See discussions, stats, and author profiles for this publication at: https://www.researchgate.

net/publication/326722514

Genome-wide researches and applications on Dendrobium

Article  in  Planta · October 2018

DOI: 10.1007/s00425-018-2960-4

CITATIONS READS

17 1,016

7 authors, including:

Shigang Zheng
Chinese Academy of Sciences
20 PUBLICATIONS   154 CITATIONS   

SEE PROFILE

Some of the authors of this publication are also working on these related projects:

Genetic, developmental and pharmaceutical researches on Dendrobium View project

All content following this page was uploaded by Shigang Zheng on 02 January 2020.

The user has requested enhancement of the downloaded file.

Planta (2018) 248:769–784
https://doi.org/10.1007/s00425-018-2960-4

REVIEW

Genome‑wide researches and applications on Dendrobium

Shi‑gang Zheng1 · Ya‑dong Hu1 · Ruo‑xi Zhao1 · Shou Yan1,2 · Xue‑qin Zhang1,2 · Ting‑mei Zhao1,2 · Ze Chun1

Received: 17 April 2018 / Accepted: 21 July 2018 / Published online: 31 July 2018
© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Abstract
Main conclusion  This review summarizes current knowledge of chromosome characterization, genetic mapping,
genomic sequencing, quality formation, floral transition, propagation, and identification in Dendrobium.

The widely distributed Dendrobium has been studied for a long history, due to its important economic values in both medicine
and ornamental. In recent years, some species of Dendrobium and other orchids had been reported on genomic sequences,
using the next-generation sequencing technology. And the chloroplast genomes of many Dendrobium species were also
revealed. The chromosomes of most Dendrobium species belong to mini-chromosomes, and showed 2n = 38. Only a few
of genetic studies were reported in Dendrobium. After revealing of genomic sequences, the techniques of transcriptomics,
proteomics and metabolomics could be employed on Dendrobium easily. Some other molecular biological techniques, such
as gene cloning, gene editing, genetic transformation and molecular marker developing, had also been applied on the basic
research of Dendrobium, successively. As medicinal plants, insights into the biosynthesis of some medicinal components
were the most important. As ornamental plants, regulation of flower related characteristics was the most important. More,
knowledge of growth and development, environmental interaction, evolutionary analysis, breeding of new cultivars, propa-
gation, and identification of species and herbs were also required for commercial usage. All of these studies were improved
using genomic sequences and related technologies. To answer some key scientific issues in Dendrobium, quality formation,
flowering, self-incompatibility and seed germination would be the focus of future research. And genome related technolo-
gies and studies would be helpful.

Keywords  Genetic studies · Genomic sequencing · Quality formation · Flowering · Propagation · Identification

Introduction mainly distributed in south of Qinling Mountains (Wang and

The currently used Dendrobium SW. was originated from
Dendrobium crumenatum, published in 1799 by Olof Swartz
(Kaewphalug et al. 2017). And it became a legal name in
1959. Dendrobium represents a big genus in Orchids. And
there are about 1500 species in the whole world, which
are mainly distributed in Tropics and Subtropics in south
of Asia, Oceanica and somewhere else (Teixeira da Silva
et al. 2016; Teixeira da Silva and Ng 2017). There are more
than 80 species of Dendrobium had been reported in China,
* Ze Chun
sczycyzgg@cib.ac.cn
1
Chengdu Institute of Biology, Chinese Academy of Sciences,
Chengdu 610041, China
2
University of Chinese Academy of Sciences, Beijing 100041,
China
Xu 1989; Niu et al. 2017d). Due to its commercial values as
ornamental and medicinal plants, more and more researches
have been reported on Dendrobium in recent years (Tang
et al. 2017; Teixeira da Silva and Ng 2017).
Genome-wide studies partially reflect the research depth
of one specific plant. Along with the rising of genomics,
sequencing technologies have also been improved to reduce
the cost, time and sample requirements (Yeh et al. 2018).
By applying the second and third generation of sequencing
technologies, the complete sequences of nuclear genome of
D. officinale/catenatum (Tang et al. 2017) and some other
species in Orchidaceae (Cai et al. 2015; Yan et al. 2015;
Zhang et al. 2016a, 2017a; Huang et al. 2016) have been
revealed. The complete chloroplast genome sequences of
many species of Dendrobium have also been published (Li
et al. 2016a; Zhong et al. 2016; Wang et al. 2017a; Niu et al.
2017c, d). Here, to find out the existing problems and the

13
Vol.:(0123456789)

770
future focus on Dendrobium, the genome related studies on
chromosomes, heredity and sequencing were summarized.
Their application on some of the basic researches in Dend-
robium was also discussed.
Studies on chromosomes of Dendrobium
Chromosome identification was the important foundation of
genomic studies. Since 1960s, many researchers had reported
the cytological identification of chromosomes on numerous
species of Dendrobium (Shindo and Kamemoto 1963; Wang
and Xu 1989; Liao et al. 2012; Zhang et al. 2016a). Some rep-
resentative reports are listed in Table 1. The previously used
procedure was mainly from flaking to staining, and to micro-
scopic examination (Wilfret and Kamemoto 1969; Wang and
Xu 1989). Nowadays, fluorescent dyes and in situ hybridi-
zation have been widely used in chromosomal identification
(Zhang et al. 2016a). As shown in those reports, most species
of Dendrobium belongs to diploid plants. The common num-
bers of chromosomes were 2n = 38, but few were 2n = 40. The
chromosome identification on D. officinale/catenatum and
D. nobile (2n = 38) had been performed by many researchers
(Wang and Xu 1989; Liao et al. 2012; Zhang et al. 2016a).
Most of them belong to mini-chromosomes with a length of
1–3 μm. Moreover, triploids and tetraploids had also been
reported on Dendrobium (Liao et al. 2012). This might be
related to the chosen methods or materials, because of that a
lot of polyploidy lines were produced for hybrid breeding or
experiments (Yam and Lee 2013; Devadas et al. 2016).
In recent years, artificial inducing of polyploids was also
conducted by many researchers. The widely used inducer
was colchicine (Sarathum et  al. 2010), and some others
like oryzalin (Miguel and Leonhardt 2011) were also used.
Numerous polyploid materials had been induced from D.
officinale/catenatum (Jiang et al. 2014), D. nobile (Vichiato
et al. 2014) and D. scabrilingue (Sarathum et al. 2010). And
homologous tetraploids (2n = 4x = 76) were the mostly reported
on Dendrobium (Vichiato et al. 2014; Jiang et al. 2014). Com-
pared to diploids, the tetraploids showed higher contents of
polysaccharide, more internodes, more petals, and bigger
flower, but less flowers per pseudobulb, later florescence, and
slower development (Vichiato et al. 2014; Jiang et al. 2014).
The polyploid technologies might be helpful for producing of
new materials, breeding of new cultivars, and some other chro-
mosome associated basic researches in Dendrobium.
Genetic studies on Dendrobium
Researches reported on genetic linkage maps were poor
in Dendrobium. Before genomic sequencing, only a few
preliminary genetic linkage maps were constructed in four
13
Planta (2018) 248:769–784
populations of Dendrobium (Xue et al. 2010; Lu et al. 2012a,
b; Feng et al. 2013). Due to the difficulty in constructing of
stable segregation populations and the limited availability of
molecular markers, it is hard for genetic studies on Dendro-
bium. As one of the perennial orchids, the whole life cycle
needs at least 3 years (Jin et al. 2016; Yan et al. 2018). More,
self-incompatibility (Yan et al. 2016a; Wang et al. 2017b),
specific survival conditions for seed germination and seed-
ling development (An et al. 2016; Chen et al. 2017a) were
also restricted the obtaining of progenies. So, only ­F1 gen-
eration and about 100 population lines were used for genetic
studies (Table 2). Moreover, the available molecular mark-
ers were also poor (Teixeira da Silva et al. 2016; Xu et al.
2017b). And this leads to a low density on each chromo-
some (Table 2). The delay on genetic studies restricted the
performing of some molecular researches (Bhattacharyya
et al. 2015, 2017) and the assembly of genomic sequences in
Dendrobium (Yan et al. 2015; Zhang et al. 2016a). However,
after the publishing of Dendrobium genome, high-density
genetic map of Dendrobium was also being constructed
(Table 2). And it was used for quantitative trait loci iden-
tification of some important traits (Lu et al. 2018). Well,
with the improvement on tissue culturing, self-breeding
and molecular marker developing, genetic studies would be
increased in Dendrobium.
Genomic sequencing on Dendrobium
Sequencing of nuclear genome
Although numerous species present in Orchidaceae, only
few of them had been reported on genomic sequencing.
Currently, the draft genome of D. officinale/catenatum
(Yan et al. 2015; Zhang et al. 2016a), Phalaenopsis eques-
tris (Cai et al. 2015), Phalaenopsis ‘KHM190’ (Huang
et al. 2016), Apostasia shenzhenica (Zhang et al. 2017a)
and Vanilla fragrans (http://fj.peopl​e.com.cn/n/2015/0208/
c3370​0 6-23835​3 72.html) had been revealed. The next-
generation high-throughput sequencing technologies (Illu-
mina and PacBio platform) were employed in these studies
(Yeh et al. 2018). The complete genome sequences of D.
officinale and D. catenatum were published successively
(Yan et al. 2015; Zhang et al. 2016a). The final genome
size of D. officinale/catenatum is about 1.1 Gb (Table 3).
After optimizing in sequencing and assembling (Zhang
et al. 2017a), the scaffold N50 of D. officinale/catenatum
were increased from 76 to 391 kb, and to 1055 kp. Com-
pared to some other medicinal plant species (Table 3), the
genome of Dendrobium showed high contents of repeat
sequences, and also showed high heterozygosity. The
high percent of repeat sequences might be associated with
Orchid evolution (Luo et al. 2014; Niu et al. 2017b), and
 Table 1  Chromosome identification of Dendrobium 
Nos. Species Chromosome Tissue Staining Published years Major affiliations
Planta (2018) 248:769–784

