Introduction

Bamboo placed to monocotyledonous plant under Poaceae family and sub family Bambusoideae [1]. There have been diversities of bamboo species found across the globe including India (Fig. 1). Bamboo has three interesting characteristics: peak development pace of 1 m per day (unique to only a few species), blossoming cycle (3 to 120 years) and widespread rhizome (sympodial and monopodial) [2,3,4,5,6]. Bamboo from base to top, as its root (rhizome), stem (culm), and leaf is used in various applications like food, fire wood, hand crafts and therapeutic [7, 8]. Bamboo is widely utilized in pulp and paper industries because of its fibre content [9, 10]. Its natural physical structure of culms (pole) is an appealing component for construction and building businesses, such as material for fortified cement beams [11, 12]. For the past two-decade bamboo has been utilized as fuel, electricity, biochar and charcoal which is an efficient way of controlling environmental contamination [13,14,15,16,17]. Previous studies on physico-chemical properties and mechanical strength of bamboo (rhizome, culm, and leaves) confirms that bamboo species are being utilized in numerous different ventures to deliver various items like furnishings, woven items, trimming/painstaking work, flooring, fibreboard, boards, mash, paper, development/building material, rustic uses, fuel, non-private/horticulture, pressing, and transport [2, 18,19,20]. Bamboo plantations and its biomass has been practiced in improvement of ecological restoration of degraded/contaminated lands and conversion of mine degraded sites into carbon sinks [11, 21]. Bamboo farming is done using rhizome, tissue culture, or small branch cutting directly without any further verification leads to mis identification and mis classification of bamboo species.

Fig. 1
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Distribution of Bamboo species in India with respect to world

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Several traditional identification and classification systems were deployed in the field of bamboo research previously. Researchers/investigators classified bamboo in to 67 genera in nine sub‐tribes, on the basis of floral characters such as flower [22], inflorescence [23], ovary and seed [24]. Bamboo species have an unusual life cycle, which diverges from one species to other; vast difference in vegetative growth phase with minimum from one year to maximum up to 120 years. Moreover, some of the species have not been reported flowering in their life cycle [25]. Further, floristic identification of these sterile bamboos is a serious problem and it does not have any solution in systematic classification, where, taxonomic studies are depended completely on floristic characters; moreover, vegetative characters could rapidly change or influenced by various environmental factors, such as soil, climatic factors etc., [26, 27]. Therefore, classification or identification of these bamboos using molecular approach is the best option to overcome problems in systematic classification [28]. Furthermore, utilizing DNA markers could provide solutions to systematic classification as an alternative approach in the studies of bamboo phylogeny and identification (Table 1). In 1997, Molecular identification studies by Clark and Kobayashi on woody bamboos have confirmed a linkage between temperate and tropical woody bamboos (New World and Old World) [29, 30].

Table 1 List of markers along with its various characteristics [31,32,33,34,35,36,37,38,39,40,41,42,43,44,45]
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Currently, the application of advance molecular-based technology has become more prominent for characterization, taxonomic and systemic studies of organisms [46,47,48]. Also, several published researches emerge out in last decade related to application of barcode in identification of plants species (Fig. 2). These methodologies consist of RAPD (random amplified polymorphic DNA) [49], AFLP (amplified fragment length polymorphism), RFLP (restriction fragment length polymorphism), ISSR (inter simple sequence repeat), iPBS (inter primer binding site), and SCoT (start codon targeted). These molecular markers give accurate and detailed information regarding the genetic diversity [41, 50, 51], phylogenetic interactions [52, 53] and species-specific marker [54]. DNA barcoding is only one of its kind methods for characterization and classification of several organisms at species level as well genus level. The last decade witnessed the potentialities of DNA barcoding as a promising tool to supplement the species recognition in plants as well as in animals. RFLP, RADP and AFLP markers used to investigate species identification and creating phylogenetic relationships between various species of Bambusa, Dendrocalamus and Phyllostachys species [55,56,57,58]. Some other researchers used ISSR markers and expressed sequence tag (EST) based primers to find molecular relationship among the bamboo species [59, 60].

