Ethnobotany Genomics is a new emerging discipline which is synthesis of ethnobotany and genomics and based on the ancient knowledge of biodiversity variation among different cultures around the world and combines with modern genomic tools such as DNA barcoding has been applied to various organisms including plants in exploring the natural genetic variability and biodiversity found among various plant groups followed by high-throughput Automated Identification Technology (AIT) system. These are novel approaches that of late have revolutionized especially botanical research and technological innovations and are founded on the concept of ‘assemblage’ of biodiversity knowledge, traditional knowledge (TK) and scientific knowledge (SK) and employs modern genomics technology, as an important tool for identifying cryptic species, which are routinely recognized as ethnotaxa using the TK classification systems of local ethnic cultures in India and elsewhere. This paper reviews some well studied plant species belonging to Acacia, Biophytum, Cardiospermum, Tripogon and minor millets of Tamil Nadu, south India, India, that have been studied recently ethnogenomically and the variations among the cryptic taxa have been identified.
The term genomics was coined by Tom Roderick to describe an approach to the study of DNA at the level of entire genomes, chromosomes, or large clusters of genes and has now emerged as a vital tool for the researchers engaged in plant biodiversity, but also deals with the inventory and management of earth’s immense biodiversity. Identification at the species level is a pre-requisite for quality assurance, identifying the crude plant product and also evaluating its pharmaceutical quality (see Wagner et al., 2011). Genomics in recent times has become a powerful tool for the identification and authentication of biodiversity species (Pereira et al., 2008). As on today, DNA bar coding (Paul D. N. Hebert, founder of DNA barcoding technology) has emerged as an important scientific area that provides a unique forum for exchange of information in biological studies and serves as a rapid and cost-effective method for identifying biodiversity. Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods and bioinformatics to sequence, assemble and analyze the function and structure of genomes, i.e., the complete set of DNA within a single cell of an organism. This study draws on the ancient body of knowledge concerning the variation in biological diversity that is present in different cultures combined
with modern genomic tools such as DNA barcoding or metabarcodes from next-generation sequencers (Wilson et al., 2016) as a modern molecular tool and system for species to identify closely related or newly evolved species. For their short gene sequencing from a standardized region of the genome (Hebert et al., 2003; Kress and Erickson, 2007, 2008, 2009; Newmaster et al., 2006, 2009a; Kun Luo et al., 2010) and enables one to explore the natural genetic variations present among plant species and other organisms. Ethnobotany genomics is a novel approach that has already impacted botanical/zoological research and is bound to create wave in the years to come. The application of DNA barcoding is a new and novel approach to ethno- botany and the term was ethnobotany genomics proposed by Newmaster and Ragupathy (2010). This new branch of science is founded on the concept of ‘assemblage’ of biodiversity knowledge, traditional knowledge (TK) and scientific knowledge (SK) and employs modern genomic technology, DNA barcoding, as an important tool for identifying cryptic species, which were already recognized as ethnotaxa using the TK classification systems of local cultures in the Velliangiri Hills of Tamil Nadu, India (Ragupathy et al., 2009). Ethnobotany genomics engages modern tools that can overcome taxonomic impediments to exploring biodiversity. Biodiversity genomics study as on today involves intensive sampling of organisms at taxonomic levels for the same genomic region and provides a link between variation in taxa, sequence evolution and genomic structure, function, and good estimate of evolutionary process. This approach helps integrate genomic thinking with natural occurring variation in ecosystems to explore biological diversity. DNA barcoding indeed is a critical technique for ethnobotany genomics research. The TK classifies three broad categories of traits: (1) morphological (plant height, seed shape, size, etc.), (2) agricultural (grain yield, drought tolerance, etc.), and (3) cultural value traits (gastronomic and medicinal) to the farmers (Newmaster et al., 2013).
The investigation of plants and their uses has been one of the most primary human concerns and has been practiced by all cultures for tens, if not hundreds, of thousands of years, though it wasn’t called ‘Ethnobotany’ then. Ethnobotany is the scientific study of plant lore and agricultural customs of a people since ancient times. Given their extensive range of knowledge of medicinal plants, indigenous people remain the ultimate resource for retrieving this information for the purpose of application, particularly in modern medicine. Ethnobotany is a rapidly growing science and is now multidisciplinary in nature, attracting people with widely varying academic
background and interests and still predominantly linked to Economic Botany, and hence pursued to determine the potential economic value of various plants as potential sources for life saving drugs that have proven important in the treatment of various serious diseases such as AIDS and cancer and improve healthcare. There is revival of ethnobotany during the last few decades and the subject has become a hot topic of research and new foci have been developed by critical research raising thereby the credibility of Traditional Knowledge (TK) in modern scientific studies which have gained credibility and have evolved considerably in recent times (Schultes, 1962; MacDonald, 2009).
Ethnobotanists describe, document and explain the complex relationships between various cultures and the utility of plants which includes how plants are used, managed and perceived across human societies around the world for food, medicines, textiles, building materials and cosmetics, etc.; within cultural deviation, rituals and religions. On the other hand ethnobotanic genomics is a novel approach that is poised to create botanical discoveries and innovations in a new era of exploratory research which is founded on the concept of assemblage of biodiversity knowledge including species variation and valorizing value to both tradition knowledge and scientific ethnobotany.
The collision, influence and to some extent convergence of eastern knowledge and advance western scientific technology has resulted in a unique synthesis of medical belief and practice, along with the development and processing of innovative and effective drugs both of Traditional Chinese Medicine and Indian Ayurveda, other systems but also the knowledge and practices that have been orally transmitted in various cultures over the centuries (Macdonald, 2009).