1 D. schuetzei, D. sanderae, D. dearei 2n = 38 Root tips buds Aceto-orcein 1963 Hawaii Agricultural Experiment Station (Shindo and
D. formosum, D. draconis 2n = 40 Kamemoto 1963)
2 D. chrysotoxum, D. draconis, D. crumenatum, D. anos- 2n = 38 Root tips Aceto-orcein 1969 University of Hawaii (Wilfret and Kamemoto 1969)
mum, D. aggregatum, D. distichum, D. trigonopus, D.
d’albertsii, D. gouldii, D. grantii, D. mirbellianum, D.
stratiotes, D. strebloceras, D. undulatum, D. canalicu-
latum, D. arachnites, D. heterocarpum, D. linguella, D.
macrostachyum, D. monile, D. moschatum, D. senile,
D. tortile, D. macrophyllum, D. spectabile, D. bulleni-
anum, D. biggibum, D. delacourii
D. leonis, D. dixanthum 2n = 40
3 D. acinaciforme, D. chrysotoxum, D. densiflorum, D. 2n = 38 Root tips Giemsa 1985 South China Botanical Garden, The Chinese Academy of
candidum, D. crepidatum, D. denneanum, D. devoni- Sciences (Chen et al. 1985)
anum, D. guangxiense, D. linawianum, D. loddigesii,
D. lohohense, D. nobile, D. clavatum, D. wangi, D.
gibsonii, D. aphyllum, D. primulinum
D. fimbriatum, D. hancockii, D. thyrsiflorum 2n = 40 Leaves buds
D. hercoglossum 2n = 57
D. chrysanthum 2n = 76
4 D. crepidatum, D. crispulum, D. denneanum, D. fimbria- 2n = 38 Root tips Carbol fuchsin 1989 Anhui University (Wang and Xu 1989)
tum, D. hercoglossum, D. jenkinsii, D. lohohense, D.
moniliforme, D. nobile, D. officinale
5 D. aphyllum, D. aggregatum 2n = 38 Root tips Chromomycin A3 2010 University of Dhaka (Begum et al. 2010)
D. moschatum 2n = 40
6 D. Fairyflake “Carmen”, D. Snowflake “Otome”, D. 4x = 76 Root tips Carbol fuchsin 2012 South China Agricultural University (Liao et al. 2012)
Utopia “Messenger”, D. Shinonome “Karen”
D. Casiflake, D. Himezakura “Fujikko”, D. Shirasagi 3x = 57
D. nobile, D. guangxiense 2x = 38
7 D. catenatum 2n = 38 Root tips Propidium iodide 2016 The National Orchid Conservation Center of China and
The Orchid Conservation and Research Center of Shenz-
hen (Zhang et al. 2016a, b)

13
771

772 Planta (2018) 248:769–784

the high heterozygosity might be related to the lack of

RAPD random amplified polymorphic DNA, SRAP sequence-related amplified polymorphism, EST expressed sequence tags, SSR simple sequence repeat, ISSR inter-simple sequence repeat,
Hangzhou Normal University (Xue

Hangzhou Normal University (Lu

Hangzhou Normal University (Lu

Hangzhou Normal University (Lu

homozygous materials (Zhang et al. 2016a, 2017a). They

Hangzhou Normal University

were also the difficulties in genomic sequencing of Dend-
robium. More, the deficiency of genetic studies restricted
the assembly from scaffolds to chromosomes (Table 3).

(Feng et al. 2013)

But still, the known genome sequences of Dendrobium and
Linkage groups Genome coverage (%) Published years Major affiliations

some other Orchids would be helpful for further sequenc-

et al. 2012b)

et al. 2012a)
et al. 2010)

et al. 2018)
ing of the other species. And they could also be applied
on cytological, genetic and molecular studies in Dendro-
bium. Meanwhile, the improvement on technologies and
basic researches will be helpful for drawing the complete
genome of Dendrobium.
2010

2012

2012

2013

2018
Sequencing of chloroplast genome

As a photosynthesis organelle, chloroplast was the most

important and common plastome in Dendrobium (Niu et al.
2017c, d). So, besides the nuclear genome, the chloroplast
2448–2304

genome was also involved in evolution and biosynthesis of

Dendrobium. Currently, the complete chloroplast genome
92.7
82.7
76.1

71.7
73.1

73.5
76.9

sequences of more than 33 Dendrobium species had been

reported (Table 4). Among them, the chloroplast genomes
of D. officinale/catenatum (Yang et al. 2016; Zhong et al.
19 + 20
17 + 20

2016; Zhang et  al. 2017b) and D. nobile (Konhar et  al.
15 + 4
11 + 3
27 + 9

15 + 2
15 + 4

2016; Yan et al. 2016b) had been reported for several times.
19

Taking together, these results indicates that the chloroplast

genome size is about 0.15 Mb, the predicted gene number
Generation Lines Molecular markers Number Average
distance

is about 130, protein coding genes are more than 70, tRNA
(cM)

11.6
11.2
11.8

10.4
10.2

14.8
14.7
0.32

and rRNA encoding genes, and pseudo-genes are about 38,

8, and 8, respectively.
112
62
265

169
165

117
116
8573

Applying of genomic sequences

RAPD, ISSR

in Dendrobium
EST-SSR

EST-SSR
RAPD

RAPD
SRAP

SRAP

SRAP

SLAF
Types

ISSR

Based on genomic sequences, some new technologies and

methods were employed to improve the basic and applied
researches in Dendrobium. In recent years, RNA-seq tech-
90

140

90

90

111

nologies were largely used for transcriptional studies in D.

Table 2  Genetic linkage maps of Dendrobium 

officinale/catenatum and D. nobile, successively (Table 5).

Proteome (Li et al. 2016b; Wang et al. 2017b) and metabo-
SLAF specific-locus amplified fragment
D. hercoglossum F1

F1

F1

F1

F1

lome (Wu et al. 2016; Jin et al. 2016) related studies were
also constructed on Dendrobium. The molecular biological
D. moniliforme

D. moniliforme

D. moniliforme

technologies, such as gene cloning (Wan et al. 2017; He

D. officinale

D. officinale
D. officinale

D. officinale
D. aduncum

et al. 2017d), genetic transformation (Azuma et al. 2016;

D. nobile

Sawettalake et al. 2017), overexpression (Liu et al. 2016),

RNA interfering (Lau et al. 2015; Yu et al. 2016) and gene
Nos. Population

editing (Kui et al. 2017) were applied on Dendrobium rap-

Female

Female

Female

Female

Female
Parents

Male

Male

Male

Male

Male

idly. The functional studies on regulation networks of tran-

scription factors, such as WRKY (Wang et al. 2018b), MYB
and MYC (Li et al. 2017a; Zhu et al. 2017), and small RNAs
1

13
 Table 3  Comparison of genome sequencing in Dendrobium, orchids and some other medicinal plants
Species Family Chromo- Sequencing Platform Depth Assembly Levels Scaffold Repeat Heterozy- Predicted Published Major affiliations
somes Genome Methods N50 (kp) sequences gosity genes years
(Gb) (%)

D. officinale Orchi- 2n = 38 1.35 Illumina 327X SOAPde- Scaffold 76.4 63.3 0.48 35,567 2015 Jilin University (Yan
daceae Hiseq2000 novo et al. 2015)
Planta (2018) 248:769–784

PacBio
D. catenatum Orchi- 2n = 38 1.01 Illumina 159X SOAPde- Scaffold 391.4 78.1 0.63 28,910 2016 The National Orchid
daceae 1.12 Hiseq2000 novo 1055.3 29,257 Conservation Center
of China and The
Orchid Conservation
and Research Center
of Shenzhen (Zhang
et al. 2016a)
Phalaenopsis Orchi- 2n = 38 1.08 Illumina 99X SOAPde- Scaffold 359.1 61.5 0.40 29,431 2015 The National Orchid
equestris daceae 1.13 Hiseq2000 novo 1217.4 29,545 Conservation Center
of China and The
Orchid Conservation
and Research Center
of Shenzhen (Cai
et al. 2015)
Phalaenopsis Orchi- 2n = 38 3.10 Illumina 90X Velvet Scaffold 100.9 59.7 3.2 41,153 2016 National Pingtung
‘KHM190’ daceae Hiseq2000 assem- University of Sci-
bler ence and Technol-
ogy (Huang et al.
2016)
Apostasia Orchi- 2n = 68 0.35 Illumina 185X ALL- Scaffold 3029.1 42 0 21,841 2017 The National Orchid
shenz- daceae Hiseq2000/X- PATHS- Conservation Center
henica Ten PacBio LG of China and The
RS II assem- Orchid Conservation
bler and Research Center
of Shenzhen (Zhang
et al. 2017a)
Vanilla Orchi- 2n = 28 0.80 Illumina 325X – Scaffold 288.0 – 1.14 29,000 – Fujian Agriculture and
fragrans daceae Hiseq2500 Forestry University
Lotus japoni- Legumi- 2n = 12 0.39 Roche 454 0.67X Arachne Chromo- 25.0 34.2 – 30,799 2008 Kazusa DNA
cus nosae assem- some Research Institute
bler (Sato et al. 2008)
Salvia miltio- Lamiaceae 2n = 16 0.54 Illumina 250X SOAPde- Scaffold 51.0 54.4 0.27 30,478 2010 China Academy of
rrhiza Hiseq2000 novo Chinese Medical
PacBio RS II Sciences (Xu et al.
2016)
Ricinus com- Euphorbi- 2n = 20 0.35 AB3730xl 4.6X Celera Scaffold 496.5 50.3 – 31,237 2010 J. Craig Venter
munis aceae sequencers assem- Institute (Chan et al.
bler 2010)

13
773


Table 3  (continued)
774

Species Family Chromo- Sequencing Platform Depth Assembly Levels Scaffold Repeat Heterozy- Predicted Published Major affiliations
somes Genome Methods N50 (kp) sequences gosity genes years

13
(Gb) (%)

