Organ Identity Research Articles

Functional retrogression of LOFSEPs in specifying floral organs in barley

AbstractThe barley genome encodes a complete set of MADS-box proteins sharing homology with components of the ABCDE model, which explains the molecular basis of floral organ identity in angiosperm flowers. Although the E-class members are universally expressed across floral whorls and crucial for flower development in Arabidopsis and rice, the functional role of the barley E-class LOFSEP subfamily (comprising MADS1, MADS5, and MADS34) remains elusive, particularly during spikelet formation. Here, we characterize the single, double and triple lofsep mutants in barley in an attempt to overcome the anticipated genetic redundancy. Surprisingly, loss of function of all LOFSEP members only disturbs lemma development, either converting this hull organ into a leaf-like structure or reducing its size. The inner organs, including lodicules, anthers and pistil remain unaffected. A systematic interrogation of how ABCDE class genes are affected in all whorls of the mutants was undertaken. Generally, in the lemma and palea of the lofsep mutants, A- and E-class genes are hyperactivated, B- and C- classes are slightly repressed, and D-class genes show unchanged expression in these inner organs. Intriguingly, loss of function of MADS6, an AGL6 member closely related to the E-class genes, leads to most organs being transformed into lemma-like organs with new spikelets generated from the center of the flower. Contrasting with rice, these findings suggest barley LOFSEPs may have regressed in determining floral organ identity, and this could be partially compensated by HvMADS6.

Deciphering the evolutionary development of the "Chinese lantern" within Solanaceae.

The key genetic variation underlying the evo-devo of ICS in Solanaceae may be further pinpointed using an integrated strategy of forward and reverse genetics studies under the framework of phylogeny. The calyx of Physalis remains persistent throughout fruit development. Post-flowering, the fruiting calyx is inflated rapidly to encapsulate the berry, giving rise to a "Chinese lantern" structure called inflated calyx syndrome (ICS). It is unclear how this novelty arises. Over the past 2decades, the role of MADS-box genes in the evolutionary development (evo-devo) of ICS has mainly been investigated within Solanaceae. In this review, we analyze the main achievements, challenges, and new progress. ICS acts as a source for fruit development, provides a microenvironment to protect fruit development, and assists in long-distance fruit dispersal. ICS is a typical post-floral trait, and the onset of its development is triggered by specific developmental signals that coincide with fertilization. These signals can be replaced by exogenous gibberellin and cytokinin application. MPF2-like heterotopic expression and MBP21-like loss have been proposed to be two essential evolutionary events for ICS origin, and manipulating the related MADS-box genes has been shown to affect the ICS size, sepal organ identity, and/or male fertility, but not completely disrupt ICS. Therefore, the core genes or key links in the ICS biosynthesis pathways may have undergone secondary mutations during evolution, or they have not yet been pinpointed. Recently, we have made some encouraging progress in acquiring lantern mutants in Physalis floridana. In addition to technological innovation, we propose an integrated strategy to further analyze the evo-devo mechanisms of ICS in Solanaceae using forward and reverse genetics studies under the framework of phylogeny.

The mammary hair of Monodelphis domestica and homology of the mammary pilosebacous unit.

The unitary mammary gland is a synapomorphy of therian mammals and is thought to have evolved from the pilosebaceous organ in the mammalian stem lineage from which the lactogenic patch of monotremes is also derived. One of the key lines of evidence for the homology of the nipple and the lactogenic patch is that marsupials have retained a transient hair associated with developing mammary glands. However, these structures have not been documented since the early 20th-century drawings of Ernst Bresslau. In this study, we examine the developing mammary organs of Monodelphis domestica and document the presence of mammary hairs in 12-week-old females, as well as their absence after 18 weeks of age. Histochemical staining for cystine confirms the structures as keratinized hairs. Milk ducts of both juvenile and adult nipples show a division between KRT18+ luminal epithelium and KRT14+ ACTA2+ myoepithelium. These patterns match those in eutherians and suggest a conserved ductal morphology and mechanism of milk expulsion. Finally, PTHLH, a peptide hormone which promotes homeotic transformation of hairy skin into hairless nipples in the mouse, was detected in the Monodelphis milk duct during the mammary hair stage, suggesting that the mutual exclusivity of "hairless nipple" and "hair" organ identity is derived in eutherian mammals. These results reveal shared characteristics of the M. domestica nipple with both the eutherian nipple and the pilosebaceous organ, consistent with the evolutionary derivation of the mammary gland from an ancestral hair organ via developmental individualization of pilosebaceous and mammary identities.