Fig. 2
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Publication status of DNA barcode and Bamboo DNA in last decade

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The present review is designed to consider above facts and focus to prepare a framework with respect to the application and mechanism of DNA barcoding in identification and characterization of bamboo species. A detailed discussion on, how this method overrides the traditional identification and classification methods, along with opportunities, challenges and prospects for future research.

Traditional System of Classification Versus DNA Barcoding

Traditional system of plant identification i.e., floral taxonomy has several problems that hinder it progress. Few plants species are only known from their original descriptions and several others are yet to be identified [61]. Morphological categorization of plant species is generally reliant on vegetative features that are simply governed by environmental variables [26]. Morphological systematic is based on morphological features, comparative anatomy and other vegetative characteristics [62]. Systematic identification would be beneficial in visual determination of species at various levels of classification by using their macromorphological characters, however, there are many drawbacks in the systematic [59]. Morphological characteristics, the properties of culm/culm sheaths and leaves are highly crucial to distinguish or identify bamboo species only in its matured state or in the farming field but this method is not always reliable. Table 2 describes 7 key attributes of bamboo which are used for species identification in the traditional method by most of the people who work in the bamboo sector from farm to industry. Bamboo culms height, diameter, and internode length are the countable quality yet can't be used in species identification purpose (Fig. 3). These three attributes (culms height, width, and internode length) are not valuable to distinguish among same genus species like Dendrocalamus (hamiltonii and latiflorus) because these two species have roughly same tallness (20 m), same width (16 cm), same internode length (45 cm). Likewise, Gigantochloa (apus and pseudoarundinacea). Not only that, but this attribute is not adequate to compare and distinguish between different genus as (Bambusa bambos and Gigantochloa levis), (Dendrocalamus asper and Bambusa balcooa), (Bambusa vulgaris and Cephalostachyum pergracile), (Bambusa tulda, Gigantochloa atroviolacea and Melocanna baccifera), (Thyrsostachys oliveri and Bambusa cacharensis) and (Bambusa nana, Gigantochloa rostrate and Ochlandra scriptoria) [7].

Table 2 A comparison of the 7 key attributes of culm, culm-sheath and leaves descriptors used to evaluate phylogenetic relationships among 22 bamboo species from 7 genera: A—average culm height (m), B—average culm diameter (cm), C—average culm internode length (cm), D—average culm-sheaths length at base (cm), E—average culm-sheaths breadth at base (cm), F—average leaves length (cm), G—average leaves width (mm)
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Fig. 3
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Species from different genus which are showing similar value for attributes of culm (height, diameter and internode length), sheaths (length and breadth), leaves (length and width) [31, 63,64,65,66]

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Therefore, the traditional method of bamboo species identification depends on these attributes is not reliable. In some species, the morphological characters typically used in the conventional taxonomic classification of bamboos show similar affinities. In addition, recognition and grouping of bamboo using anatomical characteristics have failed to prove effective. Various taxonomists have identified the same bamboo species in separate genera or same species which have culminated in several revisions in different genera during the last several decades. Due to the high degree of morphological resemblance, in the field recognition of certain bamboo species is exceedingly challenging even for a taxonomy specialist. Therefore, identifying bamboo species on their physical and morphological characteristics is not reliable.

DNA polymorphism is the substitute for traditional systematic to differentiate individuals or species and classify them according to molecular approach to overcome systematic classification problems. DNA barcoding is best biotechnological approach to subsidise the complications of traditional taxonomy [67]. Short sequence of genome (< 1000 bp) acting as a “DNA barcode’, which could be able to identify a species or a taxonomical group. The study “DNA barcode” expresses that the uniform genetic sequences can categorize taxon in the identical manner as the 11-digit Worldwide merchandise Code recognizes retail merchandises in market [68].