Selaginella Selaginel- 2n = 20 0.21 ABI3730 7.0X Arachne Scaffold 1749.8 48 – 34,782 2011 Purdue University
moellen- laceae assem- (Banks et al. 2011)
dorffii bler
Zizania Gramineae 2n = 34 0.44 Illumina Genome 140X ALL- Scaffold 604.8 37.7 – 43,703 2015 China National Rice
latifolia Analyzer II PATHS- Research Institute,
LG Chinese Academy
assem- of Agricultural
bler Sciences (Guo et al.
2015)
Ginkgo Gink- 2n = 24 10.61 Illumina 196X SOAPfil- Scaffold 1360.0 76.5 – 30,209 2016 Zhejiang University
biloba goaceae Hiseq2000/4000 ter (Guan et al. 2016)
Panax gin- Araliaceae 2n = 48 3.43 Illumina Hiseq 112X SOAPde- Scaffold 108.7 62 – 42,006 2017 China Academy of
seng X-Ten novo Chinese Medical
Sciences (Xu et al.
2017a)
Glycyrrhiza Legumi- 2n = 16 0.38 Illumina 817X ALL- Scaffold 109.2 36.4 0.33 34,445 2017 RIKEN Center
uralensis nosae Hiseq2000 PATHS- for Sustainable
PacBio RS II LG Resource Science
assem- (Mochida et al.
bler 2017)
Planta (2018) 248:769–784
Planta (2018) 248:769–784 775
(Yu et al. 2016) were expanded. Genome-wide development
and application of molecular markers, especially SSR and
single nucleotide polymorphism (SNP) markers, was also
increased (Table 6). These technologies and studies were
involved in evolution, classification, identification, devel-
opment and regulation, floral transition, propagation, bio-
synthesis and metabolism, breeding and cultivation, and
interaction with environments.
Quality formation of medicinal Dendrobium
Many species of Dendrobium could be used as plant medi-
cine. In Chinese Pharmacopoeia (State Pharmacopeia Com-
mittee of China 2015), D. officinale/catenatum, D. nobile, D.
fimbriatum and D. chrysotoxum were listed as the traditional
herbs. The quality of Dendrobium herbs was influenced by
numerous genetic and environmental factors (Tang et al.
2017; Zheng et al. 2018). At present, the biosynthesis and
metabolism of some important pharmaceutical components
were still not very clear (Zhang et al. 2016a; Li et al. 2017c).
Recently, transcriptional studies were conducted to identify
the genes involved in biosynthesis of polysaccharide (Zhang
et al. 2016b; Shen et al. 2017), dendrobine (Li et al. 2017c),
and flavonoid (Lei et al. 2018). These studies indicated that
the families of cellulose synthase and glycosyltransferase
played key roles in biosynthesis of polysaccharide (Fig. 1).
The families of cytochrome P450, aminotransferase and
methyltransferase played key roles in biosynthesis of dend-
robine (Fig. 2). The predicted pathways still need to be con-
firmed. However, only few of these genes, such as DoUGP
(Wan et al. 2017), DoUGE (Yu et al. 2017), DoCSLA6 (He
et al. 2017b), DoGMP1 (He et al. 2017c), DoPMM (He et al.
2017d) and DoNI (Gao et al. 2016), have been cloned and
functionally analyzed (Fan et al. 2016). The families of some
transcriptional factors, such as MYC and WARKY (He et al.
2017a; Zhu et al. 2017), were also reported to play roles in
the regulation map. The biosynthesis of some other impor-
tant medicinal components, such as gigantol, moscatilin,
erianin, bibenzyl, phenanthrenes and sesquiterpenes, was
rarely reported in Dendrobium.
Moreover, the effects of abiotic and biotic stresses on
the metabolism of secondary metabolites should also be
considered (Chen et al. 2017c). Cold acclimation signifi-
cantly affected the expression of numerous genes related to
metabolome in Dendrobium (Wu et al. 2016). Light inten-
sity influenced the content of dendrobine (Li et al. 2017b).
Water and salt stresses were also associated to the quality of
Dendrobium herbs (Yu et al. 2017; Li et al. 2017b). Mycor-
rhizal fungus was reported to stimulate the accumulation
of dendrobine and polysaccharide in Dendrobium (Li et al.
2017c). To understand the quality formation of Dendrobium
herbs, both genetic and environmental factors need to be
systematically studied.
Flowering in ornamental Dendrobium
Dendrobium was also one of the big families of flowering
plant. And a lot of hybrids of Dendrobium could be found
in the ornamental markets (Li et al. 2017a; Sawettalake
et al. 2017). So, floral transition was always the research
focus in worldwide. The external changes of temperature
and photoperiod in vernalization led to the change of cir-
cadian clock in Dendrobium (Huang et al. 2016; Wen et al.
2017; Kaewphalug et al. 2017). Then, many signal pathways
were activated (Fig. 3a). Some plant hormones like cyto-
kinin, auxin and gibberellin were reported to be involved in
this pathway (Liu et al. 2016; Wen et al. 2017; Chen et al.
2017c). Some key genes, such as DnVRN1 (Wen et al. 2017),
DoSOC1 (Liu et al. 2016), DoAP1 (Sawettalake et al. 2017),
DnCOL (Kaewphalug et al. 2017) and DnFT (Wang et al.
2017c), had been identified in the process of flowering. Most
of them, such as DoSOC1, DoAP1 and DnAGL19, belong
to MADS-box transcription factors (Liu et al. 2016). Other
families of transcriptional factors like DwMYB were also
involved in the regulation map (Lau et al. 2015). More, a
few genes response to ethylene in pollination and chilling
induced senescence and abscission of Dendrobium flowers
were characterized (Thongkum et al. 2015; Phetsirikoon
et al. 2016).
More, colorful and sweet flowers attracted pollinators
and customers (Dormont et  al. 2014). Different species
of Dendrobium showed diverse flower colors (Tang et al.
2017; Sawettalake et al. 2017). Even in the same species,
the flower color could be different (Fig. 3b). The changes of
flower color might be mainly caused by different constituting
of anthocyanins and flavonoids (Li et al. 2017a). Some key
genes in the biosynthesis of anthocyanins and flavonoids
were also characterized in Dendrobium (Fig. 3c). However,
more functional studies were still required to find out some
key factors in regulation of flowering. And then, they could
be utilized in molecular breeding of ornamental Dendrobium
(Azuma et al. 2016).
Propagation of Dendrobium
Sexual propagation of Dendrobium was influenced by self-
incompatibility and seed germination (Yan et al. 2016a;
Devadas et al. 2016; Niu et al. 2017a). Traditionally, cut-
ting propagation was the mostly applied method by utiliz-
ing the production of axillary bud in pseudobulb (Yan et al.
2018; Zheng et al. 2018). In the current commercial pro-
cess, hybridization and medium induced germination were
widely used for large-scale propagation (Yam and Lee 2013;
Si et al. 2017; Tang et al. 2017). However, this led to the
13

776 Planta (2018) 248:769–784

Table 4  Information of complete genome sequences of Dendrobium chloroplast

Species Size (bp) Genes Proteins tRNA rRNA Sudo-genes Published years Major affiliations

D. officinale 152221 129 76 30 4 – 2014 Nanjing Normal University (Luo et al. 2014)
D. officinale 152185 127 89 30 8 – 2016 Guangzhou University of Chinese Medicine
(Zhong et al. 2016)
D. officinale 152018 128 83 39 8 – 2016 Chinese Academy of Medical Sciences and
Peking Union Medical College (Yang et al.
2016)
D. candidum 152094 129 89 30 8 7 2017 Kunming Medical University (Zhang et al.
2017b)
D. nobile 150793 130 76 30 4 – 2016 Nanjing Normal University (Yan et al. 2016b)
D. nobile 152018 132 79 38 8 7 2016 North-Eastern Hill University (Konhar et al.
2016)
D. strongylanthum 153059 130 77 38 8 7 2016 Shaanxi Normal University (Li et al. 2016a)
D. huoshanense 153188 129 76 38 8 7 – Shaanxi Normal University
D. chrysotoxum 153953 116 63 38 8 7 – Shaanxi Normal University
D. pendulum 153248 129 76 38 8 7 2017 Shaanxi Normal University (Wang et al. 2017a)
D. moniliforme 148778 129 73 39 8 6 2017 Nanjing Normal University (Niu et al. 2017c)
D. fimbriatum 151673 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. parishii 151689 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. henryi 151850 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. parviflorum 150073 131 72 38 7 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. wilsonii 152080 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. primulinum 150767 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. lohohense 151812 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. jenkinsii 151717 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. hercoglossum 151939 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. chrysanthum 151790 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. aphyllum 151524 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. crepidatum 151717 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. gratiosissimum 151829 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. devonianum 151945 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. devonianum 151715 102 68 30 4 – 2017 Nanjing Normal University (Niu et al. 2017b)
D. denneanum 151565 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. salaccense 151104 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. exile 151294 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. ellipsophyllum 152026 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. brymerianum 151830 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. wardianum 151788 131 71 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. falconeri 151890 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. xichouense 152052 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. spatella 151829 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. fanjingshanense 152108 132 72 38 8 8 2017 Nanjing Normal University (Niu et al. 2017d)
D. loddigesii 152493 102 68 30 4 – 2017 Nanjing Normal University (Niu et al. 2017b)

deficiency of homozygous individuals (Zhang et al. 2016a).
And the phenotype traits and medicinal quality of progenies
were not stable (Bhattacharyya et al. 2015, 2017; Yan et al.
2018). Recently, the influence factors of self-incompatibil-
ity were analyzed, assisted by the genomic sequences (Yan
et al. 2016a; Devadas et al. 2016). Researches indicated that
self-incompatibility was related to evolution of Dendrobium
and characteristics of chromosomes and genomes (Pinheiro
et al. 2015; Devadas et al. 2016; Niu et al. 2017a). Some
differentially expressed proteins were revealed between
self-pollination and cross-pollination pistils in Dendrobium
(Wang et al. 2017b). More, new insights into the process
of nutrient accumulation were provided in seed develop-
ment (Ling et al. 2016). Some molecular mechanisms of

13
Planta (2018) 248:769–784 777

Table 5  Transcriptional studies on Dendrobium in recent two years

Species Sequencing platform Assembly Unique genes Research direction Published years Major affiliations

