Update on functional analysis of long non-coding RNAs in common crops

Abstract

With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.

Keywords: biological function; crops; lncRNAs; molecular mechanism; plant development.

Figure 1

Progress in the research on lncRNAs in common crop species. This review comprehensively summarizes the functions of lncRNAs in major food crops (wheat, corn, and rice), oil crops (soybean, peanut, and rapeseed), sugar crops (sugarcane and beet), fiber crops (cotton and hemp), beverage crops (tea and coffee), and vegetables (tomato).

Figure 2

Investigating the function of lncRNAs in gain crops such as maize, rice, and wheat. (A) lncRNA involved in the regulation of leaf development; (B) lncRNA involved in the regulation of rice resistance to Xanthomonas oryzae pv. Oryzae; (C) lncRNA involved in the regulation of drought stress; (D) lncRNA involved in the regulation of seed germination; (E) Involved in the regulation of tolerance to low Pi; (F) lncRNA involved in the regulation of phytohormone gibberellin; (G) lncRNA involved in the regulation of SCMV resistance; (H) lncRNA involved in the regulation of cold resistance; (I) lncRNA involved in the regulation of lipid accumulation; (J) lncRNA involved in the regulation of seed germination.

Figure 3

Investigating the function of lncRNAs in oil crops such as soybean and rapeseed. (A) lncRNA involved in salt stress regulation; (B) lncRNA involved in salt and drought stress regulation; (C) lncRNA involved in lipid synthesis regulation; (D) lncRNA involved in seed oil accumulation.

Figure 4

Investigating the function of lncRNAs in fiber crops such as cotton. (A) lncRNA involved in the regulation of Verticillium wilt; (B) lncRNA involved in the regulation of drought stress; (C) lncRNA involved in the regulation of cold-stress; (D) lncRNA involved in the regulation of salt-stress.

Figure 5

Investigating the function of lncRNAs in vegetable such as tomato. (A) lncRNA involved in the regulation of fruit ripening; (B) lncRNA involved in the regulation of carotenoids biosynthesis; (C) lncRNA involved in the regulation of trichome formation; (D) lncRNA involved in the regulation of tomato resistance to Phytophthora infestans.

Figure 6

Flow chart of the research strategy for identifying lncRNAs in crops.