Delphinium as a model for development and evolution of complex zygomorphic flowers.

The complex zygomorphic flowers of the early-diverging eudicot Delphinium provide an opportunity to explore intriguing evolutionary, developmental, and genetic questions. The dorsal perianth organs, consisting of a spurred sepal and the nectar-bearing spurred petal(s) in Delphinium, contribute to the dorso-ventralization and zygomorphic flower morphology. The seamless integration of the two or three dorsal petaloid spurred organs is considered a synorganization, and the resulting organ complex is referred to as a hyperorgan. The hyperorgan shows variability within the tribe due to variation in the number, size, and shape of the spurs. Research in recent decades within this tribe has enhanced our understanding of morphological evolution of flowers. More recently, functional studies using the RNAi approach of Virus-Induced Gene Silencing (VIGS) have unraveled interesting results highlighting the role of gene duplication in the functional diversification of organ identity and symmetry genes. Research in this early-diverging eudicot genus bridges the gaps in understanding the morphological innovations that are mostly studied in model grass and core eudicot clades. This first comprehensive review synthesizes eco-evo-devo research on Delphinium, developing a holistic understanding of recent advancements and establishing the genus as an exceptional model for addressing fundamental questions in developmental genetics, particularly in the evolution of complex flowers. This progress highlights Delphinium's significant potential for future studies in this field.

Single nucleotide polymorphisms in SEPALLATA 2 underlie fruit length variation in cucurbits.

Complete disruption of critical genes is generally accompanied by severe growth and developmental defects, which dramatically hinder its utilization in crop breeding. Identifying subtle changes, such as single-nucleotide polymorphisms (SNPs), in critical genes that specifically modulate a favorable trait is a prerequisite to fulfill breeding potential. Here, we found 2 SNPs in the E-class floral organ identity gene cucumber (Cucumis sativus) SEPALLATA2 (CsSEP2) that specifically regulate fruit length. Haplotype (HAP) 1 (8G2667A) and HAP2 (8G2667T) exist in natural populations, whereas HAP3 (8A2667T) is induced by ethyl methanesulfonate mutagenesis. Phenotypic characterization of 4 near-isogenic lines and a mutant line showed that HAP2 fruits are significantly longer than those of HAP1, and those of HAP3 are 37.8% longer than HAP2 fruit. The increasing fruit length in HAP1-3 was caused by a decreasing inhibitory effect on CRABS CLAW (CsCRC) transcription (a reported positive regulator of fruit length), resulting in enhanced cell expansion. Moreover, a 7638G/A-SNP in melon (Cucumis melo) CmSEP2 modulates fruit length in a natural melon population via the conserved SEP2-CRC module. Our findings provide a strategy for utilizing essential regulators with pleiotropic effects during crop breeding.

Genome-wide analysis of MADS-box genes and their expression patterns in unisexual flower development in dioecious spinach

Evolution of unisexual flowers involves extreme changes in floral development. Spinach is one of the species to discern the formation and evolution of dioecy. MADS-box gene family is involved in regulation of floral organ identity and development and in many other plant developmental processes. However, there is no systematic analysis of MADS-box family genes in spinach. A comprehensive genome-wide analysis and transcriptome profiling of MADS-box genes were undertaken to understand their involvement in unisexual flower development at different stages in spinach. In total, 54 MADS-box genes found to be unevenly located across 6 chromosomes and can be divided into type I and type II genes. Twenty type I MADS-box genes are subdivided into Mα, Mβ and Mγ subgroups. While thirty-four type II SoMADSs consist of 3 MIKC*, and 31 MIKCC -type genes including sixteen floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in spinach. Gene structure, motif distribution, physiochemical properties, gene duplication and collinearity analyses for these genes are performed in detail. Promoters of both types of SoMADS genes contain mainly MeJA and ABA response elements. Expression profiling indicated that MIKCc genes exhibited more dynamic and intricate expression patterns compared to M-type genes and the majority of type-II genes AP1, SVP, and SOC1 sub-groups showed female flower-biased expression profiles, suggesting their role in carpel development, while PI showed male-biased expression throughout flower developmental stages, suggesting their role in stamen development. These results provide genomic resources and insights into spinach dioecious flower development and expedite spinach improvement.