D. officinale Illumina Hiseq2000 Trinity 114,098 Polysaccharide synthesis 2016 South China Botanical Garden,
Chinese Academy of Sciences
(Zhang et al. 2016b)
D. officinale Illumina Hiseq2000 – – Protocorm development 2016 Southwest Jiaotong University
(An et al. 2016)
D. officinale Illumina Hiseq2500 Trinity 79,256 Cold acclimation 2016 Zhejiang Academy of Agricul-
tural Sciences (Wu et al. 2016)
D. officinale Illumina Hiseq2500 Trinity 299,107 Organ-specific study 2016 Hangzhou Normal University
(Meng et al. 2016)
D. chrysanthum Illumina Hiseq2000 Trinity 91,457 Self-incompatibility 2016 Shenzhen University (Wang
et al. 2017a, b, c)
D. officinale Ion Torrent PGM™ Trinity 40,405 SSR analysis 2017 Nanjing Forestry University (Xu
et al. 2017b)
D. officinale Illumina Hiseq2500 Trinity 18,721 Synthesis of polysaccha- 2017 Hangzhou Normal University
rides and alkaloids (Shen et al. 2017)
D. officinale Illumina Hiseq2000 – – Symbiotic germination 2017 Chinese Academy of Medical
Sciences and Peking Union
Medical College (Chen et al.
2017a)
D. officinale – Trinity 2645 Flowering 2017 Zhejiang Academy of Agri-
culture Science (Chen et al.
2017b)
D. officinale Illumina Hiseq1500 Trinity – Translocation of sugars 2017 Chinese Academy of Medical
Sciences and Peking Union
Medical College (He et al.
2017e)
D. nobile Illumina HiSeq4000 – 207,283 SSR analysis 2017 Chinese Academy of Medical
Sciences and Peking Union
Medical College (Li et al.
2017d)
D. nobile Illumina Hiseq2000 Trinity 99,686 Floral transition 2017 South China Agricultural Uni-
versity (Wen et al. 2017)
D. nobile Illumina HiSeq4000 Trinity 207,283 Dendrobine biosynthesis 2017 Chinese Academy of Medical
Sciences and Peking Union
Medical College (Li et al.
2017c)
D. catenatum Illumina HiSeq4000 – 23,139 Flavonoid biosynthesis 2018 Guangzhou University of Chi-
nese Medicine (Lei et al. 2018)

asymbiotic germination (An et  al. 2016) and symbiotic
germination (Chen et al. 2017a; Li et al. 2018) were inves-
tigated in Dendrobium. And mycorrhizal fungi were used
for enhancing seed germination, protocorm formation and
seedling development in D. devonianum (Huang et al. 2018).
Simultaneously, improvements on the technologies of tissue
culturing and micro-propagation were also performed (Kui
et al. 2017). The suitable conditions and potential mecha-
nisms in differentiation of somatic cell (da Silva and Winarto
2016), development of protocorm (An et al. 2016) and repro-
duction of plants (Sawettalake et al. 2017) had been reported
successively. High-efficient, stable and non-toxic propaga-
tion methods were required for resource restoring and com-
mercial producing of Dendrobium.
Identification of Dendrobium
There are many wild species and cultivated varieties in Den-
drobium genus. Phenotypic identification of this big fam-
ily of Orchids was limited. So, genetic identification was
required. To further utilize Dendrobium resources and qual-
ity control of these herbs, multi-type of molecular markers
had been developed (Table 6). Previously, based on sequenc-
ing, some genomic fragments such as ITS1 and ITS2 from
nuclear genome (Feng et al. 2015b; Srikulnath et al. 2015;
Wang et al. 2018a), matK and trnH-psbA from chloroplast
genome (Xu et al. 2015; Peng et al. 2015), and nad1 from
mitochondria genome (Ye et al. 2017b), were widely used
for classification and evolution analysis of Dendrobium
(Teixeira da Silva et al. 2016; Hou et al. 2017). Based on

13

778 Planta (2018) 248:769–784

Table 6  Development and application of molecular markers on Dendrobium in recent years

Molecular markers Materials Published Major affiliations
years
Types Total Screened Origin Species Samples Target species
number number

PCR and ITS, ITS2 11 5 Ribosome 184 1698 Dendrobium 2015 Institute of Botany, Chinese Academy
sequencing matK Chloroplast of Sciences (Xu et al. 2015)
rbcL
trnH-psbA
ITS2 1 1 Ribosome 64 364 Dendrobium 2015 Hangzhou Normal University (Feng
et al. 2015b)
matK 2 2 Chloroplast 9 27 Dendrobium 2015 Kasetsart University (Srikulnath et al.
ITS Ribosome 2015)
psbA-trnH 1 1 Chloroplast 12 32 D. denneanum 2015 Chengdu Institute of Biology, Chi-
nese Academy of Sciences (Peng
et al. 2015)
trnC-petN 2 2 Chloroplast 18 135 D. moniliforme 2017 Nanjing Normal University (Ye et al.
trnE-trnT 2017a)
nad 1/b-c 2 2 Mitochondria 18 143 D. moniliforme 2017 Nanjing Normal University (Ye et al.
nad 7/2-3 2017b)
ITS 1 1 Ribosome 73 320 Dendrobium 2018 Chengdu University of Traditional
Chinese Medicine (Wang et al.
2018a)
ITS 4 4 Ribosome 5 475 D. officinale 2017 Nanjing Normal University (Hou
accD-psaI Chloroplast et al. 2017)
trnC-petN
rps15-ycf1
PCR and elec- SCoT 36 22 Translation initiation 36 38 Dendrobium 2015 Hunan Agricultural University (Feng
trophoresis TRAP 13 13 codon et al. 2015a)
Known sequences
RAPD 13 13 Random primers 6 60 D. nobile 2015 North-Eastern Hill University (Bhat-
tacharyya and Kumaria 2015)
ISSR 35 13 Repeat spacer 6 60 D. nobile 2015 North-Eastern Hill University (Bhat-
DAMD 25 12 Minisatellite DNA tacharyya et al. 2015)

SSR 10 10 Microsatellite DNA 7 102 D. nobile 2015 Nanjing Normal University (Yan and
Ding 2015)
SSR 48 19 Microsatellite DNA 5 24 D. calamiforme 2015 University of Georgia (Trapnell et al.
2015)
SSR 320 109 Microsatellite DNA 44 44 Dendrobium 2015 Hangzhou Normal University (Kang
et al. 2015)
AFLP 20 9 Restricted site 5 50 D. thyrsiflorum 2017 North-Eastern Hill University (Bhat-
tacharyya et al. 2017)
SSR 68 17 Transcriptome 1 31 D. officinale 2017 Nanjing Forestry University (Xu et al.
2017b)
SSR 20 13 Transcriptome 3 3 D. nobile 2017 Chinese Academy of Medical Sci-
ences and Peking Union Medical
College (Li et al. 2017d)
ITS, trnL-F 8 8 Ribosome, Chlo- 8 115 Dendrobium 2018 China Academy of Chinese Medical
roplast Sciences (Jiang et al. 2018)
Real-time PCR trnL-F 3 3 Chloroplast 3 226 D. officinale 2018 China Academy of Chinese Medical
Sciences (Dong et al. 2018)
rpl32-trnL 14 6 Plastome 20 127 D. huoshanense 2018 Nanjing Normal University (Niu et al.
trnS-trnG 2018)
atpB-rbcL
trnT-trnL
trnL intron
Sequencing ddRAD – – Restricted site 4 4 D. densiflorum 2017 University of North Bengal (Roy
et al. 2017)

ITS internal-transcribed spacer, SCoT start codon targeted polymorphism, TRAP target region amplification polymorphism, DAMD direct ampli-
fication of polymorphic DNA, AFLP amplified fragment length polymorphism, ddRAD double digest restriction site-associated DNA sequencing

gene sequences and SNP variances, real-time PCR was and evolutionary process of Dendrobium species in China,
also used for fast identification (Dong et al. 2018; Niu et al. India, Thailand, and Australia were identified successively
2018). Then, the genetic diversity, phylogenetic relationship (Xu et al. 2015; Srikulnath et al. 2015; Ye et al. 2017a; Wang

13
Planta (2018) 248:769–784 779

Sucrose
cellulose synthase beta-fructofuranosidase Melibiose
Galcatan Arabinose Xylose
galactosyltransferase galactinol-sucrose Raffinose alpha-galactosidase
galactosyltransferase alpha-galactosidase Aldehyde Xylose
Lactose synthase Lactose Lactase Galactose
galactinol-raffinose Stachyose beta-fructofuranosidase Manninotriose reductase isomerase
Tagatose galactosyltransferase
inositol 3-alpha Aldehyde reductase Galactitol 2-dehydrogenase
Galactinol Arabitol Lyxose
galactosyltransferase Glucono-1,5-
lactone Arabinitol Lyxose
sucrose
UDP-4-keto- Glucose 2-dehydrogenase ketol-isomerase
6-deoxy-glucose 1-dehydrogenase gluconolactonase
UDP-rhamnose Arabinitol
sucrose synthase
3,5-epimerase-4-reductase Invertase DoNI Xylose isomerase Gluconate Ribulose 4-dehydrogenase
UDP-glucose
Glucose Iditol-2- gluconokinase ribulokinase Xylulose
UDP-rhamnose 4,6-dehydratase aldose reductase Sorbitol UDP-glucose
DoUGE dehydrogenase
hexokinase Sorbitol Ribose
UDP-galactose epimerase UDP-glucose sorbose Gluconate-6-
dehydrogenase phosphate Glycolysis
Glucose- Phosphoglucose Fructosyltransferase Fructan ribokinase
UDP-galactose UDP-glucose Mannitol mannitol dehydrogenase Fructose
6-phosphate isomerase Phosphogluconate
UDP-glucose pyrophosphorylase DoUGP phosphatase ketohexokinase Ribose-5-
dehydrogenase phosphate
6-dehydrogenase Mannitol Fructose-1-phosphate Glyceraldehyde-
Glucose-1-phosphate phosphoglucomutase fructose-2,6-bisphosphate
Phospho- Ribulose-5- 3-phosphate
fructokinase 1-phospho fructokinase ribose-5-phosphate
UDP-glucuronate GDP-glucose GDP-glucose transferase phosphate
fructose-2,6-bisphosphate isomerase Triose-phosphate
ADP-glucose pyrophosphorylase hexokinase Fructose-1,6-bisphosphate
2-phosphatase isomerase
UDP-apiose/xylose pyrophosphorylase ribulose-phosphate
synthase cellulose synthase cellulose synthase mannitol- mannitol-1-phosphate fructose-6-phosphate 3-epimerase
ADP-glucose xylosyltransferase glucosyltransferase 5-dehydrogenase Glycerone-1-
1-phosphate 1-phosphotransferase Xylulokinase
UDP-xylose Xylulose-5-phosphate phosphate
Starch Cellulose Fructose-6-phosphate transketolase
Xyloglucan Glucan Erythrose-4-phosphate
synthase synthase GDP-mannose epimerase phosphomannose isomerase Rhamnulose-1-
UDP-arabinose
4-epimerase cellulose Fucose- Fucose-1-phosphate Mannose phosphate aldolase
Amylose Mannuronan Mannose-6-phosphate mannokinase
1-phosphate guanylyltransferase
UDP-arabinose Starch Rhamnulose-
phosphomannomutase DoPMM mannan 1,2-(1,3)- mannan endo-1,4-
branching Mannuronan alpha-mannosidase beta-mannosidase 1-phosphate
cellulose synthase enzyme Fucokinase synthase Mannose-1-phosphate
arabinosyltransferase Fucan Mannan 1,4-β-Mannan Rhamnulokinase
GDP-mannuronate mannose-1-phosphate DoGMP1
Starch Fucose DoCSLA6
Arabinan guanylyltransferase Rhamnulose
Amylase Cellulose synthase cellulose synthase Galactoglucomannan
Fucose GDP-mannose
cellulose synthase Fucosyltransferase GDP-mannose mannosyltransferase Rhamnose
Maltose isomerase 6-dehydrogenase
arabinosyltransferase isomerase
GDP-fucose GDP-mannose cellulose synthase cellulose synthase
Maltose Fuculose GDP-fucose Glucomannan
synthase 4,6-dehydratase glucosyltransferase galactosyltransferase Rhamnose
Arabino-1,4-β-xylan phosphorylase
Fuculokinase GDP-6-deoxy-talose GDP-6-deoxy-talose GDP-4-oxo- GDP-4-dehydro-rhamnose cellulose synthase
cellulose synthase Glucose GDP-rhamnose Rhamnan
4-dehydrogenase 6-deoxy-mannose reductase galactosyltransferase Rhamnofuranose
xylosyltransferase Trehalose synthase
Fuculose-1- Fuculose-phosphate 2-Dehydro-3-deoxy- Rhamnonate Rhamnono- Rhamnose
Lactaldehyde aldolase Rhamnonate Rhamnono-1,4-lactone
Xylan Trehalose phosphate aldolase rhamnonate dehydratase 1,4-lactonase 1-dehydrogenase