Molecular operational taxonomic unit (MOTU) is a molecular system for identification of various taxa. It is fast and perfect identification tool, and also useful in solving problems in species evolution point of view. Lambert et al., [69] studied diversity of the Earth’s biota by using molecular approach by means of DNA barcoding. Generally, to study DNA barcode includes several key attributes, which include the DNA marker used as a barcode sequence should be appropriate for wide range of taxa, it should able to differentiate among various species and should be conserved within the species, therefore the intraspecific deviation will be non-significant [70, 71]. DNA barcode correspond to the sequence in the form of nucleotides ATCG, which representing adenine, thymine, cytosine and guanine. DNA barcoding could able to serve dual purpose as an advanced device in the new era taxonomists in the enhancement of systematic knowledge as well as being an modern tool for non-taxonomists who require to create a speedy classification [72]. In recent days, there are several researchers are attempting and creating multiple genomic databases, these databases are open for all and any one can use out of it for the classifying the organism/s [73]. The purpose of creating this molecular systematic approach is to facilitate and validate the existing morphological species identifications and support the speeding up of species discoveries and solving the problems in systematic approach through creation of these barcode databases [74]. Molecular database is relatively an easy approach to compare species in a group or identify individual species and to determine distance correlation between the species [75].

Application of DNA Barcoding Technology in Bamboos

Utilization of molecular marker is one of best approaches to overcome the difficulties in identification of genotypes in bamboos [76]. Various DNA sequences were worked out to surmise phylogenetic interactions among the bamboos, however, deviation among the studied DNA sequence was very less or various DNA markers have showed similarity in the studied species [77,78,79,80]. Table 3 summarizes the molecular approaches consequently carry light to the challenging field in the taxonomical classification of several bamboos sp. at various systematic level.

Table 3 Summary of work done on molecular taxonomy of different bamboos
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Molecular markers techniques such as SSR, ISSR, RFLP, RAPD, SCoT, AFLT and SNP were in use by several researchers to distinguish the bamboos at species or generic levels. Glimpses of these techniques being used in identification, classification, characterization, cluster analysis or genetic mapping of bamboo species across the world as follows:

Simple Sequence Repeat (SSR)

Microsatellites also known as simple sequence repeats (SSR), which are comprised of short tandem repeated sequence motifs (1–6 bp in length). Genomic SSR markers have become the most common markers of choice for mapping the genes, fingerprinting of genomes and study the genetic diversity with highly reproducible data [112]. In previous studies, by Nayak and Rout, demonstrated the polymorphism of different bamboo species by Locus Ba10 amplified and characterized four bamboo species such as Bamboosa clarata, B. vulgaris, B. vulgaris var striata and B. ventricosa; further, Locus Ba20 was amplified in Dendrocalamus strictus. In recent studies, the species diversity was demonstrated among 803 moso bamboo genotypes from 34 populations with the help of 20 fluorescently labelled SSR markers [56]. Previous studies have developed 15 caespitose bamboo EST-SSR markers to identify the sequence polymorphism across the bamboo species of Bambusa edulis, Bambusa oldhamii, Phyllostachys pubescens and related species [113]. Moreover, the transferability among various bamboo species varies from 30–100%. Characteristics of 20 polymorphic microsatellite loci for Phyllostachys edulis was established with primer sequences, which will be useful in study the population genetics and conservation of the species [114]. Biogeographic history of Bambusa arnhemica from Australia was established using SSR primers [115]. SSR markers will be useful as a tool in understanding the relationship between various intra/inter bamboo species, phylogeny, ecological structure and its diversity. Characteristics of some of SSR markers being used in identification and classification of bamboo species were tabulated in Table 4.

Table 4 Various SSR primers used in identification of bamboo species
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Inter Simple Sequence Repeat (ISSR)

ISSR markers are more resourceful and reliable as it is based on longer primer sequence. ISSR markers have been widely used to identify taxonomic classification of closely resembled species, population genetics studies and phylogenetic characterization. Amom et al. [32] constructed a phylogenetic tree using ten ISSR primers and found similarity matrix between 15 North-East Indian bamboos such as Bambusa tulda, B. nutan, B. mizorameana, B. vulgaris and B. manipureana; Dendrocalamus giganteus, D. hamiltonii, D. sikkimensis, D. hookeri, D. Longispathus and D. Manipureanus; and Schizotachyum dullooa, S. pergracile, S. Munroi and S. fuchsianum. They constructed a genetic relationship between the genus and between the species and expressed disagreement with traditional system of classification. ISSR markers also found beneficial in identifying cross bred of Phyllostachys kwangsiensis and Phyllostachys bambusoides [116]. Mukherjee et al., [60] studied genetic relationships among 22 taxa of bamboo by using twelve ISSR random primers, resulting in amplification of 220 loci and classified several bamboo species (Table 5). Gami et al., [83] collected twenty bamboo accessions from different regions of India and classified bamboo species based on eight ISSR primers. Some known ISSR primers have been used in previous studies to classify bamboo species are given in Table 5.