Genomics draws on the ancient body of knowledge concerning the variation in biological diversity that is found in different cultures combined with modern genomic tools such as DNA barcoding also explores the natural genetic variations found among higher plants and other organisms. The application of DNA barcoding in a new and novel approach to ethnobotany and Newmaster and Ragupathy (2010) proposed the term “ethnobotany genomics” ‘which is founded on the concept of ‘assemblage’ of biodiversity knowledge, traditional knowledge (TK) and Scientific Knowledge (SK). They employed modern genomic technology, DNA barcoding, as an important tool for identifying cryptic species, which were already recognized ethnotaxa using the TK classification systems of local cultures in the Velliangiri Hills
of Tamil Nadu, India. Ethnobotany genomics engages modern tools that can overcome taxonomic impediments to exploring biodiversity. Contemporary biodiversity genomics include intensive sampling of organisms at taxonomic levels for the same genomic region. This study provides a link between variation in taxa, sequence evolution and genomic structure and function, providing thereby reasonably good estimate of evolutionary process. The approach integrates genomic thinking with natural variation encountered in ecosystems to explore biological diversity. DNA barcoding is an important technique for studying ethnobotany genomics. Bar coding systems in land plants is much more challenging as the plant genome substitution rates are considerably lower than those observed in animal mitochondria, suggesting that a much greater amount of sequence data from multiple loci is needed to barcode plants using a tiered approach wherein highly variable loci are nested under a core barcoding gene. Analysis of over 10,000 rbcL sequences from GenBank demonstrated that this locus could serve well as the core region, with sufficient variation to discriminate among species in approximately 85% of congeneric pair-wise comparisons (Newmaster et al., 2006).
Modern Automated Identification Technology (AIT), using DNA barcoding, provides a rapid, repeatable and reliable tool for identifying ethnotaxa and variation in cryptic species. Recent development of this system for plants identification indicates the efficacy of an AIT system in saving of time, resources, and provides quick, reliable automatable identification (Newmaster et al., 2009a). DNA barcoding has been used widely to discriminate the cryptic ethno-taxa for several plants and to mention few cases: Tripogon (Newmaster et al., 2008b), Cardiospermum halicacabum (Ragupathy et al., 2008a), Biophytum (Newmaster et al., 2010) and Rutaceae (72 genera, 192 species) of China (Kun Luo et al., 2010). These authors proposed that a DNA bar code to be a quick and reliable tool to identify ethnotaxa, which also legitimizes the validity of (TK), rendering it stable, testable, meaningful and globally acceptable.
The impact of ethnobotany genomics has been phenomenal and now has been extended beyond biodiversity science and is being used effectively even for lower and higher animal species. Explorations of the genomic properties across the expanse of life are now possible using DNA barcoding to assemble sequence information for a standard portion of the genome from large assemblages of species. This is in contrast to the usual focus of large- scale genomics projects which acquire sequence information for all genes in single taxon. The barcode region is a genomics entity in which nucleotide
composition of the plant barcode region closely mirror those in the rest of the genome. As the library of species expands it will be possible to flag species whose genomes show unusual nucleotide composition, allowing them to be probed in more detail. Shifts in sequence composition may also reveal idiosyncrasies of sequence and amino acid change. The most important contribution of barcode projects will leave/impact an important legacy; a comprehensive repository of high-quality DNA extracts that will facilitate future genomic investigations. This will also help in correct authentication of genuine ethnobotanicals. The paper reviews some best studied plants from Tamil Nadu, South India.
The genus Acacia family Mimosaceae is an economically important and comprises of about 1350 species and sub-divided into three subgenera: subg. Acacia (c. 161 species), subg. Aculiferum (c. 235 species), and subg. Phyllodineae (c. 960 species), with many cryptic sister species showing pantropical distributions (Maslin et al., 2003; Newmaster and Ragupathy, 2009b). Acacia species are well adapted to arid conditions are of great utility in the forest industry; timber, fuel wood, fiber, medicine, food, handicrafts, domestic utensils, environmental amelioration, soil fertility, livestock fodder, ornamental/horticultural planning, gum, and tannins, etc. (Wickens et al., 1995; McDonald et al., 2001: Midgley and Turnbull, 2003). However, taxonomic ambiguity exits because many Acacia species are difficult to identify on morphological and micromorphological and other related characters (Bentham, 1842; Wardill et al., 2005). Therefore, correct identification is essential to distinguish the rare species (Byrne et al., 2001) and economically useful species (Midgley and Turnbull, 2003). Prickly Acacia (A. nilotica subsp. indica) is an invasive species in northern Australia and believed to have been introduced from India into Australia but the present distribution pattern appears variable throughout India. This variability perhaps includes new species, which could be due to invasive weedy nature and new food/ medicinal value. The aboriginal cultures recognize several ethnotaxa of this species, which have been commonly used as timber, tools, furniture, fodder for sheep and used for personal hygiene; the young twigs are used as
toothbrush by tribals to cure infected gums while Acacia leucophloea is used for making liquor.
