9.11: The Role of Seed Plants - Biology

9.11: The Role of Seed Plants - Biology

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Learning Objectives

  • Discuss the roles that plants play in ecosystems

Without seed plants, life as we know it would not be possible. Plants play a key role in the maintenance of terrestrial ecosystems through stabilization of soils, cycling of carbon, and climate moderation. Large tropical forests release oxygen and act as carbon dioxide sinks. Seed plants provide shelter to many life forms, as well as food for herbivores, thereby indirectly feeding carnivores. Plant secondary metabolites are used for medicinal purposes and industrial production.

Animals and Plants: Herbivory

Coevolution of flowering plants and insects is a hypothesis that has received much attention and support, especially because both angiosperms and insects diversified at about the same time in the middle Mesozoic. Many authors have attributed the diversity of plants and insects to pollination and herbivory, or consumption of plants by insects and other animals. This is believed to have been as much a driving force as pollination. Coevolution of herbivores and plant defenses is observed in nature. Unlike animals, most plants cannot outrun predators or use mimicry to hide from hungry animals. A sort of arms race exists between plants and herbivores. To “combat” herbivores, some plant seeds—such as acorn and unripened persimmon—are high in alkaloids and therefore unsavory to some animals. Other plants are protected by bark, although some animals developed specialized mouth pieces to tear and chew vegetal material. Spines and thorns (Figure 1) deter most animals, except for mammals with thick fur, and some birds have specialized beaks to get past such defenses.

Herbivory has been used by seed plants for their own benefit in a display of mutualistic relationships. The dispersal of fruit by animals is the most striking example. The plant offers to the herbivore a nutritious source of food in return for spreading the plant’s genetic material to a wider area.

An extreme example of collaboration between an animal and a plant is the case of acacia trees and ants. The trees support the insects with shelter and food. In return, ants discourage herbivores, both invertebrates and vertebrates, by stinging and attacking leaf-eating insects.

Animals and Plants: Pollination

Grasses are a successful group of flowering plants that are wind pollinated. They produce large amounts of powdery pollen carried over large distances by the wind. The flowers are small and wisp-like. Large trees such as oaks, maples, and birches are also wind pollinated.

Explore this website for additional information on pollinators.

More than 80 percent of angiosperms depend on animals for pollination: the transfer of pollen from the anther to the stigma. Consequently, plants have developed many adaptations to attract pollinators. The specificity of specialized plant structures that target animals can be very surprising. It is possible, for example, to determine the type of pollinator favored by a plant just from the flower’s characteristics. Many bird or insect-pollinated flowers secrete nectar, which is a sugary liquid.

They also produce both fertile pollen, for reproduction, and sterile pollen rich in nutrients for birds and insects. Butterflies and bees can detect ultraviolet light. Flowers that attract these pollinators usually display a pattern of low ultraviolet reflectance that helps them quickly locate the flower’s center and collect nectar while being dusted with pollen (Figure 2). Large, red flowers with little smell and a long funnel shape are preferred by hummingbirds, who have good color perception, a poor sense of smell, and need a strong perch. White flowers opened at night attract moths. Other animals—such as bats, lemurs, and lizards—can also act as pollinating agents. Any disruption to these interactions, such as the disappearance of bees as a consequence of colony collapse disorders, can lead to disaster for agricultural industries that depend heavily on pollinated crops.

Testing Attraction of Flies by Rotting Flesh Smell

Question: Will flowers that offer cues to bees attract carrion flies if sprayed with compounds that smell like rotten flesh?

Background: Visitation of flowers by pollinating flies is a function mostly of smell. Flies are attracted by rotting flesh and carrions. The putrid odor seems to be the major attractant. The polyamines putrescine and cadaverine, which are the products of protein breakdown after animal death, are the source of the pungent smell of decaying meat. Some plants strategically attract flies by synthesizing polyamines similar to those generated by decaying flesh and thereby attract carrion flies.

Flies seek out dead animals because they normally lay their eggs on them and their maggots feed on the decaying flesh. Interestingly, time of death can be determined by a forensic entomologist based on the stages and type of maggots recovered from cadavers.

Hypothesis: Because flies are drawn to other organisms based on smell and not sight, a flower that is normally attractive to bees because of its colors will attract flies if it is sprayed with polyamines similar to those generated by decaying flesh.