Table 5 Various ISSR primers used in identification of bamboo species
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Random Amplified Polymorphic DNA (RAPD)

RAPD is rapid and efficient technique to screen polymorphism among the species as it is directed with a single, arbitrary and short oligonucleotide primer. In this technique arbitrary primers will be used as a tool for the detection of DNA polymorphism. RAPD technique has showed positive results in identification of genetic relationships between various bamboo genera and species such as, Cephalostachyum, Dendrocalamus, Dinocloa and Sasa using 10 RAPD primers [117]. Several other researchers studied the phylogenetic relationships among the bamboo species viz., Bambusa, Denderocalamus, Melocana, Oxytenanthera, Phyllostachys, Schizostachyum, Teinostachyum, Thyrsostachysby with the help of polymorphic loci of the genomic DNA generated by RAPD [100]. Further, Annisa et al., [118] also studied the genetic relationship between 25 bamboo species of Indonesia such as Bambusa, Dendrocalamus, Dinochloa, Gigantochloa and Schizostachyum by using RAPD technique. Moreover, RAPD technique could be used to draw phylogenetic tree between closely resembled species and to eliminate distantly related species of bamboos [117]. Some characteristics of known RAPD primer sequences have been given in Table 6.

Table 6 Various known RAPD primers used in identification of bamboo species
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Amplified Fragment Length Polymorphism (AFLP)

AFLP method is a robust and reliable assay to detect genetic polymorphism. Moreover, this technique will be of great use in comparing a large number of genetic loci parallel being functioning under rigorous conditions of experimentation and thereby providing high reproducible results with good precision rate. In previous studies, AFLP was used to prepare cluster analysis of species among bamboo genera such as Bambusa, Dendrocalamus, Gigantochloa and Thyrsostachys [55]. Several researchers are in the opinion that AFLPs will be the best tool in identification of inter/inter specific bamboo species and useful in systematic studies and cluster analysis within the sub tribe. In China, Phyllostachys violascens cultivars were studied by using fifteen primer combinations of AFLP markers to identify genetic diversity among cultivars and found it is more efficient than other genomic techniques [119]. Some known AFLP markers have been presented in Table 7.

Table 7 Various known primer and adapter sequences for AFLP analysis of bamboo species
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Restriction Fragment Length Polymorphism (RFLP)

The technique RFLP uses the combination of restriction enzymes and finds the variation in the banding pattern and reveals the genetic diversity. It is a significant molecular tool in the field of fingerprinting, mapping and paternity testing. Konzen et al., [120] studied variation among species of Bambusa, Dendrocalamus, Guadua and Phyllostachys by using RFLP techniques and constructed genomic library. Previously, Friar and Kochert distinguished 20 species of Phyllostachys by using RFLP and examined the degree of genetic variation, genetic distances and constructed dendrograms for 61 accessions [121].

Start Codon Targeted (SCoT)

SCoT technique will find the polymorphisms using reproducible markers based on the short-conserved region of the genomic sequence surrounding the ATG codon translation start or initiation codon. Previous studies showed that ScoT markers have been useful in discriminating the Bamboo species compared to other molecular techniques [31]. Recently, Amom et al., [2020], used SCoT technique to identify genetic relationship between commercial Bamboo species such as Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. Sikkimensis from North-East India. Furthermore, dendrogram analysis based on UPGMA (Unweighted Pair Group Arithmetic Mean Method) demonstrated species-specific clustering of this five bamboo species and found that all molecular techniques used for this study were having close association except RAPD [31].