In view of the importance of Acacia described above, Newmaster and Ragupathy (2009b) developed a reliable identification method to differentiate Acacia species using only leaf samples. A classification of tree based on DNA barcoding sequence data (rbcl, ribulose-1,5-bisphospate carboxylase matK - Maturase K and trnH-psbA) clearly resolved 12 Acacia species and identified considerable intraspecific variation. In this study the authors chose sister species of Acacia that are difficult to distinguish. The defining characters of many acacias are found in the small flowers that appear during short periods of time during the year. Since the vegetative characters are variable and hence less reliable for species identification. Their study revealed wrongly identified herbarium specimens that only had vegetative material, which hampered identification of the species. In contrast, molecular studies utilizing DNA bar to classify previously/unidentified species/undetermined specimens due to lack of morphological characters and as a classification tool where specimens have proven difficult to classify (Wardill et al., 2005). Many of these studies employed fragments of DNA from various regions such as ITS1 and trnL which are useful for subspecies identification (Fagg and Greaves, 1990; Wardill et al., 2005) and created an ITS1 genotype library that was used as an identification tool to match exactly to the genotypes of other herbarium specimens identified by taxonomists. Although this ITS1 genotype library is a useful tool for Acacias, this has not been found to be a suitable region for DNA barcoding because it is not possible to sequence this region for many different groups of plants (see Erickson et al., 2008). Their findings indeed confirmed a recent taxonomic split in the genus Acacia. In the classification, DNA barcode using rbcl, matK or trnH-psbA and enables distinguish a new taxon Vachellia from Acacia species. Variation in rbcl alone could be used to differentiate Vachellia species from that of the Acacia species. These results are also supported by previous phonetic analysis (see Newmaster and Raghupathy, 2009a). These results are also supported by other phylogenetic studies in which Vachellia species are placed in a separate clad (100% bootstrap support); all Acacia species other than Vachellia species be replaced in a different clad (66% boot strap support), suggesting that Vachellia is distantly related to Acacia (Luckow et al., 2003; Miller and Bayer, 2001; Seigler et al., 2006), Vachellia (Acacieae, Acacia subg. Acacia) and thus rightly recognized as a distinct taxon from the ‘true’ Acacia as described in the earlier taxonomic literature (see Wight and Arnott, 1834).
The family Myrsticaceae is comprised of about 500 species of canopy to sub- canopy woody trees and native to tropical rainforest including some recently evolved species (Janovec and Harrison, 2002). Although information on its history and cultivation have been studied earlier, ethnobotanical studies of several Myristica species was unavailable till recently. Myristica fragrans Houtt., is a species endemic to the Maluku Province of Indonesia and has long been used both as a spice was studied in the Indonesian provinces of Maluku and Central and East Java. Historical and current indigenous uses of the fruit and seed and information on medicinal aspects is well known. It is well known that M. fragrans is still commonly used for culinary and medicinal purposes not only in its area of origin but in south India in particular. Identification of Myristica species in the past was difficult because many species share similar leaf morphology, hence difficult to identify and identification of species relies mainly on small flowers that bloom for just few weeks during the flowering season. Incorrect or misidentification of Myristicaceae species is c. 25% and is considered as ecological. Plastid DNA barcode and multilocus gene marker have been used for diagnostic method of all the genes mat k (maturase k) appears to have evolved rapidly and shows high level of variation making it a perfect marker for Nutmeg species. Using mat k, the genus Myristica can be separated from the genus Virola (up to 99.25%). Other related taxa viz., Virola and Compsoneura are used in several South American countries, as wood for veneer and timber while in some Neotropical countries, Brazil and Coloumbia, exports of Virola sp. are comparable in economic importance to big leaf mahogany (Macedo and Anderson, 1993). Thus, the genera Virola and Compsoneura show considerable intraspecific genomic variation (Newmaster et al., 2008a).
The genus Compsoneura, is considered as an ideal group for testing bar- coding in plants as the species present a taxonomic hinderance since the family has low levels of molecular variation compared to other closely related families of Magnoliales (see Sauquet et al., 2003) Compsoneura contains some recently described taxa (Janovec and Neill, 2002) and a new species split (Janovec and Harrison, 2002). A recent ethnobotany genomic study by Newmaster et al. (2008b) showed the utility of six coding (Universal Plastid Amplicon UPA, rpoB, rpoc1, accD, rbcl, matK) and one non-coding (trnH- psbA) chloroplast loci for barcoding in the genus Compsoneura using both single and multi region approaches. Five of the regions tested by them were predominantly invariant across species (UPA, rpoB, rpoCl, accD, rbcl). Two of the regions (matK and trnH-psbA) showed significant variation and hence considered ideal for barcoding in Myristicas. This study clearly demonstrated that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsoneura species sampled including C. sprucei and C. mexicana. A classification analyzes based on non metric multi dimensional scaling ordination concluded that the use of two regions showed a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples being correctly identified in a sequence identification analysis (see Newsmaster et al., 2008a; Newmaster and Ragupathy, 2010). Further research by them revealed cryptic diversity within the current species concepts, which has been recognized earlier by various aboriginal cultures. The classification tree from recent DNA barcoding sequence data (rbcl, matK and trnH-p sbA) reveals considerable intraspecific variation.
