alternative splicing. It was first reported in Arabidopsis, where lncRNA behaved as an alternative splicing competitor (ASCO) [67]. Together with the nuclear speckle RNAbinding protein (NSR), ASCO-lncRNA forms an alternative splicing regulatory module. The expression of AtNSR in primary and lateral root meristems regulates the development of lateral roots. The interaction of AtNSR with overexpressing ASCO-lncRNA affects the splicing pattern of mRNA targeted by NSR in transgenic plant [67, 87]. This indicates the role of

Most of the plant growth and developmental processes are regulated by different climatic factors among them light is one of the most important factor [88]. The role of lncRNA in the regulation of photomorphogenesis is still an interesting area of research because most of the identified regulatory molecules are proteins. In *A. thaliana*, several light responsive lncRNAs have been identified associated with histone modifications [89]. Identification and functional characterization of *HIDDEN TREASURE 1* (*HID1*), a novel lncRNA, involved in photomorphogenesis have been accomplished [89]. It may control the process of photomor phogenesis by regulating the expression of PHYTOCHROME INTERACTING FACTOR 3 (PIF3), a transcription factor involved in light response [89]. It could negatively regulate the expression of *PIF3* gene by binding to its promoter directly or in association with chromatin [89]. The occurrence of *HID1* homologs has been described in other plant species exhibiting conserved functions. The findings also shed light on the involvement of other ncRNAs in

The selection of lncRNAs from the complete set of RNAs is broadly based on three criteria: (i) transcript length of ≥200 bp, (ii) small open reading frame with ≤300 bp, and (iii) transcripts without homology to known proteins. In addition to this, several other factors like the type of cDNA libraries or transcriptional sequence data, depth of sequencing, and coding potential of transcripts, also contribute in the screening of lncRNAs. The challenges during computational analysis come when some protein-coding gene which fulfill the basic selection criteria and encode a functional peptide. Besides this, the functional long non-coding transcript may have ORF >300 bp and share homology with known protein-coding genes will also produce hindrance in the identification [90]. Another challenge comes with the transcripts that not only function as an RNA molecule, but also encodes a peptide [91]. The advancement in computational approaches have been made to overcome these limitations and for more accurate

duction of light and temperature sensitive male sterile lines of rice [82].

**8. Limitations in computational analysis of lncRNAs**

**7.2. Role in alternate splicing**

light responses.

lncRNA as a regulator of alternative splicing.

**7.3. Plant lncRNAs in photomorphogenesis**

**Table 2.** List of some annotated lncRNAs.

breeding processes. lncRNAs are known to induce photoperiod-sensitive genetic male sterility (PSMF) in *O. sativa* [82, 86], but the mechanism is not completely well understood. But according to the available reports, two different mechanisms of lncRNA can be possible [23]. In one mechanism, the high expression of the *long day* (*LD*)*-specific male-fertility-associated RNA* (*LDMAR*), a type of lncRNA, is important for the fertility of rice plant during long day (LD) conditions. During male sterility, the programme cell death (PCD) of anther cells occur due to lowered expression of *LDMAR* under LD conditions. The reduced expression of *LDMAR* is mediated by over expressing psi-LDMAR (a siRNA), transcribed in the promoter region of *LDMAR*. Enhanced expression of Psi-LDMAR caused methylation in promoter region through RdDM mechanism [81]. The other mechanism suggested the involvement of osa-sm R5864w (a 21-nt sRNA) which was formed from a unique ncRNA encoded by *LDMAR*. The point mutation of C to G in osa-sm R5864w, resulting in the loss of function, leads to the production of light and temperature sensitive male sterile lines of rice [82].