Single-Nucleotide Nolymorphism (SNP)

These are position in genome where some individuals have one nucleotide (G) and others have a different nucleotide (T) and it is referred as single-nucleotide polymorphism (SNP) or ‘Snips’ [122]. For example, two sequenced DNA fragments from different individuals—CTTAGGTTCGAA and CTGAGGTTCGAA—contain variation in a single nucleotide, that is, G or T. It is genes specific marker and its detection is more rapid because it is based on oligonucleotide hybridization analysis. Species identification was achieved by detecting allelic variations of these type of markers.

Complete phylogeny of bamboo which included bamboo tribes and its subtribes was presented in the form of molecular database by using chloroplast genome of 6.7 kb of coding nucleotide and noncoding nucleotide sequence data and characteristics of 37 microstructure [123]. Classical taxonomy contributes a major role in classifying various bamboo species. However, molecular approach i.e., DNA barcoding can certainly support the traditional system of classification and also make possible identification process more consistent and easier. In India, several researchers are working on preparation of barcodes belong to various plant and animal species (Table 8).

Table 8 Barcoding efforts in India made so far
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Recognizing bamboo species by DNA barcode is fundamental, since it can precisely distinguish bamboo species in their adolescent stage [81]. Along with these, recognizable proof of the species is useful in bamboo industries as well as in commercial bamboo farming. Surrounding atmosphere plays a critical role in the development and growth of bamboo, hence, this barcoding technology can help the farmer in choosing the species that are the best for growth and development of bamboo in specific climatic conditions [137]. DNA standardized barcode is additionally utilized for building DNA barcode library which further utilized for contrasting and recognizing DNA barcode sequences recuperated from obscure DNA samples [138]. This technology is not only used for identification and classification of species but also has to protect endangered species, preserving natural resources, pharmaceutical, wildlife forensic, authentication of natural health products, illegitimate trading and even amusing activities [74, 90, 139, 140].

Bamboo identification is regularly troublesome because of its sporadic flowering pattern and its long reproducing cycle which changes in each species [141], yet by utilizing DNA barcoding, identification can be made with much simplicity and accuracy. Bamboo has genetic material as DNA, and despite the fact that two closely species have a place with a similar family or genera have contrasted in their DNA [142]. DNA is the genomic material which differs in size from millions to billion according to species and their family, the Moso bamboo’s (Phyllostachys pubescens) whole genome size has been evaluated to be around 2034 Mb [143]. DNA barcoding isn't new, yet the first run through came well known in the year 2003, when Paul Hebert's published a research namely ‘Biological identifications through DNA barcodes’, that presented a global biological distinguishing proof framework for creatures utilizing mitochondrial gene cytochrome c oxidase I (COI) [67]. The COI has been broadly exploited in the animal kingdom and suggested to be an appropriate DNA barcode at several taxonomical levels [144, 145]. But due to its lowering rate of evolution, it is not considered as a suitable DNA marker [146]. A variety of DNA markers have been assessed for their performance as a barcode for a variety of land plants [147]. Numerous combinations of DNA markers have been recommended for the barcoding of plants [148].

The technique of DNA barcoding has been advanced for most of the taxonomic challenging lineages in the Poaceae family. DNA barcoding has been proposed a great technique for the identification of grasses species that can be challenging to recognize at the species level [67]. In 2011 Drumwright et al., [149] demonstrated the identification of grass species with 95% accuracy with the use of matK + rbcL as the main core barcode. The maximum coverage of genes in gene bank to study the species diversity of grass and barcoding included gbss1, matK, ndhF, nrITS, phB, rps16, rpoA, rbcL, rpoc2, and trnL, etc. [150,151,152].

In Bamboo, chloroplast region could be utilized as a marker region for identification. In previous study, seven up-and-comer barcoding loci from chloroplast region used to make barcoding with four coding genes such as matK, rbcL, rpoB and rpoC1, and non-coding inserts such as atpF-atpH, psbA-trnH and psbK-psbI. These 7 barcode loci show diverse oppressive force and their position as rpoC1 < rpoB < atpF-atpH < rbcL < matK < psbK-psbI < psbA-trnH [153]. Consortium for the Barcode of Life (CBOL) mentioned that loci rbcL and matK genes are well-known barcodes for the characterization of terrestrial plant species [71, 148]. Moreover in bamboo species, ITS2 and psbA-trnH barcode would be considered as effective barcodes [154]. In previous study by Cai et al., [93] it is demonstrated that some barcoding loci would be useful in species identification in bamboos viz., ITS2, matK, psbA-trnH, and rbcL. Further, the combination of these loci example rbcL + ITS2 would be better barcodes for identification of bamboo species [88]. Figure 4 illustrates the general procedures of DNA barcoding.