Transcriptomic Analysis of Alfalfa Flowering and the Dual Roles of MsAP1 in Floral Organ Identity and Flowering Time

Transcriptomic Analysis of Alfalfa Flowering and the Dual Roles of MsAP1 in Floral Organ Identity and Flowering Time

Genome-wide identification and expression pattern analysis of MIKC-Type MADS-box genes in Chionanthus retusus, an androdioecy plant

BackgroundThe MADS-box gene family is widely distributed in the plant kingdom, and its members typically encoding transcription factors to regulate various aspects of plant growth and development. In particular, the MIKC-type MADS-box genes play a crucial role in the determination of floral organ development and identity recognition. As a type of androdioecy plant, Chionanthus retusus have unique gender differentiation. Manifested as male individuals with only male flowers and female individuals with only bisexual flowers. However, due to the lack of reference genome information, the characteristics of MIKC-type MADS-box genes in C. retusus and its role in gender differentiation of C. retusus remain largely unknown. Therefore, it is necessary to identify and characterize the MADS-box gene family within the genome of the C. retusus.ResultsIn this study, we performed a genome-wide identification and analysis of MIKC-type MADS-box genes in C. retusus (2n = 2x = 46), utilizing the latest reference genome, and studied its expression pattern in individuals of different genders. As a result, we identified a total of 61 MIKC-type MADS-box genes in C. retusus. 61 MIKC-type MADS-box genes can be divided into 12 subfamilies and distributed on 18 chromosomes. Genome collinearity analysis revealed their conservation in evolution, while gene structure, domains and motif analysis indicated their conservation in structure. Finally, based on their expression patterns in floral organs of different sexes, we have identified that CrMADS45 and CrMADS60 may potentially be involved in the gender differentiation of C. retusus.ConclusionsOur studies have provided a general understanding of the conservation and characteristics of the MIKC-type MADS-box genes family in C. retusus. And it has been demonstrated that members of the AG subfamily, CrMADS45 and CrMADS60, may play important roles in the gender differentiation of C. retusus. This provides a reference for future breeding efforts to improve flower types in C. retusus and further investigate the role of MIKC-type MADS-box genes in gender differentiation.

BdRCN4, a Brachypodium distachyon TFL1 homologue, is involved in regulation of apical meristem fate.

In higher plants, the shift from vegetative to reproductive development is governed by complex interplay of internal and external signals. TERMINALFLOWER1 (TFL1) plays a crucial role in the regulation of flowering time and inflorescence architecture in Arabidopsis thaliana. This study aimed to explore the function of BdRCN4, a homolog of TFL1 in Brachypodium distachyon, through functional analyses in mutant and transgenic plants. The results revealed that overexpression of BdRCN4 in B. distachyon leads to an extended vegetative phase and reduced production of spikelets. Similar results were found in A. thaliana, where constitutive expression of BdRCN4 promoted a delay in flowering time, followed by the development of hypervegetative shoots, with no flowers or siliques produced. Our results suggest that BdRCN4 acts as a flowering repressor analogous to TFL1, negatively regulating AP1, but no LFY expression. To further validate this hypothesis, a 35S::LFY-GR co-transformation approach on 35::BdRCN4 lines was performed. Remarkably, AP1 expression levels and flower formation were restored to normal in co-transformed plants when treated with dexamethasone. Although further molecular studies will be necessary, the evidence in B. distachyon support the idea that a balance between LFY and BdRCN4/TFL1 seems to be essential for activating AP1 expression and initiating floral organ identity gene expression. This study also demonstrates interesting conservation through the molecular pathways that regulate flowering meristem transition and identity across the evolution of monocot and dicot plants.

GmDFB1, an ARM-repeat superfamily protein, regulates floral organ identity through repressing siRNA- and miRNA-mediated gene silencing in soybean.

The development of flowers in soybean (Glycine max) is essential for determining the yield potential of the plant. Gene silencing pathways are involved in modulating flower development, but their full elucidation is still incomplete. Here, we conducted a forward genetic screen and identified an abnormal flower mutant, deformed floral bud1-1 (Gmdfb1-1), in soybean. We mapped and identified the causal gene, which encodes a member of the armadillo (ARM)-repeat superfamily. Using small RNA sequencing (sRNA-seq), we found an abnormal accumulation of small interfering RNAs (siRNAs) and microRNA (miRNAs) in the Gmdfb1 mutants. We further demonstrated that GmDFB1 interacts with the RNA exosome cofactor SUPER KILLER7 (GmSKI7). Additionally, GmDFB1 interacts with the PIWI domain of ARGONAUTE 1 (GmAGO1) to inhibit the cleavage efficiency on the target genes of sRNAs. The enhanced gene silencing mediated by siRNA and miRNA in the Gmdfb1 mutants leads to the downregulation of their target genes associated with flower development. This study revealed the crucial role of GmDFB1 in regulating floral organ identity in soybean probably by participating in two distinct gene silencing pathways.