Species of the genus Biophytum, family Oxalidaceae are predominantly pantropical to sub-tropical in distribution. Biophytum species in India are distributed mostly in the south India and show a considerable diversity. There are 17-19 species of which 4 of them are said to be endangered and many are heterostylous including B. sensitivum (Mayura Devi, 1964). The various aboriginals/tribes the “Malasara and Irulas” living in the Velliangiri hills of south India, reportedly used 177 different plant species for various purposes including some Biophytum species [Thottal sinungi in Tamil] meaning “Touch me not” (Murugesan et al., 2009; Ragupathy et al., 2008b). Taxonomists identified taxa with 97% accuracy, the various species based on traditional and scientific knowledge. DNA barcoding has validated the presence of cryptic species including ‘Vishamuruchi’ (meaning detoxification of the poison); Biophytum coimbatorense, a new species), which is used as an antidote for poisonous scorpion bite, ‘Thear chedi’ (translation from Tamil - Chariot umbrella; Biophytum tamilnadense, a new species) is used as a bait plant for fish and crab and ‘Idduki poondu’ (translation from Tamil - between the rock; Biophytum velliangirianum; yet another new species) is used for curing ear ache. A classification tree from DNA barcoding sequence data (rbcL, matK and trnH-psbA 41 quantitative variables) resolved 19 Biophytum species and varieties including the new species stated above. DNA barcoding clearly discriminated the cryptic new ethnotaxa Biophytum coimbatorense from the morphologically similar species B. longipedunculatum (Thottal sinungi). DNA amplification data were found to be highly specific with a clear background in the agarose gel. Although there were no differences in the rbcL or atpF sequences for these two cryptic species, the matK and more variable non-coding spacer regions such astrnH-psbA sequences were found to be consistently distinct and different. Several segregating sites in the matK sequences were recorded consistently among the five distant populations. Studies by Newmaster and Raghupathy (2010) have also shown that closely related species are not distinguished by several plastid regions like rbcL or atpF.
The genus Tripogon Roem. & Schult. family Poaceaeae comprise of about 40 species of tropics and sub-tropics (Peterson et al., 1997; Clayton et al., 2006).The diversity of this taxon has been studied by Peterson et al. (1997) while Ruguolo-Agrasar and Vega (2004) reported that Indo-Asian region constitutes the center of diversity for this genus, with 23 species of which 16 species are native to China and 21 species including eight species endemics are native to India (Newmaster and Raghupaty, 2009a). A new species of Tripogon cope Newm. has recently been discovered during an ethnobotanical and genomics study in the Nilgiri Biosphere Reserve, Western Ghats, India by Newmaster and Raghupaty (2009b). Taxonomic identification of seven taxa from the 40 specimens with 96% (RF) accuracy among individuals. Aboriginal informants local tribes identified eight taxa from the same 40 specimens with 98% RF among the informants. DNA barcoding revealed the new species. Classification tree from DNA barcoding sequence data (rbcL, matK and trnH-psbA) clearly distinguished the 12 Tripogon known species from T. cope. The DNA amplifications were found to be highly specific with a clear background in the agarose gel. The matK and trnH-psbA sequences showed several segregating sites in sequences that were found consistently among the distant populations. However, TK classification of Tripogon is hierarchical, employing a series of characters, that is, morphological, nutritional, medicinal and ritual. For more informatiom the reader may refer Newmaster and Ragupathy (2010).
The genus Cardiospermum, family Sapindaceae has about 14 species world- wide (Willis, 1951) The species C. halicacabum is a dioecious climber with dissected leaves, small white flowers and balloon like heart shaped fruits hence the common name “balloon vine”or Heart seed Vine. The traditional classification of Cardiospermum is complex and many aboriginal communities such as the Irulas of Tamil Nadu, India and elsewhere in south India use for various purposes. Traditionally, the Irulas tribals are mainly gatherers and depend on the forest produce for food and medicine. A study of the Irulas and Malasras tribals of Tamil Nadu, West coast of India, provides evidence for the use of an ancient traditional remedy that has been used for centuries to treat rheumatoid arthritis (Newmaster et al., 2006; Newmaster and Ragupathy, 2007; Ragupathy et al., 2008a,b). This medicinal recipe is made from a plant (Cardiospermum halicacabum) “Modakathon”(Tamil translation) modaku = crippling joint pain; thon = remedy) and is still being used by some locals of Tamil Nadu to treat rheumatoid arthritis as well as by other communities of Asia and Africa. Support for this claim was substantiated by Kumaran and Karunakaran (2006), Venkatesh Babu and Krishnakumari (2005) and Naik et al. (2014) reported that the tender, young shoots of C. halicacabum have been traditionally used to treat stiffness of limbs and several other ailments, in addition used as a vegetable. Their phytochemical, ethnopharmacological activity of crude ethanolic extract has anti-inflammatory, antioxidant, analgesic, antipyretic and antidiabetic activities that are yet to be commercially formulated as modern herbal medicines, even though they have been acclaimed for their therapeutic properties in the traditional systems of medicine by the Irula tribals. Unfortunately, C. halicacabum is said to be poisonous as it contains cyanide. Hence, it is necessary that one should search for the non-cyanide accessions among the haplotypes which can be commercialized with no side effects.
Ragupathy and Newmaster (2009) in his ethnobotanical survey of the Irulas, which is comprised of small Dravidian tribal community of Negroid race in Thanjavur district of Tamil Nadu recorded the food and medicinal uses of several ethnotaxa especially C. halicacabum. They noted that most tribal informants were familiar with this species as a food and could identify other ethnotaxa used for various purposes. The stem and leaves of this plant are routinely used to make soup/curry, while the seeds of some ethnotaxa are used as oral pain relievers/applied to aching joints as a paste. This clearly indicates that the Irulas classify several ethnotaxa with a specific utility as these tribals believed in the concept ‘Neenda aauil’, in Tamil meaning “living a long healthy life”. Surveys from non-traditional communities indicate that around 20% people are familiar even now with some of the basic traditional knowledge concerning the utility of balloon vine. Interestingly it was also noted that over 75% people in modern urban centers still use balloon vine to treat rheumatoid arthritis, but less than 5% are familiar with the traditional knowledge of balloon vine. It is presently not known if the balloon vine remedies of urban centers are made from balloon vine and therefore recognizing a complex traditional classification system. Team of researchers at the Biodiversity Institute of Ontario Herbarium, University of Guelph in association with University of Madras and Bharatihiar University, Tamil Nadu, India have investigated the ethnobiological classification of balloon vine using a unique approach that bridges the aboriginal multi-mechanistic approach (Newmaster et al., 2006, 2007, 2010) with modern molecular tools such as DNA barcoding and biochemical analyzes to evaluate the classification at genomic and other levels (Newmaster and Ragupathy, 2009a).