Fig. 1  Biosynthesis of polysaccharides in Dendrobium. This path- yellow cells indicate polysaccharides, purple cells indicate activated
way was constructed based on recent transcriptional studies on Den- units of monosaccharides, blue cells indicate enzymes, white cells
drobium (Table 5) and related KEGG pathways listed in http://www. indicate intermediates, and orange cells indicate the cloned and func-
brend​a-enzym​es.org/. The green cells indicate monosaccharides, tionally studied genes in Dendrobium 

Glycolysis glyceraldehyde- 1-deoxy-D-xylulose- 1-deoxy-D-xylulose- 1-deoxy-D-xylulose- 2-C-methyl-erythritol 4- 2-C-methyl-D-erythritol 4-(Cytidine 5’-diphospho)-2-

3-phosphate 5-phosphate synthase 5-phosphate 5-phosphate reductoisomerase phosphate 4-phosphate cytidylyltransferase C-methyl-erythritol
Erythrose-
4-phosphate Phosphoenolpyruvate pyruvate DoDXS DoDXR
4-(cytidine 5'-diphospho)-
hydroxymethylglutaryl- 3-hydroxy-3-methyl- hydroxymethylglutaryl- Mevalonate- 2-C-methyl-D-erythritol kinase
3-deoxy-7-phosphoheptulonate Acetyl-CoA Mevalonate mevalonate kinase
CoA synthase glutaryl-CoA CoA reductase 5-phosphate
synthase 2-Phospho-4-(Cytidine 5’-
Mevalonate-3,5- mevalonate-3- Mevalonate- Mevalonate diphospho)-2-C-methyl-
7-Phosphate-2-dehydro-3- acetyl-CoA C-
Acetoacetyl-CoA disphosphate phosphate 5-kinase 3-phosphate 3-kinase Phosphomevalonate erythritol
deoxy-arabinoheptonate acetyltransferase
kinase
Phosphomevalonate 2-C-methyl-D-erythritol
3-dehydroquinate synthase 2,4-cyclodiphosphate synthase
decarboxylase Mevalonate-5-
Diphosphomevalonate
3-Dehydroquinate decarboxylase diphosphate 2-C-methyl-D-erythritol
Isopentenyl Isopentenyl Isopentenyl
2,4-cyclodiphosphate
3-dehydroquinate dehydratase phosphate phosphate kinase diphosphate
(E)-4-hydroxy-3-methylbut-
3-Dehydro-shikimate Sesquiterpene farnesyl farnesyl Isopentenyl-diphosphate 2-enyl-diphosphate synthase
sesquiterpene synthases diphosphate diphosphate synthase DELTA-isomerase
Shikimate dehydrogenase 4-hydroxy-3- 4-hydroxy-3-
methylbut-2-enyl methylbut-2-enyl
Shikimate geranyl diphosphate Geranyl Dimethylallyl- diphosphate reductase diphosphate
(6E)-8-hydroxygeraniol geraniol 8-hydroxylase Geraniol diphosphatase diphosphate transtransferase Dimethylallyl
shikimate kinase
8-hydroxygeraniol diphosphate
Shikimate-3-phosphate dehydrogenase

(6E)-8-oxogeranial hydroxylase iridotrial hydroxylase 7-deoxyloganetate hydroxylase loganate Loganate O-methyltransferase loganin
3-phosphoshikimate
1-carboxyvinyltransferase
Methyltransferase 7-deoxyloganin 7-deoxyloganin 7-hydroxylase
secologanin synthase
5-O-(1-Carboxyvinyl)-3- Chorismate anthranilate Anthranilate
chorismate anthranilate
phosphoshikimate synthase synthase phosphoribosyltransferase Indole Trytophan aromatic-L-amino-acid Tryptamine secologanin
decarboxylase
tryptophan synthase
N-(5-phospho-β- Phosphoribosylanthranilate 1-(2-Carboxyphenylamino)- indole-3-glycerol-
nbosyl)-anthranilate isomerase 1’-deoxy-nbulose 5-phosphate (3-Indoyl)-glycerolphosphate
phosphate synthase
4,21-Dehydrocorynantheine Strictosidine- 3alpha(S)-strictosidine Strictosidine
4,21-Dehydrogeissoschizine Dialdehyde 3-α(S)-Strictosidine
aldehyde aglycone beta-glucosidase synthase
cytochrome P450
Geissoschizine Polyneuridine Polyneuridine
dehydrogenase
Geissoschizine
aldehyde aldehyde esterase
16-Epivellosimine Aminotransferase Dendrobine
N-methyltransferase

Fig. 2  Biosynthesis of dendrobine in Dendrobium. This pathway was a-enzym​es.org/. The green cells indicate intermediates, blue cells
constructed based on recent transcriptional studies on Dendrobium indicate enzymes, and orange cells indicate the cloned and function-
(Table  5) and related KEGG pathways listed in http://www.brend​ ally studied genes in Dendrobium 

et al. 2018a). Currently, ITS might be suitable and cred- More, the PCR and electrophoresis based molecu-
ible for interspecific identification of Dendrobium (Xu et al. lar markers, such as AFLP, TRAP, RAPD, DAMD, ISSR
2015; Jiang et al. 2018; Wang et al. 2018a). and SCoT, had also been employed for identification of

13

780 Planta (2018) 248:769–784

circadian clock photoperiod

a Vernalization
pollination
Low temperature DnGI gibberellin
DcCOL
DnELF
ethylene
DnEMF2 DnVRN1
DnCLF DnVRN3 DoGID DSCKX1
DoFRI DnCO
DnVIN3 DnMSI1 DhCKX
chilling
DnHOS1 DwMYB4 DthyrAG1
DnAGL19 Cytokinin DthyrAG2
DnLFY DwMYB9
DnFPA DcOAG1
Den-ERS1 DenCEL
DoFCA DnFT
Denb-GAL
DoAP1 DnFY DnSOC1
Auxin DenPME
DcOAP3A DoSOC1
DOMADS1 ovule development
DOH1 DOMADS2 DnARF
DOMADS3

DcOAP3A DcOPI DcOSEP senescence

flowering abscission
b

PH Anthocyanins
c p-coumaroyl-
Leucoanthocyanidins Orange
dihydroflavonol anthocyanidin synthase
Dihydroquercetin Leucocyanidin cyanidin
CoA 4-reductase
malonyl-CoA flavonoid 3’-
DhMYB2 DhbHLH1 DnANS Red
hydroxylase DnDFR
DnCHS dihydroflavonol
chalcone synthase Dihydrokaempferol Leucopelargolidin anthocyanidin synthase pelargonidin
4-reductase
DmF3’5’H Magenta
Chalcones flavonoid 3’,5’- dihydroflavonol Leucodelphinidin delphinidin
Dihydromyricetin anthocyanidin synthase
flavanone hydroxylase 4-reductase
White Purple
chalcone isomerase 3β-hydroxylase
flavonol
Flavonols Yellow
synthase
Naringenin flavonesynthase flavones

Fig. 3  Regulation of flowering and flower colors in Dendrobium. Dendrobium nobile with different colors. c Biosynthesis of anthocya-
a Environmental factors and genes involved in flowering and senes- nins and flavonoids involved in flower color
cence of Dendrobium. b Under-flowering and flowered flowers of

Dendrobium (Feng et al. 2015a; Bhattacharyya and Kuma-
ria 2015; Bhattacharyya et al. 2015, 2017). However, more
or less of deficiencies presented in these markers, such as
limited number of available markers, low rate of genome
coverage, difficulty of polymorphism distinguishing, and
poor of repeatability (Feng et al. 2013, 2015a; Bhattacharyya
et al. 2017). Along with insights into Dendrobium genome,
development and application of SSR markers were increased
rapidly in recent years (Table 6). And they showed potential
values in identification of Dendrobium species and herbs
(Xu et al. 2017b; Li et al. 2017d). SNP markers and reduced-
representation genome sequencing were also employed for
identification (Roy et al. 2017; Lu et al. 2018). The newly
developed molecular markers would meet the requirement