Fig. 4
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Schematic representation of DNA barcoding

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Methodology involved in DNA barcoding

The methodology of DNA barcoding includes the following phases starting from DNA extraction, amplification of DNA by polymerase chain reaction (PCR) with the help of universal barcode primers has been shown in Fig. 5. Combination of several primers has been reported to be useful in identification and discrimination of various taxa at species level as well at genus level in the system of molecular approach (Table 9).

Fig. 5
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Schematic representation of PCR components with cycle involve in DNA barcoding

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Table 9 List of routinely used primers in DNA barcoding
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The grouping of the primers sequence from coding region (rbcL, matK and rpoC1) and non-coding region (trnH2-psbA) displayed potential differential insight among the chosen species. Some molecular studies confirmed to identify 48 phylogenetically diverse plant genera by molecular approach i.e. DNA barcoding using nine 9 loci such as, accD, ITS1, matK, rpoC1 ycf5, rbcL-a, rpoB2, trnH-psbA and ndhJ [152, 155]. The DNA barcoding practices involves two fundamental steps: (1) construction of barcode library of identified species and (2) blast the barcode sequence of unidentified species compared to the barcode library intended for identification. Gene Bank has databases of some commercial bamboo species of various genera as Bambusa, Dendrocalamus, Melocanna, Oxytenanthera with their standardized identification for the species-specific region both essential and optional (rbcL, matK and psbA-trnH) (https://www.ncbi.nlm.nih.gov/genbank/). Google has an additional desktop search engine for DNA barcoding. This barcode library can be useful to various government and private agencies for providing agriculture certification to different crops [81, 156,157,158].

Concluding remarks and future prospects

Among the huge diversity of bamboo species, some are more commercial and ecologically important therefore it is necessary to identify such species accurately. Bamboo species recognition, based only on morphology, is a difficult task because it continuously changing and dependent on the environment and mainly due to the absence or long flowering cycle in their entire lifespan. Bamboo plant species characterization with recognizable proof is one of the troublesome errands in agribusiness because of its assortment and distinctive field conditions. Incorrect identification and classification of bamboo species appropriate for various agro-climatic zones can prompt a noteworthy decrease in profitability. It can likewise prompt striking misfortune to farmers if an inappropriate species personality is found a lot later particularly when the species is inadmissible for a particular end-use it was grown for.

DNA barcoding a well-known molecular technique has been observed to be an alternative tool for addressing several taxonomical complexities predominant in bamboo species. DNA barcoding is short and novel for every species of bamboo and its outcome is increasingly accurate, unlike morphological identification. It recognizes species as well as builds up connections between various bamboo species. In addition, it characterizes and recognizes bamboo species without knowing its age, physico-chemical and mechanical properties. This technique has the probability to serve as an innovative method for identifying taxonomically distinct species of bamboo. When, DNA barcode library is well-known and the classification and identification of commercial bamboo species are affordable, it can be used for standardization and certification. DNA barcode can also help to identify the genes which are responsible for quick development, high compressive strength, and high fiber content. DNA barcoding is used to handle the complexity at a taxonomic level not only in the identification of species but also for the selection of planting materials. This technology can act as an innovative molecular tool complementing modern approaches for distinguishing taxonomically difficult species of bamboo. For DNA barcoding, the entire genome sequence and expressive region must be notable ahead of time. Building a DNA barcode library for all bamboo species is expensive and challenging since it has 1575 species and tremendous genome sizes extending from 100 Mbp to 150 Gbp. However, the technology is accurate and reliable, yet expensive because of the inaccessibility of the standardized barcode library for all species. At full scale, this method can be utilized by all bamboo ventures and ranchers for distinguishing species according to their requirements. The government or private agency may give accreditation data modest rate that improves the bamboo trade.