Minor millets are important for local food security and genetic diversity in the arid and semi-arid regions of southern India and are widely cultivated because of their short duration and drought tolerance, constitute a group characterized by shorter, slender culms and small coarse seeded nutritionally rich cereals viz., Eleusine coracana, Setaria italica, Panicum miliaceum, Echinochloa frumentacea, Paspalum scorbiculatum, etc.
Maloles et al. (2011) investigated variation in minor millets of Kolli Hills, southern India in the context of traditional and scientific knowledge including ethnobotany genomics to understand and examine the biodiversity, and to detect natural variation in plastid regions rbcL, trnH-psbA and matK among 19 TK landraces, but noted that these regions were invariant among species within the context of existing classifications among 19 TK landraces, Elaborating on this study, Newmaster et al. (2013) using the nuclear regions ITS (ITS, ITS1 and ITS2) to examine variation between 15 landraces of 174 millet samples for both TK and SK Malayali informants and recorded 96 morphological characters and even studied DNA barcoding. Quantitative multivariate classification analysis of these plants revealed that the Malayali millet classification to be hierarchical and recognized considerable fine scale variation with high consensus which was analyzed using morphometric and DNA barcoding methods that revealed existence of fewer taxa. Furthermore, they also found that the plastid region trnH-psbA allowed differentiation for eight out of 15 landraces.
Recently, Ragupathy et al. (2016) based on their DNA bar coding studies utilized a tiered approach using ITS2 DNA barcode to make 100% accurate landrace (32 landraces) and six species assignments for all 160 blind samples used by indigenous farmers located in the rain fed areas of rural India and noted considerable variation in various traits and DNA sequences. They provided details of the various millet species studied by them. They also recorded precious TK of nutritional value, ecological and agricultural traits used by the local farmers for each of these traditional landraces. This work clearly demonstrates the immense potential of DNA barcoding as a reliable identification tool for evaluating and conserving genetic diversity of small millets, documenting protecting farmers rights and Traditional Knowledge.
Genomic diversity of landraces of millet was investigated by Newmaster et al. (2013) a key uncertainty that will provide a framework for a DNA bar- code method that could be used for fast, sensitive, and accurate identification of millet landraces, and millet landrace conservation including biocultural diversity. They found considerable intraspecific variation among 15 landraces representing six species of small millets using nuclear regions (ITS, ITS1, and ITS2); without any variation in plastid regions (rbcL, matK, and trnH-psbA). An efficient ITS2 DNA barcode enabled them make 100% accurate landrace assignments for 150 blind samples representing 15 landraces revealing that genomic variation is aligned with a fine-scale classification of landraces using traditional knowledge (TK) of local farmers. Significantly the landrace classification was found to be highly correlated with traits morphological, agricultural, and cultural traits of utility associated with factors such as yield, drought tolerance, growing season, medicinal properties, and nutrition. This could provide a DNA-based model for conservation of genetic diversity and the associated bicultural diversity (TK) of millet landraces, which has sustained marginal farming communities in harsh environments for many generations. It may be recalled that Kun Luo et al. (2010) proposed that ITS2 is a promising candidate barcode for plant species identification region exhibited the highest inter-specific divergence, and that this is significantly higher than the intra- specific variation in the “DNA barcoding gap” assessment and Wilcoxon two- sample tests. The ITS2 locus had the highest identification efficiency among all tested regions which works as internal species tags.
Despite the extensive use of small millet landraces as an important source of nutrition for people living in semi-arid regions, they are presently marginalized and their diversity and distribution are threatened at a global scale. Local farmers have developed ancient breeding programs entrenched in TK that has sustained rural cultures for thousands of years. The convention on biological diversity seeks fair and equitable sharing of genetic resources arising from local knowledge and requires signatory nations to provide appropriate policy and legal framework to farmers’ rights over plant genetic resources and associated TK. DNA barcoding employed in this study is proposed as a model for conservation of genetic diversity and an essential step towards documenting and protecting farmers’ rights and TK. Study by Ragupathy et al. (2016) focuses on 32 landraces of small millets that are still used by indigenous farmers located in the rain fed areas of rural India and Nepal. Traditional knowledge of traits and utility was gathered using participatory methods and semi-structured interviews with key informants. DNA was extracted and sequenced (rbcL, trnH-psbA and ITS2) from 160 samples. Both multivariate analysis of traits and phylogenetic analyzes were used to assess diversity among small millet landraces. Their research revealed considerable variation in traits and DNA sequences among the 32 small millet landraces. They utilized a tiered approach using ITS2 DNA barcode to make 100% accurate landrace (32 land- races) and species (6 species) assignments for all 160 blind samples in our study. They also recorded precious TK of nutritional value, ecological and agricultural traits used by local farmers for each of these traditional landraces. This research demonstrates the potential of DNA barcoding as a reliable identification tool and for use in evaluating and conserving genetic diversity of small millets. They suggest ways in which DNA barcodes could be used in the Protection of Plant Varieties and Farmers’ Rights in India and Nepal.