13
Planta (2018) 248:769–784 781
for intraspecific identification, fast and convenient detection
of herbs (Jiang et al. 2018; Wang et al. 2018a). Additionally,
the linkages of molecular markers to some biochemical traits
were also identified (Bhattacharyya et al. 2015, 2017; Lu
et al. 2018). And more molecular markers closely linked
to medicinal and ornamental traits would be necessary for
further commercial application of Dendrobium.
Conclusions
The aim of this review was to summarize the genome-related
studies in recent years, and to provide some insights into
research interests in Dendrobium. Along with the reveal-
ing of genomic sequences in D. officinale/catenatum, some
well-used methods and technologies in other plants had
been applied on Dendrobium. And the biosynthesis of some
important metabolites, such as polysaccharide and dendrob-
ine, and process of plant development, such as floral transi-
tion and seed germination, were better understudied. Some
other basic researches, such as genetic studies, gene cloning,
and molecular marker developments were also improved.
But still, there are difficulties in genomic sequencing, genetic
mapping, functional characterizing of genes, conjoint analy-
sis of omics. To better understand the mechanisms and uti-
lize the resources, genome-wide researches and applications
might be a breakthrough direction in Dendrobium.
Author contribution statement  ZS, HY and ZR designed the
outline of the article, ZS wrote the paper, HY and ZR com-
posed the manuscript and figures. YS, ZX and ZT completed
literature retrieval and primary analysis. CZ provided scien-
tific feedback and critical comments and revised content. All
authors read and approved the manuscript.
Acknowledgements  Financial supports from Sichuan Provincial
13th Five-Year Breeding Program of Traditional Chinese Medicine
(2016NYZ0036), Science and Technology Service Network Initiative
(STS) Program of China Academy of Science, Keypoint Research Pro-
gram of Sichuan Province (2017SZ0020, 2017SZ0022), Science and
Technology Support Program of Sichuan Province (2016JZ0015), and
Science and Technology Basic Condition Platform Program of Sichuan
Province (2017TJPT0022) are gratefully acknowledged.
References
An H, Zhu Q, Pei W, Fan J, Liang Y, Cui Y (2016) Whole-transcrip-
tome selection and evaluation of internal reference genes for
expression analysis in protocorm development of Dendrobium
officinale Kimura et Migo. PLoS ONE 11:e0163478
Azuma M, Morimoto R, Hirose M, Morita Y, Hoshino A, Iida S,
Oshima Y, Mitsuda N, Ohme-Takagi M, Shiratake K (2016) A
petal-specific InMYB1 promoter from Japanese morning glory:
a useful tool for molecular breeding of floricultural crops. Plant
Biotechnol J 14:354–363
Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M,
dePamphilis VAAC, Aono N, Aoyama T, Ambrose BA, Ashton
NW et al (2011) The compact Selaginella genome identifies
changes in gene content associated with the evolution of vas-
cular plants. Science 332:960–963
Begum R, Sultana SS, Alam SS (2010) Comparison of CMA-karyo-
types in three Dendrobium spp. Cytologia 75:185–188
Bhattacharyya P, Kumaria S (2015) Molecular characterization of
Dendrobium nobile Lindl., an endangered medicinal orchid,
based on randomly amplified polymorphic DNA. Plant Syst
Evol 301:201–210
Bhattacharyya P, Kumaria S, Tandon P (2015) Applicability of ISSR
and DAMD markers for phyto-molecular characterization and
association with some important biochemical traits of Dendro-
bium nobile, an endangered medicinal orchid. Phytochemistry
117:306–316
Bhattacharyya P, Ghosh S, Mandi SS, Kumaria S, Tandon P (2017)
Genetic variability and association of AFLP markers with
some important biochemical traits in Dendrobium thyrsiflo-
rum, a threatened medicinal orchid. S Afr J Bot 109:214–222
Cai J, Liu X, Vanneste K, Proost S, Liu KW, Tsai WC, Chen LJ,
He Y, Xu Q, Bian C et al (2015) The genome sequence of the
orchid Phalaenopsis equestris. Nat Genet 47:65–72
Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-
Berhan A, Jones KM, Redman J, Chen G et al (2010) Draft
genome sequence of the ricin-producing oilseed castor bean.
Nat Biotechnol 28:951–956
Chen SJ, Hu ZH, Li XL, Cheng RY (1985) A preliminary report on
the chromosomes of the homemade Dendrobium. Acta Hortic
Sin 12:119–124
Chen J, Liu SS, Kohler A, Yan B, Luo HM, Chen XM, Guo SX
(2017a) iTRAQ and RNA-Seq analyses provide new insights
into regulation mechanism of symbiotic germination of
Dendrobium officinale seeds (Orchidaceae). J Proteome Res
16:2174–2187
Chen Y, Shen Q, Lin R, Zhao Z, Shen C, Sun C (2017b) De novo
transcriptome analysis in Dendrobium and identification of
critical genes associated with flowering. Plant Physiol Biochem
119:319–327
Chen ZH, Yuan Y, Fu D, Shen CJ, Yang YJ (2017c) Identification and
expression profiling of the auxin response factors in Dendrobium
officinale under abiotic stresses. Int J Mol Sci 18:927
da Silva JA, Winarto B (2016) Somatic embryogenesis in two
Orchid genera (Cymbidium, Dendrobium). Methods Mol Biol
1359:371–386
Devadas R, Pattanayak SL, Singh DR (2016) Studies on cross com-
patibility in Dendrobium species and hybrids. Indian J Genet
76:344–355
Dong XM, Jiang C, Yuan Y, Peng DY, Luo YQ, Zhao YY, Huang
LQ (2018) Application of high-resolution melting analysis for
authenticity testing of valuable Dendrobium commercial prod-
ucts. J Sci Food Agric 98:549–558
Dormont L, Delle-Vedove R, Bessière JM, Schatz B (2014) Floral scent
emitted by white and coloured morphs in orchids. Phytochem-
istry 100:51–59
Fan HH, Wu QJ, Wang X, Wu LS, Cai YP, Lin Y (2016) Molecu-
lar cloning and expression of 1-deoxy-d-xylulose-5-phosphate
synthase and 1-deoxy-d-xylulose-5-phosphate reductoisomer-
ase in Dendrobium officinale. Plant Cell Tissue Organ Cult
125:381–385
Feng S, Zhao H, Lu J, Liu J, Shen B, Wang H (2013) Preliminary
genetic linkage maps of Chinese herb Dendrobium nobile and
D. moniliforme. J Genet 92:205–212
13

