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Long non-coding RNA (lncRNA) is a kind of RNA widely present in plant genome, which plays a crucial role in various regulatory processes in plants. LncRNA refers to RNA with a nucleotide length greater than 200 nt and has no or almost no protein coding ability. Most plant lncRNAs are transcribed by RNA polymerase Ⅱ and are mainly produced from gene structural variation, gene replication, chromosome recombination, or transposon insertion. There are many types of lncRNA in plants, which can be divided based on their relative positions and forms of functions. The structure of lncRNA is similar to mRNA, which has the cap and poly (A) structure and foldability, but its transcript is longer than mRNA, and has low transcriptional abundance, extremely high expression specificity, and low conservation. The functional mechanisms of lncRNA in horticultural plants are complex, which can play roles in pre-/post- transcription, pre-/post- translation, and epigenetics. It mainly plays a role through cis-/trans-regulating gene transcription, acting as a precursor or endogenous target mimic of miRNA, interacting with transcription factors, modulating mRNA alternative splicing, modulating protein localization, and participating in chromatin remodeling. Horticultural plants are closely related to human life, and its study is an important part of agricultural development. With the continuous development of sequencing technology, research on plant lncRNA has also expanded from model plants such as Arabidopsis to horticultural plants. Different types and quantities of lncRNAs have been identified in horticultural plants and found to be involved in seed germination, reproductive growth, as well as in response to biotic stresses such as diseases and pests, and abiotic stresses such as high temperature, cold, drought, and salt. In this paper, the research progress of lncRNA in horticultural plants in recent years was reviewed, and the generation, characteristics, classification and mechanism of lncRNA were summarized, as well as the identified lncRNAs and their main biological functions in horticultural plants. It also puts forward prospects for future research directions of lncRNA, in order to provide reference and foundation for further research on lncRNA in horticultural plants. [ABSTRACT FROM AUTHOR]

The development of the horticultural industry is largely limited by disease and excessive pesticide application. MicroRNAs constitute a major portion of the transcriptomes of eukaryotes. Various microRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycle of plants. Recently, small RNA sequencing has been applied to study gene regulation in horticultural plants. In this review, we summarize the current understanding of the biogenesis and contributions of microRNAs in horticultural plant disease resistance. These microRNAs may potentially be used as genetic resources for improving disease resistance and for molecular breeding. The challenges in understanding horticultural plant microRNA biology and the possibilities to make better use of these horticultural plant gene resources in the future are discussed in this review. [ABSTRACT FROM AUTHOR]

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is extensively applied technique to investigate the transcript abundance of target genes in various organisms. Selection of appropriate reference genes (RGs) for qRT-PCR normalization is a crucial prerequisite for accurately quantifying gene expression level. RGs should exhibit minimal variation in gene expression. However, the actual expression stability of RGs fluctuates greatly in different species or under different experimental conditions. Due to rapid advancements in next-generation sequencing (NGS) technology, it is no longer difficult to get massive transcriptome data, which has greatly promoted the development of RGs. In this review, we elaborate on the strategies for developing RGs using Northern blotting, expressed sequence tags (ESTs), qRT-PCR, and high-throughput technologies such as microarray and RNAsequencing (RNA-Seq). The process for developing RGs based on RNA-Seq is further addressed, including processing and normalization of RNA-Seq data, evaluation of gene expression stability, and screening and validation of RGs. The most frequently used RGs in horticultural plants are summarized, and the strategies for developing these RGs are introduced in detail. The information provided here will help to design effective strategies for the development of RGs in horticultural plants, with a focus on using big data generated by RNA-Seq. [ABSTRACT FROM AUTHOR]