'Organ'ising Floral Organ Development.

Flowers are plant structures characteristic of the phylum Angiosperms composed of organs thought to have emerged from homologous structures to leaves in order to specialize in a distinctive function: reproduction. Symmetric shapes, colours, and scents all play important functional roles in flower biology. The evolution of flower symmetry and the morphology of individual flower parts (sepals, petals, stamens, and carpels) has significantly contributed to the diversity of reproductive strategies across flowering plant species. This diversity facilitates attractiveness for pollination, protection of gametes, efficient fertilization, and seed production. Symmetry, the establishment of body axes, and fate determination are tightly linked. The complex genetic networks underlying the establishment of organ, tissue, and cellular identity, as well as the growth regulators acting across the body axes, are steadily being elucidated in the field. In this review, we summarise the wealth of research already at our fingertips to begin weaving together how separate processes involved in specifying organ identity within the flower may interact, providing a functional perspective on how identity determination and axial regulation may be coordinated to inform symmetrical floral organ structures.

B-class floral homeotic gene MapoAPETALA3 may play an important role in the origin and formation of multi-tepals in Magnolia polytepala

In angiosperms, floral architecture diversity reflects its significance in exploring plant evolution. Magnolia polytepala, an endemic and ancient species in China, possesses a unique multi-tepal trait. Notably, the origin and formation of these multi-tepals are poorly understood. In this study, we investigated the origin and formation of multi-tepals from the inner floral whorl and elucidated the underlying molecular regulatory mechanisms by combining phenotypic analysis, sequencing, and molecular experiments. We found that the multi-tepals exhibited morpho-anatomical characteristics similar to normal tepals but differed from petaloid and normal stamens. The temporal dynamics of a large number of differentially expressed genes (DEGs) involved in multiple signaling (transduction) pathways contributed to multi-tepal primordia initiation during early floral differentiation. In particular, the dynamic expression of MpWOX4, MpCLE41, MpULT1, and MpKN1 might be responsible for floral meristem activation and maintenance, while MpTGA1 and MpEJ2 potentially regulated floral organ initiation. Floral homeotic genes, such as MapoAP3, contributed to subsequent organ identity specialization. We further isolated a nucleus-localized APETALA3 homolog from M. polytepala, terming it the MapoAPETALA3 (MapoAP3) gene, which was expressed in almost all vegetative and reproductive tissues. Ectopically expressing MapoAP3 in Arabidopsis resulted in altered phenotypes of rosette leaves, inflorescences, and florets, particularly generating extra petals instead of undergoing homeotic organ conversion. This discovery revealed an additional function of MapoAP3 in regulating organ initiation in addition to its conserved B-function in floral architecture plasticity. In summary, the multi-tepals of M. polytepala originated from the early tepal primordia initiation event rather than stamen petalody. The formation of the multi-tepal trait was attributed to the coordinated regulation of several vital DEGs, with the MapoAP3 gene playing an important role. These results provide additional insight into the regulation underlying the floral architecture formation in ancient Magnolia species and suggest that manipulating the MapoAP3 gene may hold promising potential for genetic breeding in ornamental plants.

SEPALLATA-driven MADS transcription factor tetramerization is required for inner whorl floral organ development.

MADS transcription factors are master regulators of plant reproduction and flower development. The SEPALLATA (SEP) subfamily of MADS transcription factors is required for the development of floral organs and plays roles in inflorescence architecture and development of the floral meristem. SEPALLATAs act as organizers of MADS complexes, forming both heterodimers and heterotetramers in vitro. To date, the MADS complexes characterized in angiosperm floral organ development contain at least 1 SEPALLATA protein. Whether DNA binding by SEPALLATA-containing dimeric MADS complexes is sufficient for launching floral organ identity programs, however, is not clear as only defects in floral meristem determinacy were observed in tetramerization-impaired SEPALLATA mutant proteins. Here, we used a combination of genome-wide-binding studies, high-resolution structural studies of the SEP3/AGAMOUS (AG) tetramerization domain, structure-based mutagenesis and complementation experiments in Arabidopsis (Arabidopsis thaliana) sep1 sep2 sep3 and sep1 sep2 sep3 ag-4 plants transformed with versions of SEP3 encoding tetramerization mutants. We demonstrate that while SEP3 heterodimers can bind DNA both in vitro and in vivo and recognize the majority of SEP3 wild-type-binding sites genome-wide, tetramerization is required not only for floral meristem determinacy but also for floral organ identity in the second, third, and fourth whorls.