782
Feng S, He R, Yang S, Chen Z, Jiang M, Lu J, Wang H (2015a) Start
codon targeted (SCoT) and target region amplification polymor-
phism (TRAP) for evaluating the genetic relationship of Dend-
robium species. Gene 567:182–188
Feng S, Jiang Y, Wang S, Jiang M, Chen Z, Ying Q, Wang H (2015b)
Molecular identification of Dendrobium species (Orchidaceae)
based on the DNA barcode ITS2 region and its application for
phylogenetic study. Int J Mol Sci 16:21975–21988
Gao F, Cao XF, Si JP, Chen ZY, Duan CL (2016) Characterization of
the alkaline/neutral invertase gene in Dendrobium officinale and
its relationship with polysaccharide accumulation. Genet Mol
Res. https​://doi.org/10.4238/gmr.15027​647
Guan R, Zhao Y, Zhang H, Fan G, Liu X, Zhou W, Wang J, Shi C, Liu
W, Liang X et al (2016) Draft genome of the living fossil Ginkgo
biloba. GigaScience 5:49
Guo L, Qiu J, Han Z, Ye Z, Chen C, Xin X, Liu C, Ye CY, Wang YY,
Xie H et al (2015) A host plant genome (Zizania latifolia) after a
century-long endophyte infection. Plant J 83:600–609
He C, Teixeira da Silva JA, Tan J, Zhang J, Pan X, Li M, Luo J, Duan
J (2017a) A genome-wide identification of the WRKY family
genes and a survey of potential WRKY target genes in Dendro-
bium officinale. Sci Rep 7:9200
He C, Wu K, Zhang J, Liu X, Zeng S, Yu Z, Zhang X, Teixeira da
Silva JA, Deng R, Tan J, Luo J, Duan J (2017b) Cytochemical
localization of polysaccharides in Dendrobium officinale and the
involvement of DoCSLA6 in the synthesis of Mannan polysac-
charides. Front Plant Sci 8:173
He C, Yu Z, Teixeira da Silva JA, Zhang J, Liu X, Wang X, Zhang X,
Zeng S, Wu K, Tan J, Ma G, Luo J, Duan J (2017c) DoGMP1
from Dendrobium officinale contributes to mannose content
of water-soluble polysaccharides and plays a role in salt stress
response. Sci Rep 7:41010
He CM, Zeng SJ, Teixeira da Silva JA, Yu ZM, Tan JW, Duan J (2017d)
Molecular cloning and functional analysis of the phosphoman-
nomutase (PMM) gene from Dendrobium officinale and evidence
for the involvement of an abiotic stress response during germina-
tion. Protoplasma 254:1693–1704
He L, Fu S, Xu Z, Yan J, Xu J, Zhou H, Zhou J, Chen X, Li Y, Au
KF, Yao H (2017e) Hybrid sequencing of full-length cDNA
transcripts of stems and leaves in Dendrobium officinale. Genes
(Basel) 8:E257
Hou B, Luo J, Zhang Y, Niu Z, Xue Q, Ding X (2017) Iteration expan-
sion and regional evolution: phylogeography of Dendrobium
officinale and four related taxa in southern China. Sci Rep
7:43525
Huang JZ, Lin CP, Cheng TC, Huang YW, Tsai YJ, Cheng SY, Chen
YW, Lee CP, Chung WC, Chang BC, Chin SW, Lee CY, Chen
FC (2016) The genome and transcriptome of Phalaenopsis yield
insights into floral organ development and flowering regulation.
PeerJ 4:e2017
Huang H, Zi XM, Lin H, Gao JY (2018) Host-specificity of symbiotic
mycorrhizal fungi for enhancing seed germination, protocorm
formation and seedling development of over-collected medicinal
orchid, Dendrobium devonianum. J Microbiol 56:42–48
Jiang JL, Ye W, Li YQ, Zhou JJ, Lei FG, Wei DZ (2014) Growth
and polysaccharides accumulation in autotetraploid Dendrobium
officinale. Plant Physiol J 50:519–526
Jiang C, Luo YQ, Yuan Y, Dong XM, Zhao YY, Huang LQ (2018)
Conventional octaplex PCR for the simultaneous identification of
eight mainstream closely related Dendrobium species. Ind Crops
Prod 112:569–576
Jin Q, Jiao C, Sun S, Song C, Cai Y, Lin Y, Fan H, Zhu Y (2016)
Metabolic analysis of medicinal Dendrobium officinale and Den-
drobium huoshanense during different growth years. PLoS ONE
11:e0146607
13
Planta (2018) 248:769–784
Kaewphalug W, Huehne PS, Sriboonlert A (2017) Characterization of
a CONSTANS-like gene from pigeon Orchid (Dendrobium cru-
menatum Swartz) and its expression under different photoperiod
conditions. Hortic J 86:252–262
Kang JY, Lu JJ, Qiu S, Chen Z, Liu JJ, Wang HZ (2015) Dendrobium
SSR markers play a good role in genetic diversity and phyloge-
netic analysis of Orchidaceae species. Sci Hortic 183:160–166
Konhar R, Biswal DK, Debnath M, Parameswaran S, Sundar D,
Tandon P (2016) Complete chloroplast genome sequence
of Dendrobium nobile from Northeastern India. Genome
Announc. https​://doi.org/10.1128/genom​eA.01088​-16
Kui L, Chen H, Zhang W, He S, Xiong Z, Yan L, Zhang Y, Zhong C,
Chen J, He F, Zeng P, Zhang G, Dong Y, Yang S, Wang W, Cai
J (2017) Building a genetic manipulation tool box for Orchid
biology: identification of constitutive promoters and applica-
tion of CRISPR/Cas9 in the Orchid, Dendrobium officinale.
Front Plant Sci 7:2036
Lau SE, Schwarzacher T, Othman RY, Harikrishna JA (2015) dsRNA
silencing of an R2R3-MYB transcription factor affects flower
cell shape in a Dendrobium hybrid. BMC Plant Biol 15:194
Lei Z, Zhou C, Ji X, Wei G, Huang Y, Yu W, Luo Y, Qiu Y (2018)
Transcriptome analysis reveals genes involved in flavonoid bio-
synthesis and accumulation in Dendrobium catenatum from
different locations. Sci Rep 8:6373
Li J, Chen C, Wang ZZ (2016a) The complete chloroplast genome
of the Dendrobium strongylanthum (Orchidaceae: Epiden-
droideae). Mitochondrial DNA A 27:3048–3049
Li XB, Jackson A, Xie M, Wu DX, Tsai WC, Zhang S (2016b) Pro-
teomic insights into floral biology. Biochem Biophys Acta
1864:1050–1060
Li C, Qiu J, Ding L, Huang M, Huang S, Yang G, Yin J (2017a)
Anthocyanin biosynthesis regulation of DhMYB2 and Dhb-
HLH1 in Dendrobium hybrids petals. Plant Physiol Biochem
112:335–345
Li JL, Zhao Z, Liu HC, Luo CL, Wang HL (2017b) Influence of light
intensity and water content of medium on total dendrobine of
Dendrobium nobile Lindl. Asian Pac J Trop Med 10:1095–1100
Li Q, Ding G, Li B, Guo SX (2017c) Transcriptome analysis of genes
involved in dendrobine biosynthesis in Dendrobium nobile Lindl.
infected with mycorrhizal fungus MF23 (Mycena sp.). Sci Rep
7:316
Li Q, Li B, Guo SX (2017d) SSR information in transcriptome of Den-
drobium nobile. China J Chin Mater Med 42:63–69
Li YY, Chen XM, Zhang Y, Cho YH, Wang AR, Yeung EC, Zeng
X, Guo SX, Lee YI (2018) Immunolocalization and changes of
hydroxyproline-rich glycoproteins during symbiotic germination
of Dendrobium officinale. Front Plant Sci 9:552
Liao DL, Xie L, Zeng RZ, Li YH, Yi MS, Zhang ZS (2012) Relation-
ship between chromosome ploidy and morphology characters in
Dendrobium. Acta Bot Boreal Occident Sin 32(10):2023–2029
Ling H, Zeng X, Guo S (2016) Functional insights into the late embry-
ogenesis abundant (LEA) protein family from Dendrobium offici-
nale (Orchidaceae) using an Escherichia coli system. Sci Rep
6:39693
Liu XR, Pan T, Liang WQ, Gao L, Wang XJ, Li HQ, Liang S (2016)
Overexpression of an Orchid (Dendrobium nobile) SOC1/TM3-
like ortholog, DnAGL19, in Arabidopsis regulates HOS1-FT
expression. Front Plant Sci 7:99
Lu JJ, Zhao HY, Suo NN, Wang S, Shen B, Wang HZ, Liu JJ (2012a)
Genetic linkage maps of Dendrobium moniliforme and D. offici-
nale based on EST-SSR, SRAP, ISSR and RAPD markers. Sci
Hortic 137:1–10
Lu JJ, Wang S, Zhao HY, Liu JJ, Wang HZ (2012b) Genetic linkage
map of EST-SSR and SRAP markers in the endangered Chi-
nese endemic herb Dendrobium (Orchidaceae). Genet Mol Res
11:4654–4667
Planta (2018) 248:769–784 783
Lu J, Liu Y, Xu J, Mei Z, Shi Y, Liu P, He J, Wang X, Meng Y, Feng S,
Shen C, Wang H (2018) High-density genetic map construction
and stem total polysaccharide content-related QTL exploration
for Chinese endemic Dendrobium (Orchidaceae). Front Plant Sci
9:398
Luo J, Hou BW, Niu ZT, Liu W, Xue QY, Ding XY (2014) Com-
parative chloroplast genomes of photosynthetic orchids: insights
into evolution of the Orchidaceae and development of molecular
markers for phylogenetic applications. PLoS ONE 9:e99016
Meng YJ, Yu DL, Xue J, Lu JJ, Feng SG, Shen CJ, Wang HZ (2016)
A transcriptome-wide, organspecific regulatory map of Dend-
robium officinale, an important traditional Chinese orchid herb.
Sci Rep 6:18864
Miguel TP, Leonhardt KW (2011) In vitro polyploid induction of
orchids using oryzalin. Sci Hortic 130:314–319
Mochida K, Sakurai T, Seki H, Yoshida T, Takahagi K, Sawai S, Uchi-
yama H, Muranaka T, Saito K (2017) Draft genome assembly
and annotation of Glycyrrhiza uralensis, a medicinal legume.
Plant J 89:181–194
Niu SC, Huang J, Zhang YQ, Li PX, Zhang GQ, Xu Q, Chen LJ, Wang
JY, Luo YB, Liu ZJ (2017a) Lack of S-RNase-based gameto-
phytic self-incompatibility in Orchids suggests that this system
evolved after the monocot–eudicot split. Front Plant Sci 8:1106
Niu Z, Xue Q, Wang H, Xie X, Zhu S, Liu W, Ding X (2017b) Muta-
tional biases and GC-biased gene conversion affect GC content
in the plastomes of Dendrobium genus. Int J Mol Sci 18:E2307
Niu Z, Xue Q, Zhu S, Sun J, Liu W, Ding X (2017c) The complete
plastome sequences of four Orchid species: insights into the evo-
lution of the Orchidaceae and the utility of plastomic mutational
hotspots. Front Plant Sci 8:715
Niu Z, Zhu S, Pan J, Li L, Sun J, Ding X (2017d) Comparative analysis
of Dendrobium plastomes and utility of plastomic mutational
hotspots. Sci Rep 7:2073
Niu Z, Pan J, Xue Q, Zhu S, Liu W, Ding X (2018) Plastome-wide
comparison reveals new SNV resources for the authentication of
Dendrobium huoshanense and its corresponding medicinal slice
(Huoshan Fengdou). Acta Pharm Sin B 8:466–477
Peng XF, He T, Chun Z, Hu YD, Wan RL (2015) Interspecific and
intraspecific identification of Dendrobium based on the psbA-
trnH intergenic region sequences and the 5S rRNA gene spacer
sequences. Chin J Appl Environ Biol 21:887–896
Phetsirikoon S, Paull RE, Chen N, Ketsa S, Doornd WG (2016)
Increased hydrolase gene expression and hydrolase activity in
the abscission zone involved in chilling-induced abscission of
Dendrobium flowers. Postharvest Biol Technol 117:217–229
Pinheiro F, Cafasso D, Cozzolino S, Scopece G (2015) Transitions
between self-compatibility and self-incompatibility and the evo-
lution of reproductive isolation in the large and diverse tropical
genus Dendrobium (Orchidaceae). Ann Bot 116:457–467
Roy SC, Moitra K, De Sarker D (2017) Assessment of genetic diversity
among four orchids based on ddRAD sequencing data for conser-
vation purposes. Physiol Mol Biol Plants 23:169–183
Sarathum S, Hegele M, Tantiviwat S, Nanakorn M (2010) Effect of
concentration and duration of colchicine treatment on poly-
ploidy induction in Dendrobium scabrilingue L. Eur J Hortic
Sci 75:123–127
Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M,
Sasamoto S, Watanabe A, Ono A, Kawashima K et al (2008)
Genome structure of the Legume, Lotus japonicus. DNA Res
15:227–239
Sawettalake N, Bunnag S, Wang Y, Shen L, Yu H (2017) DOAP1 pro-
motes flowering in the Orchid Dendrobium Chao Praya Smile.
Front Plant Sci 8:400
Shen C, Guo H, Chen H, Shi Y, Meng Y, Lu J, Feng S, Wang H (2017)
Identification and analysis of genes associated with the synthesis
of bioactive constituents in Dendrobium officinale using RNA-
Seq. Sci Rep 7:187
Shindo K, Kamemoto H (1963) Chromosome numbers and genome
relationships of some species in the nigrohirsutae section of Den-
drobium. Cytologia 28:68–75
Si JP, Wang Q, Liu ZJ, Liu JJ, Luo YB (2017) Breakthrough in key sci-
ence and technologies in Dendrobium catenatum industry. China
J Chin Mater Med 42:2224–2227
Srikulnath K, Sawasdichai S, Jantapanon TK, Pongtongkam P, Peya-
choknagul S (2015) Phylogenetic relationship of Dendrobium
species in Thailand inferred from chloroplast matK gene and
nuclear rDNA ITS region. Hortic J 84:243–252
State Pharmacopeia Committee of China (2015) Pharmacopoeia of
People’s Republic of China. The Medicine Science and Tech-
nology Press of China, Peking
Tang H, Zhao T, Sheng Y, Zheng T, Fu L, Zhang Y (2017) Dendro-
bium officinale Kimura et Migo: a review on its ethnopharma-
cology, phytochemistry, pharmacology, and industrialization.
Evid Based Complement Altern Med 2017:7436259
Teixeira da Silva JA, Ng TB (2017) The medicinal and pharma-
ceutical importance of Dendrobium species. Appl Microbiol
Biotechnol 101:2227–2239
Teixeira da Silva JA, Jin XH, Dobránszki J, Lu JJ, Wang HZ, Zotz G,
Cardoso JC, Zeng SJ (2016) Advances in Dendrobium molecu-
lar research: applications in genetic variation, identification
and breeding. Mol Phylogenet Evol 95:196–216
Thongkum M, Burns P, Bhunchoth A, Warin N, Chatchawankan-
phanich O, van Doorn WG (2015) Ethylene and pollination
decrease transcript abundance of an ethylene receptor gene in
Dendrobium petals. J Plant Physiol 176:96–100
Trapnell DW, Beasley RR, Lance SL, Field AR, Jones KL (2015)
Characterization of microsatellite loci for an Australian epi-
phytic orchid, Dendrobium calamiforme, using Illumina
sequencing. Appl Plant Sci 3:1500016
Vichiato MRDM, Vichiato M, Pasqual M, Rodrigues FA, Castro
DMD (2014) Morphological effects of induced polyploidy in
Dendrobium nobile Lindl. (Orchidaceae). Crop Breed Appl
Biotechnol 14:154–159
Wan RL, Sun J, He T, Hu YD, Zhao Y, Wu Y, Chun Z (2017) Cloning
cDNA and functional characterization of UDP-glucose pyroph-
osphorylase in Dendrobium officinale. Biol Plant 61:147–154
Wang LA, Xu JL (1989) The chromosome number of Dendrobium I.
10 species. J Wuhan Bot Res 7:112–114 + 209–210
Wang LR, Wang SQ, Niu JF, Wang SP, Wang ZZ (2017a) The com-
plete chloroplast genome sequence of an endangered species,
Dendrobium pendulum Roxb. (Orchidaceae). Conserv Genet
Resour 13:1–3
Wang W, Yu HY, Li TH, Li LX, Zhang GQ, Liu ZJ, Huang TB,
Zhang YX (2017b) Comparative proteomics analyses of pol-
lination response in endangered orchid species Dendrobium
chrysanthum. Int J Mol Sci 18:2496
Wang Y, Liu L, Song S, Li Y, Shen L, Yu H (2017c) DOFT and
DOFTIP1 affect reproductive development in the orchid Den-
drobium Chao Praya Smile. J Exp Bot 68:5759–5772
Wang S, Hou F, Zhao J, Cao J, Peng C, Wan D, Guo J (2018a)
Authentication of Chinese herbal medicines Dendrobium spe-
cies and phylogenetic study based on nrDNA ITS sequence. Int
J Agric Biol 20:369–374
Wang T, Song Z, Wei L, Li LB (2018b) Molecular characterization
and expression analysis of WRKY family genes in Dendrobium
officinale. Genes Genomics 40:265–279
Wen Z, Guo W, Li J, Lin H, He C, Liu Y, Zhang Q, Liu W (2017)
Comparative transcriptomic analysis of vernalization- and
cytokinin-induced floral transition in Dendrobium nobile. Sci
Rep 7:45748
13

