Orchids are horticultural plants with significant ornamental and economic value. Increasing market circulation and rising trade in orchids is forcing breeders to develop varieties with unique characteristics, including flower color, morphology, and resistance using a range of approaches, including traditional and molecular breeding. Advances in high-throughput technologies have generated extensive data sets with greater sequencing depths and broader coverage, providing the potential for discovering new genes/pathways that give rise to key traits. Several attempts have been made to use emerging molecular and omics methods to accelerate the breeding process in certain of the commercially valuable orchids. This review consolidates current approaches and achievements in orchid breeding and discusses their future applications for improving the resistance, ornamental, and other valuable characteristics of these plants.

As an important horticultural plant, the orchid is widely distributed in its natural habitat and faces various environmental stresses, among which nutrient recycling and stress resistance are of great concern. During these processes, autophagy is an essential pathway, which is a conserved self-eating process that degrades macromolecular components and recycles cell materials or nutrients during developmental processes or under stress conditions. Two ubiquitin-like systems (UBLs) play a major role in the initiation of autophagy and are associated with two key proteins: ATG8 and ATG12. In this study, we identified and refined the UBL-related genes in orchids and performed phylogenetic reconstruction together with other plant species. We found that the orchid had unique domains in UBL-related genes, indicating potential functional diversification in the ATG8 system in plants. Transcriptome and protein tertiary structure prediction indicated that conserved domains that are vital for the canonical function of ATG12 are incomplete in orchids, in which a novel mechanism of autophagy may have evolved.

Orchid origin and evolution are common topics in evolutionary biology. Orchidaceae have approximately 30000 orchid species distributed in diverse habitats and account for approximately 10% of the flowering plant species worldwide. Orchids provide us with materials to explore coevolution and organic evolution. In this review, we highlighted the genome study progress of orchids. In addition, we revealed the role of MADS-box gene families in the floral morphology and evolution of orchids. Genomics studies confirmed that all five subfamilies of existing orchids evolved from a common ancestor. Loss of Mβ MADS-box genes resulted in the endosperm from the seed of all existing orchids being absent. Perianth reversion to the ancestral state occurred because Apostasia and Apostasioideae lost B-AP3 and E class paralogous genes. Loss of P-subclade members of MIKC*-Type in Phalaenopsis equestris, Dendrobium catenatum, and Epidendroideae caused the formation of pollinium. In addition, the combined loss of AGL12 and contraction of ANR1 gave orchids the ability to be successfully epiphytic on trees or rocks and to develop a unique root system. Both pollinium and epiphytic production on trees are beneficial for orchid adaptations, and Epidendroideae evolved more species (~ 20000) than Apostasioideae (16 species). Genome studies shed new light on determining the evolutionary history of orchids and understanding the genetic mechanisms of orchid morphological evolution.