From the foregoing discussion of various case studies it is obvious that DNA barcoding and ethnogenomics is a rapidly developing frontier technology and science that is gaining not only global attention but has proved beyond doubt its utility in solving problems by providing reliable results in distinguishing species and other cryptic species. Similar work in India is being carried out
at some Indian universities but elsewhere abroad in advanced countries considerable work has been carried out in this direction. It may be mentioned here that ethnobotany is different from agri-genomics which deals with the study of the make up of and interaction between genes in crops and combinatorial chemistry and should not be confused with ethnobotany. Varah and Desai (2015) have recently made the first ever scientometric global analysis of the number of publications on genomics in relation to ethnobotany genomics programs for their biodiversity and observed noticeable increase of research in the subject globally, as seen by increasing number of publications originating mostly from USA, Canada, UK, and China. According to the Scopus database, the ethnobotany genomics researches are being published in 23 different subject like Agricultural and Biological Sciences and Biochemistry, Genetics, Molecular Biology, Medicine, Pharmacology, Toxicology and Pharmaceutics, etc., the latter are concerned with medicinal properties of plants. Presently, 72 countries are participating in the ethnobotany genomics research. United States is much ahead with 171, followed by China (158), Canada (78), UK (75), France (60), and India (43). In terms of average citation per article, the highest (35.21) is achieved by UK, followed by Canada (24.17), France (19.55), USA (18.42), followed by others. On the other hand, developing countries including China and India have shown an increase in their publications share in ethnobotany genomics (see Varah and Desai, 2015) since China and India share old history and tradition of advanced development in the field of medicine, especially Ayurvedic medicines in India are one such ancient tradition which are still in existence. However, in the case of genomics research, western countries dominate advancement in modern science and technology, largely because of better resources in terms trained manpower and sound finance. In Chapter 14, the authors have briefly discussed how the various modern Omic technologies, and System biology would likely to impact in the coming years better understanding of identification of various active bio-components, clinical testing and development of quality standards for safety and efficacy of ancient medical systems. Thus, the ethnogenomic approach is gaining considerable edge in validating indigenous drugs vis-a-vis, traditional knowledge much needed by the present day society for sustained and cheaper health care practices. It may be relevant to point out that Saslis-Lagoudakis et al. (2011) have shown the use of phylogeny to interpret cross cultural patterns in plant use and guide medicinal plant discovery using Pterocarpus. Traditional knowledge of medicinal plants has led to important discoveries that have helped
combat several diseases and has improved healthcare. However, the development of quantitative measures that can assist in our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last few decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are rare and needs more intensive investigations. Furthermore, ethnobotany genomics can also be used profitably to determine the distribution of rare species, their ecological requirements, including traditional ecological knowledge so that conservation strategies can be implemented. This aspect incidentally is aligned with the Convention on Biological Diversity (CBD) which was signed by over 150 nations, and thus the “world’s complex array of human-natural-technological relationships has effectively been reorganized” as rightly stated by Ragupathy et al. (2016).
We are thankful to National Centre for Biotechnology Information at the U.S. National Library of Medicine for providing some of the literature cited in this paper.
Bentham, G. (1842). Notes on Mimoseae with a short synopsis of species. J. Botany (Hooker) , 4 , 323–418.
Byrne, M., Tischler, G., Macdonald, B., Coates, D. J., & McComb, J. (2001). Phylogenetic relationships between two rare Acacias and their common, wide spread relatives in south-western Australia. Conservation Genetics. , 2 , 157–166.
Clayton, W. D., Harman, K. T., & Williamson, H. (2006). Grassbase—the Online World Grass Flora. Available from URL: https://www.kew.org/data/grasses-db/sppindex.htm#T (accessed 8 November 2006).
Erickson, D. L., Spouge, J., Resch, A., Weigt, L. E., & Kress, W. J. (2008). DNA barcoding in land plants: developing standards to quantify and maximize success. Taxon , 57 , 1304–1316.
Fagg, C. W., & Greaves, A. (1990). Acacia nilotica 1869-1988, Annotated Bibliography No. F42 (ed. LangdonK), CAB International, published in collaboration with the Oxford Forestry Institute, Wallingford, UK.
Hebert, P. D. N., Cywinska, A., Ball, S. L., & De Waard, J. R. (2003). Biological identification through DNA barcodes. Proc. Roy. Soc. B: Biol Sci. , 270 , 313–321.
Janovec, J. P. & Harrison, J. S. (2002). A morphological analysis of the Compsoneura sprucei complex (Myristicaceae), with a new combination for the Central American species Compsoneura mexicana. Sys. Bot. , 27 , 662–673.
Janovec, J. P. & Neill, A. K. (2002). Studies of the Myristicaceae: an overview of the Compsoneura atopa complex, with descriptions of new species from Columbia. Brittonia , 54 , 251–261.
Kress, W. J. & Erickson, D. L. (2007). A two-locus global DNA barcode for land plants: the coding rbcl gene complements the non-coding trnH-psbA spacer region. PLoS. , 2 , e508. doi:10.1371/journal.pone.0000508.
Kress, W. J. & Erickson, D. L. (2008). DNA barcodes: genes, genomics, and bioinformatics. Proc. Natl. Acad. Sci. USA , 105 , 2761–2762.
