Advances and prospects of orchid research and industrialization

Abstract

Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.

Figure 1

Knowledge mapping of orchid conservation. Visualization of keywords and their frequencies for orchid conservation by time series (2010–2022). Each node represents a keyword that first appears in the analysed data set. The published articles from 2010 to 2022 were retrieved from the Web of Science core collection.

Figure 2

Phylogenetic relationship and divergence time of 15 published orchid genomes. Maximum likelihood phylogenetic tree was constructed using single-copy orthologous sequences from 15 published orchids covering four subfamilies, with Asparagus officinalis as an outgroup. Divergence time was calculated by MCMCTree in PAML v.4.9 package. The orange star indicates the lineage-specific WGD (Orchid WGD) event for Orchidaceae. Subfamilies are listed to the right of the tree. Sequencing techniques for each study were marked in dots with different colors.

Figure 3

Genes related to key horticulture traits of orchids. Genes involved in floral scent biosynthesis include FDPS, AACT, HMGR, LIS, HMGS, and JMT in methyl jasmonate (MeJA) biosynthesis. Genes regulating chlorophyll degradation such as CLH2 and RCCR, and photosynthesis-related genes PsbP are responsible for orchid colorful leaves. Flower color is mainly determined by genes involved in carotenoid biosynthesis (CBP) and anthocyanin biosynthesis pathway (ABP), as well as TFs like R2R3 MYBs, AGL6, and B-class MADS-box. The transition from vegetative development to reproductive growth requires the mediation of multiple flowering repressors (SVP-like, TFL1-like genes) and promotors (CO-like, FT-like, SOC1-like genes).

Figure 4

The proposed ‘Orchid Code’, ‘Homeotic Orchid Tepal’ (HOT) model, ‘Perianth code’ (P code) and Cymbidium ensifolium’s MADS-box model for flower development of orchids.a Orchid code (left) and HOT model (right). In ‘orchid code’, clades 1–4 of B-class DEF/AP3-like genes specify the orchid perianth formation, upon which ‘HOT model’ proposed that PI and AP3B clades of B-class MADS-box genes determine all four whorls of flower identity. The joint contribution of PI and both AP3A1 and AP3Bs regulate the formation of lateral petals. Both PI and AP3 clade genes are involved in the formation of the lip. C- and D-class MADS-box genes specify column development. b Perianth code based on Oncidium. For ‘P code’, PI is expressed in lip, sepal and petal and interacts with different AP3-like and AGL-like proteins leading to lip or sepal/petal development. OPI combines with OAP3–2 and two OAGL6–2 to form L complex (Lip program) that determines lip development. SP complex (Sepal/Petal program) is composed of OPI, OAP3–1, and two OAGL6–1, regulating sepal and petal development. c MADS-box model of Cymbidium ensifolium. In C. ensifolium, E-class SEP-like and B-class PI and AP3-like genes are expressed in all flora whorls with C-and D- class genes expressed in column. Co, column; Ds, dorsal sepal; Ls, lateral sepal; Pe, petal; Se, sepal. Numbers 1, 2, 3/4 represent flower whorls.