EuAP2a, a key gene that regulates flowering time in peach (Prunus persica) by modulating Thermo-responsive transcription programming

Abstract Frequent spring frost damage threatens temperate fruit production, and the breeding of late-flowering cultivars is an effective strategy for preventing such damage, but the lack of specific genes and markers and a lack of understanding of the mechanisms make it difficult. We examined a Late-Flowering Peach (LFP) germplasm and found that its floral buds require a longer chilling period to release from their dormancy and a longer warming period to bloom than the control cultivar, two key characteristics associated with flowering time. We discovered that a 983-bp deletion in euAP2a, an APETALA2 (AP2)-related gene with known roles in regulating floral organ identity and flowering time, was primarily responsible for late flowering in LFP. This deletion disrupts an miR172 binding site, resulting in a gain-of-function mutation in euAP2a. Transcriptomic analyses revealed that at different stages of floral development, two chilling-responsive modules and four warm-responsive modules, comprising approximately 600 genes, were sequentially activated, forming a unique transcription programming. Furthermore, we found that euAP2a was transiently downregulated during the activation of these thermal-responsive modules at various stages. However, the loss of such transient, stage-specific downregulation of euAP2a caused by the deletion of miR172 binding sites resulted in the deactivation or delay of these modules in the LFP flower buds, suggesting that euAP2a acts as a transcription repressor to control floral developmental pace in peaches by modulating the thermo-responsive transcription programming. The findings shed light on the mechanisms behind late flowering in deciduous fruit trees, which is instrumental for breeding frost-tolerant cultivars.

OsMADS6-OsMADS32 and REP1 control palea cellular heterogeneity and morphogenesis in rice

Precise regulation of cell proliferation and differentiation is vital for organ morphology. Rice palea, serving as sepal, comprises two distinct regions: the marginal region (MRP) and body of palea (BOP), housing heterogeneous cell populations, which makes it an ideal system for studying organ morphogenesis. We report that the transcription factor (TF) REP1 promotes epidermal cell proliferation and differentiation inthe BOP,resulting in hard silicified protrusion cells, by regulating the cyclin-dependent kinase gene, OsCDKB1;1. Conversely, TFs OsMADS6 and OsMADS32 are expressed exclusively in the MRP, where they limit celldivision rates by inhibiting OsCDKB2;1 expression and promote endoreduplication, yielding elongatedepidermal cells. Furthermore, reciprocal inhibition between the OsMADS6-OsMADS32 complex andREP1 fine-tunes the balance between cell division and differentiation during palea morphogenesis. Wefurther show the functional conservation of these organ identity genes in heterogeneous cell growthin Arabidopsis, emphasizing a critical framework for controlling cellular heterogeneity in organ morphogenesis.

The transcription factor RhMYB17 regulates the homeotic transformation of floral organs in rose (Rosa hybrida) under cold stress.

Low temperatures affect flower development in rose (Rosa hybrida), increasing petaloid stamen number and reducing normal stamen number. We identified the low-temperature-responsive R2R3-MYB transcription factor RhMYB17, which is homologous to Arabidopsis MYB17 by similarity of protein sequences. RhMYB17 was up-regulated at low temperatures, and RhMYB17 transcripts accumulated in floral buds. Transient silencing of RhMYB17 by virus-induced gene silencing decreased petaloid stamen number and increased normal stamen number. According to the ABCDE model of floral organ identity, class A genes APETALA 1 (AP1) and AP2 contribute to sepal and petal formation. Transcription factor binding analysis identified RhMYB17 binding sites in the promoters of rose APETALA 2 (RhAP2) and APETALA 2-LIKE (RhAP2L). Yeast one-hybrid assays, dual-luciferase reporter assays, and electrophoretic mobility shift assays confirmed that RhMYB17 directly binds to the promoters of RhAP2 and RhAP2L, thereby activating their expression. RNA sequencing further demonstrated that RhMYB17 plays a pivotal role in regulating the expression of class A genes, and indirectly influences the expression of the class C gene. This study reveals a novel mechanism for the homeotic transformation of floral organs in response to low temperatures.

The Birth and Death of Floral Organs in Cereal Crops.