784
Wilfret GJ, Kamemoto H (1969) Genome and karyotype relation-
ships in the genus Dendrobium (Orchidaceae). I. Crossability.
Am J Bot 56:521–526
Wu ZG, Jiang W, Chen SL, Mantri N, Tao ZM, Jiang CX (2016)
Insights from the cold transcriptome and metabolome of Den-
drobium officinale: global reprogramming of metabolic and
gene regulation networks during cold acclimation. Front Plant
Sci 7:1653
Xu S, Li D, Li J, Xiang X, Jin W, Huang W, Jin X, Huang L (2015)
Evaluation of the DNA barcodes in Dendrobium (Orchidaceae)
from mainland Asia. PLoS ONE 10:e0115168
Xu H, Song J, Luo H, Zhang Y, Zhu Y, Li Q, Xu J, Li Y, Song C, Wang
B et al (2016) Analysis of the genome sequence of the medicinal
plant Salvia miltiorrhiza. Mol Plant 9:949–952
Xu J, Chu Y, Liao B, Xiao S, Yin Q, Su H, Bai R, Dong L, Li X, Qian J
et al (2017a) Panax ginseng genome examination for ginsenoside
biosynthesis. GigaScience 6:1–15
Xu M, Liu X, Wang JW, Teng SY, Shi JQ, Li YY, Huang MR (2017b)
Transcriptome sequencing and development of novel genic SSR
markers for Dendrobium officinale. Mol Breed 37:18
Xue D, Feng S, Zhao H, Jiang H, Shen B, Shi N, Lu J, Liu J, Wang H
(2010) The linkage maps of Dendrobium species based on RAPD
and SRAP markers. J Genet Genomics 37:197–204
Yam TW, Lee YI (2013) Chromosome pairing behaviour in the inter-
specific hybrids of Dendrobium section spatulata. Acta Hortic
977:109–113
Yan WJ, Ding XY (2015) Isolation and characterization of 10 micro-
satellite markers for Dendrobium nobile, a traditional Chinese
tonic medicine. Conserv Genet Resour 7:303–304
Yan L, Wang X, Liu H, Tian Y, Lian J, Hao S, Yang R, Wang X, Yang
S, Li Q et al (2015) The genome of Dendrobium officinale illu-
minates the biology of the important traditional Chinese Orchid
herb. Mol Plant 8:922–934
Yan S, Wan RL, Li Y, He T, Hu YD, Zhang H, Chun Z (2016a)
Researches on the mechanism of self incompatibility of plant S
loci. Sci Focus 11:9–18
Yan W, Niu Z, Zhu S, Ye M, Ding X (2016b) The complete chloroplast
genome sequence of Dendrobium nobile. Mitochondrial DNA A
27:4090–4092
Yan S, Zhao TM, Li YF, Hu YD, Chun Z (2018) Agronomic and qual-
ity traits of different Dendrobium nobile in Hejiang. Chin J Exp
Tradit Med Formulae 24:73–77
Yang P, Zhou H, Qian J, Xu H, Shao Q, Li Y, Yao H (2016) The com-
plete chloroplast genome sequence of Dendrobium officinale.
Mitochondrial DNA A 27:1262–1264
Ye M, Liu W, Xue Q, Hou B, Luo J, Ding X (2017a) Phylogeography
of the endangered orchid Dendrobium moniliforme in East Asia
13
View publication stats
Planta (2018) 248:769–784
inferred from chloroplast DNA sequences. Mitochondrial DNA
A 28:880–891
Ye M, Liu W, Xue Q, Yan WJ, Hou B, Luo J, Ding X (2017b) Phylo-
geography of endangered Dendrobium moniliforme in East Asia
based on mitochondrial DNA sequence variations. Biodivers
Conserv 26:1659–1674
Yeh CM, Liu ZJ, Tsai WC (2018) Advanced applications of next-gen-
eration sequencing technologies to Orchid biology. Curr Issues
Mol Biol 27:51–70
Yu D, Meng Y, Zuo Z, Xue J, Wang H (2016) NATpipe: an integra-
tive pipeline for systematical discovery of natural antisense tran-
scripts (NATs) and phase-distributed nat-siRNAs from de novo
assembled transcriptomes. Sci Rep 6:21666
Yu ZM, He CM, Teixeira da Silva JA, Zhang GH, Dong W, Luo JP,
Duan J (2017) Molecular cloning and functional analysis of
DoUGE related to water-soluble polysaccharides from Dendro-
bium officinale with enhanced abiotic stress tolerance. Plant Cell
Tissue Organ Cult 131:579–599
Zhang GQ, Xu Q, Bian C, Tsai WC, Yeh CM, Liu KW, Yoshida K,
Zhang LS, Chang SB, Chen F et al (2016a) The Dendrobium
catenatum Lindl. genome sequence provides insights into poly-
saccharide synthase, floral development and adaptive evolution.
Sci Rep 6:19029
Zhang J, He C, Wu K, Teixeira da Silva JA, Zeng S, Zhang X, Yu Z,
Xia H, Duan J (2016b) Transcriptome analysis of Dendrobium
officinale and its application to the identification of genes associ-
ated with polysaccharide synthesis. Front Plant Sci 7:5
Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin
YC, Xu Q, Chen LJ et al (2017a) The Apostasia genome and the
evolution of orchids. Nature 549:379–383
Zhang YJ, Song J, Cheng X (2017b) The complete chloroplast genome
sequence of an endangered traditional Chinese medicine plant
Dendrobium candidum (Orchidaceae). Conserv Genet Resour
17:1–3
Zheng SG, Yan S, Hu YD, Zhao RX, Zhao TM, Zhang XQ, Chun Z
(2018) Introduction and imitative wild cultivation of Dendrobium
nobile in north of Sichuan. J Sichuan Univ (Nat Sci Ed). https​://
doi.org/10.3969/j.issn.0490-6756.2018.03.039
Zhong ZM, Zhang GF, Lai XP, Huang S (2016) The complete chloro-
plast genome sequence of a new variety of Dendrobium officinale
‘zhong ke IV hao’. Mitochondrial DNA B 1:669–670
Zhu YF, Meng CC, Zhu LQ, Li DH, Jin Q, Song C, Cai YP, Fan
HH, Lin Y (2017) Cloning and characterization of DoMYC2
from Dendrobium officinale. Plant Cell Tissue Organ Cult
129:533–541