Kress, W. J. & Erickson, D. L. (2009). Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc. Nat. Acad. Sci. USA , 106 , 18621–18626.
Kumaran, A. & Karunakaran, R. J. (2006). Antioxidant activities of the methanol extract of Cardiospermum halicacabum. Pharm. Biol. , 44 , 146–151.
Luo, Kun, Chen, Shi Lin, Chen, Ke Li, Song, Jing Yuan, Yao, Hui, Ma, Xinye, Zhu, Ying Jie, Pang, Xiao Hui, & Hua, Yu (2010). Assessment of candidate plant DNA barcodes using the Rutaceae family. China Life Sciences , 53 (6), 701–708.
Luckow, M., Miller, J. T., Murphy, D. J., & Livshultz, T. (2003). A phylogenetic analysis of the Mimosoideae (Leguminosae) based on chloroplast DNA sequence data. In B. B.Klitgaard & A.Bruneau (Eds.), Advances in Legume Systematics, Part 10, Higher Level Systematics. Royl Bot Gard, Kew, UK. pp. 197–220.
MacDonald, I. (2009). Current trends in Ethnobotany: Editorial. Trop. J. Pharmaceut. Res , 8 (4), 295–296.
Macedo, D. S. & Anderson, A. B. (1993). Early ecological changes associated with logging in an Amazon Floodplain. Biotropica. , 25 (2), 151–163.
Maloles, J. R., Berg, K., Ragupathy, K., Balasubramaniam, C., Nirmala, K., Althaf, A., Vadaman Palanisamy, C, & Newmaster, S. G. (2011). The fine scale ethnotaxa classification of millets in Southern India. J. Ethnobiol. , 31 (2), 262–287.
Maslin, B. R., Miller, J. T., & Seiger, D. S. (2003). Overview of the generic status of Acacia (Leguminosae: Mimosoideae). Austral. Sys. Bot. , 16 , 1–18.
Mayura Devi, P. (1964). Heterostyly in Biophytum sensitivum DC. J. Genet. , 59 , 41–48.
McDonald, M. W., Maslin, B. R., & Butcher, P. A. (2001). Utilisation of Acacias. In A. E.Orchard & A. J. G.Wilson (Eds.), Flora of Australia, Volume 11A, Mimosaceae, Acacia Part 1. ABRS/CSIRO Publishing, Melbourne, Australia. pp. 30–40.
Midgley, S. J. & Turnbull, J. W. (2003). Domestication and use of Australian Acacias: an overview. Austral. Sys. Bot. , 16 (1), 89–102.
Miller, J. T. & Bayer, R. J. (2001). Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on the chloroplast matK coding sequence and flanking trnK intron spacer region. Am. J. Bot. , 88 (4), 697–705.
Murugesan, M., Ragupathy, S., Balasubramaniam, V., Nagarajan, N., & Newmaster, S. G. (2009). Three new species of the genus Biophytum DC. (Oxalidaceae-Geraniales) from Velliangiri hills in the Nilgiri Biosphere Reserve, Western Ghats. India. J. Econ. Taxon. Bot. , 33 , 10–26.
Naik, V. K. M., Babu, S. K., Latha, J., & Prabhakar, V. (2014). A review on its ethnobotany, phytochemical and pharmacological profile of Cardiospermum halicacabum (L). Intl. J. Pharmaceut. Biosci. , 3 (6), 392–401.
Newmaster, S. G., Fazekas, A. J., & Ragupathy, S. (2006). DNA barcoding in the land plants: evaluation of rbcL in a multigene tiered approach. Canad. J. Bot. , 84 , 335–341.
Newmaster, S. G., Fazekas, A. J., Steeves, R., & Janovec, J. (2008a). Testing candidate plant barcode regions in the Myristicaceae. Mole. Ecol. Resour. , 8 , 480–490.
Newmaster, S. G., Murugesan, M., Ragupathy, S., & Balasubramaniam, V. (2009a). Ethno- botany Genomics study reveals three new species from the Velliangiri Holy Hills in the Nilgiri Biosphere Reserve, Western Ghats, India. Ethnobotany , 21 , 2–24.
Newmaster, S. G. & Ragupathy, S. (2007). Exploring ethnobiological classifications for novel alternative medicine: A case study of Cardiospermum halicacabum L (Modakathon, Balloon Vine) as a traditional herb for treating arthritis. Ethnobot. , 19 , 1–20.
Newmaster, S. G. & Ragupathy, S. (2009a). Ethnobotany genomics - use of DNA barcoding to explore cryptic diversity in economically important plants. Indian J. Sci. Technol. , 2 (5), 1–8.
Newmaster, S. G. & Ragupathy, S. (2009b). Testing plant barcoding in a sister species complex of pantropical Acacias (Mimosoideae, Fabaceae). Mol. Ecol. Resour. , 9 (Suppl. 1), 172–180.
Newmaster, S. G. & Ragupathy, S. (2010). Ethnobotany Genomics - Discovery and innovation in a new era of exploratory research. Bio. Med. J. Ethnobiol. Ethnomed. , 6 , 1–11.
Newmaster, S. G., Ragupathy, S., Balasubramaniam, N. C., & Ivanoff, R. F. (2007). The multi-mechanistic taxonomy of the Irulas in Tamil Nadu, South India. J. Ethnobiol. , 27 , 31–44.
Newmaster, S. G., Ragupathy, S., & Janovec, J. (2009b). A botanical renaissance: State-of- the-art DNA Barcoding Facilitates an Automated Identification Technology (AIT) System for Plants. Intl. J. Comput. Appl. Technol. , 35 (1), 51–60.