Florets of cereal crops are the basic reproductive organs that produce grains for food or feed. The birth of a floret progresses through meristem initiation and floral organ identity specification and maintenance. During these processes, both endogenous and external cues can trigger a premature floral organ death, leading to reproductive failure. Recent advances in different cereal crops have identified both conserved and distinct regulators governing the birth of a floret. However, the molecular underpinnings of floral death are just beginning to be understood. In this review, we first provide a general overview of the current findings in the field of floral development in major cereals and outline different forms of floral deaths, particularly in the Triticeae crops. We then highlight the importance of vascular patterning and photosynthesis in floral development and reproductive success and argue for an expanded knowledge of floral birth-death balance in the context of agroecology.

Function of LcAGL19 in the flowering regulation of Arabidopsis and Litchi chinensis

Litchi (Litchi chinensis Sonn.) is an important evergreen woody fruit tree. Appropriate low temperatures during autumn and winter are necessary for floral transition in litchi. However, global warming causes defective flowering, which seriously impedes the production of litchi. AGAMOUS-LIKE 19 (AGL19), a vernalization-related gene, had been found to control flowering time in Arabidopsis thaliana. However, its role in litchi remains unknown. In this study, we performed phylogenetic analysis. The results showed that LcAGL19 belonged to the SOC1/TM3-like protein family. Subcellular localization assay showed that LcAGL19 was localized on the nucleus. Ectopic expression of LcAGL19 in Arabidopsis thaliana resulted in early flowering, active inflorescence growth, and floral defects. Yeast two-hybrid assay and Firefly luciferase complementation imaging (LCI) assays showed that LcAGL19 might interact with MADS-box proteins to determine flowering time and floral organ identity. These results demonstrated that LcAGL19 might play important roles in floral transition, inflorescence and floral organ development in litchi. Our studies provided new insights into the regulation mechanisms of litchi flowering and offered meaningful references for AGL19 functional studies on other woody fruit trees. The functional study of LcAGL19 provided a genetic reference for litchi breeding.

Reflections on the ABC model of flower development.

The formulation of the ABC model by a handful of pioneer plant developmental geneticists was a seminal event in the quest to answer a seemingly simple question: how are flowers formed? Fast forward 30 years and this elegant model has generated a vibrant and diverse community, capturing the imagination of developmental and evolutionary biologists, structuralists, biochemists and molecular biologists alike. Together they have managed to solve many floral mysteries, uncovering the regulatory processes that generate the characteristic spatio-temporal expression patterns of floral homeotic genes, elucidating some of the mechanisms allowing ABC genes to specify distinct organ identities, revealing how evolution tinkers with the ABC to generate morphological diversity, and even shining a light on the origins of the floral gene regulatory network itself. Here we retrace the history of the ABC model, from its genesis to its current form, highlighting specific milestones along the way before drawing attention to some of the unsolved riddles still hidden in the floral alphabet.

Transcriptome Analysis Provides Insights into Korean Pine Tree Aging and Response to Shading

Age controls a tree’s responses to environmental cues and shading influences tree growth and physiology. These are basic principles of “Afforestation under canopy”, an approach that is widely used in the regeneration of Korean pine forests. Studying the underlying mechanism helps us to understand tree adaptation and utilize it in forest management. In this study, we investigated the transcriptomic changes in the uppermost main stems of the Korean pine tree (Pinus koraiensis, Sieb. et Zucc.) at different ages (5, 7, 10, 14, and 17 years) and in different growth conditions (open-grown and shade-grown trees) using RNA-Seq. In total, 434,005,837 reads were produced and assembled into 111,786 unigenes. After pairwise comparisons, 568 differentially expressed unigenes (DEUs) were identified. The greatest number of DEUs was identified in the comparison between 5-year-old open-grown trees and 17-year-old shade-grown trees, while no DEUs were identified in 15 pairwise comparisons. Among these 568 DEUs, 45 were assigned to gene ontology (GO) terms associated with response to environmental changes, including “response to stress” (26) and “response to light and temperature” (19); 12 were assigned to GO terms associated with sexual reproduction, such as “sexual reproduction”, “specification of floral organ identity”, “pollen tube guidance”, and “fruit ripening”; 15 were heat shock protein genes and showed decreased expression patterns with age; and one, annotated as Pinus tabuliformis DEFICIENS-AGAMOUS-LIKE 1, showed an increased expression pattern with age, independent of the reproductive state or growth conditions of Korean pine trees. Altogether, these findings not only demonstrate the molecular aspects of the developmental and physiological effects of age and shading on Korean pine trees, but also improve our understanding of the basic principles of “Afforestation under canopy”.