Newmaster, S. G., Velusamy, B., Murugesan, M., & Ragupathy, S. (2008b). Tripogon cope, a new species of Tripogon (Poaceae: Chloridoideae) in India with a morphometric analysis and synopsis of Tripogon in India. Syst. Bot. , 33 (4), 695–701.
Newmaster, S. G., Ragupathy, S., Dhivya, S., Jijo, C. J., Sathishkumar, R., & Patel, K. (2013). Genomic valorization of the fine scale classification of small millet landraces in southern India. Genome , 56 (2), 123–127.
Pereira, F., Carneiro, J., & Amorim, A. (2008). Identification of species with DNA based technology: Current Progress and Challenges. Recent Pat DNA Gene Seq , 2 (187), 99.
Peterson, P. M., Webster, R. D., & Valdes Reyna, J. (1997). Genera of new world Eragrostideae (Poaceae: Chloridoideae). Smithsonian Contrib. Bot , 87 , 1–50.
Ragupathy, S. & Newmaster, S. G. (2009). Valorizing the ‘Irulas’ traditional knowledge of medicinal plants in the Kodiakarai reserve forest. India. J. Ethnobiol. Ethnomed. , 5 , 10. doi:10.1186/1746-4269-5-10.
Ragupathy, S., Newmaster, S. G., Gopinadhan, P., & Newmaster, C. (2008a). Exploring ethnobiological classifications for novel alternative medicine: a case study of Cardiospermum halicacabum L. (Modakathon, Balloon Vine) as a traditional herb for treating rheumatoid arthritis. Ethnobotany. , 19 , 1–20.
Ragupathy, S., Newmaster, S. G., Murugesan, M., Velusamy, B., & Huda, M. (2008b). Consensus of the ‘Malasars’ traditional aboriginal knowledge of medicinal plants in the Velliangiri holy hills. Indian. J. Ethnobiol. Ethnomed. , 4 (8), 1–14.
Ragupathy, S., Newmaster, S. G., Velusamy, B., & Murugesan, M. (2009). DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India. Mol. Ecol. Res. , 9 (Suppl), 1172–1180.
Ragupathy, S., Dhivya, S., Pate, K., Sritharan, A., Sambandan, K., Gartaula, H., Sathishkumar, R., Balasubramanian, K., Nirmala, C., Kumari, A. N., & Newmaster, S. G. (2016). DNA record of some traditional small millet landraces in India and Nepal. Biotech. , 6 (2), 133.
Ruguolo de Agrasar, Z. E. & Vega, A. S. (2004). Tripogon nicorae a new and synopsis of Tripogon (Poaceae: Chorloideae) in America. Systematic Botany , 29 (4), 874–882.
Saslis-Lagoudakis, C. H., Klitgaard, B. B., Forest, F., Francis, L., Savolainen, V., Williamson, E. M., & Hawkins, J. A. (2011). The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae). PLoS One. , 6 (7), e22275.
Sauquet, H., Doyle, J. A., Scharaschkin, T., Borsch, T., Hilu, K. W., Chatrou, L. W., & Le Thomas, A. (2003). Phylogenetic analysis of Magnoliales and Myristicaceae based on multiple data sets: implications for character evolution. Bot. J. Linn. Soc. , 142 , 125–186.
Schultes, R. E. (1962). The role of the ethnobotanists in the search for new medicinal plants. Lloydia , 25 , 257–266.
Seigler, D. S., Ebinger, J. E., & Miller, J. T. (2006). New combinations in the genus Senegalia (Fabaceae: Minosoideae) from the New World. Phytologia , 88 , 38–93.
Varah, F. & Desai, P. N. (2015). Ethnobotany genomics research: Status and future prospects. J. Scientometric Res. , 4 , 29–39.
Venkatesh Babu, K. C. & Krishnakumari, S. (2005). Anti-inflammatory and antioxidant compound, rutin in Cardiospermum halicacabum leaves. Ancient Sci. Life. , 25 (2), 47–49.
Wagner, H., Bauer, R., Melchart, D., Xiao, P. G., & Staudinger, A. (2011). Chromatographic Fingerprint Analysis of Herbal Medicines: Thin layer and High Performance Liquid Chromatography of Chinese Drugs (2nd ed.)., Vol. I. Wien, II: Springer.
Wardill, T. J., Graham, G. C., Zalucki, M., Palmer, M., William, A., Playford, & Julia, P (2005). The importance of species identity in the biocontrol process: identifying the subspecies of Acacia nilotica (Leguminosae: Mimosoideae) by genetic distance and the implications for biological control. J. Biogeography. , 32 , 2145–2159.
Wickens, G. E., Seif-El-Din, A. G., Sita, G., & Nahal, I. (1995). Role of Acacia species in the rural economy of dry Africa and the Near East. FAO Conservation Guide No. 27, Food and Agriculture Organization, Rome, Italy.
Wight, R., & Arnott, G. A. W. (1834). Prodromus Florae Peninsulae Indiae Orientalis. Par- bury, Allen & Amp. Co., London.
Wilson, J. J., Sing, Kong-Wah, Lee, Ping-Shin, & Wee, A. K. S. (2016). Application of DNA barcodes in wild life conservation in Tropical East Asia. Conservation Biol. , 30 (5), 982–989.
Willis, J. C. (1951). A Dictionary of the Flowering Plants and Ferns. Cambridge University Press.