Test the hypothesis:

  1. Select flowers usually pollinated by bees. White petunia may be good choice.
  2. Divide the flowers into two groups, and while wearing eye protection and gloves, spray one group with a solution of either putrescine or cadaverine. (Putrescine dihydrochloride is typically available in 98 percent concentration; this can be diluted to approximately 50 percent for this experiment.)
  3. Place the flowers in a location where flies are present, keeping the sprayed and unsprayed flowers separated.
  4. Observe the movement of the flies for one hour. Record the number of visits to the flowers using a table similar to Table 1. Given the rapid movement of flies, it may be beneficial to use a video camera to record the fly–flower interaction. Replay the video in slow motion to obtain an accurate record of the number of fly visits to the flowers.
  5. Repeat the experiment four more times with the same species of flower, but using different specimens.
  6. Repeat the entire experiment with a different type of flower that is normally pollinated by bees.
Table 1. Results of Number of Visits by Flies to Sprayed and Control/Unsprayed Flowers
Trial #Sprayed FlowersUnsprayed Flowers

Analyze your data: Review the data you have recorded. Average the number of visits that flies made to sprayed flowers over the course of the five trials (on the first flower type) and compare and contrast them to the average number of visits that flies made to the unsprayed/control flowers. Can you draw any conclusions regarding the attraction of the flies to the sprayed flowers?

For the second flower type used, average the number of visits that flies made to sprayed flowers over the course of the five trials and compare and contrast them to the average number of visits that flies made to the unsprayed/control flowers. Can you draw any conclusions regarding the attraction of the flies to the sprayed flowers?

Compare and contrast the average number of visits that flies made to the two flower types. Can you draw any conclusions about whether the appearance of the flower had any impact on the attraction of flies? Did smell override any appearance differences, or were the flies attracted to one flower type more than another?

Form a conclusion: Do the results support the hypothesis? If not, how can this be explained?

The Importance of Seed Plants in Human Life

Seed plants are the foundation of human diets across the world (Figure 3). Many societies eat almost exclusively vegetarian fare and depend solely on seed plants for their nutritional needs. A few crops (rice, wheat, and potatoes) dominate the agricultural landscape. Many crops were developed during the agricultural revolution, when human societies made the transition from nomadic hunter–gatherers to horticulture and agriculture. Cereals, rich in carbohydrates, provide the staple of many human diets. Beans and nuts supply proteins. Fats are derived from crushed seeds, as is the case for peanut and rapeseed (canola) oils, or fruits such as olives. Animal husbandry also consumes large amounts of crops.

Staple crops are not the only food derived from seed plants. Fruits and vegetables provide nutrients, vitamins, and fiber. Sugar, to sweeten dishes, is produced from the monocot sugarcane and the eudicot sugar beet. Drinks are made from infusions of tea leaves, chamomile flowers, crushed coffee beans, or powdered cocoa beans. Spices come from many different plant parts: saffron and cloves are stamens and buds, black pepper and vanilla are seeds, the bark of a bush in the Laurales family supplies cinnamon, and the herbs that flavor many dishes come from dried leaves and fruit, such as the pungent red chili pepper. The volatile oils of flowers and bark provide the scent of perfumes. Additionally, no discussion of seed plant contribution to human diet would be complete without the mention of alcohol. Fermentation of plant-derived sugars and starches is used to produce alcoholic beverages in all societies. In some cases, the beverages are derived from the fermentation of sugars from fruit, as with wines and, in other cases, from the fermentation of carbohydrates derived from seeds, as with beers.

Seed plants have many other uses, including providing wood as a source of timber for construction, fuel, and material to build furniture. Most paper is derived from the pulp of coniferous trees. Fibers of seed plants such as cotton, flax, and hemp are woven into cloth. Textile dyes, such as indigo, were mostly of plant origin until the advent of synthetic chemical dyes.

Lastly, it is more difficult to quantify the benefits of ornamental seed plants. These grace private and public spaces, adding beauty and serenity to human lives and inspiring painters and poets alike.

The medicinal properties of plants have been known to human societies since ancient times. There are references to the use of plants’ curative properties in Egyptian, Babylonian, and Chinese writings from 5,000 years ago. Many modern synthetic therapeutic drugs are derived or synthesized de novo from plant secondary metabolites. It is important to note that the same plant extract can be a therapeutic remedy at low concentrations, become an addictive drug at higher doses, and can potentially kill at high concentrations. Table 2 presents a few drugs, their plants of origin, and their medicinal applications.

Table 2. Plant Origin of Medicinal Compounds and Medical Applications
Deadly nightshade (Atropa belladonna )AtropineDilate eye pupils for eye exams
Foxglove (Digitalis purpurea)DigitalisHeart disease, stimulates heart beat
Yam (Dioscorea spp.)SteroidsSteroid hormones: contraceptive pill and cortisone
Ephedra (Ephedra spp.)EphedrineDecongestant and bronchiole dilator
Pacific yew (Taxus brevifolia)TaxolCancer chemotherapy; inhibits mitosis
Opium poppy (Papaver somniferum)OpioidsAnalgesic (reduces pain without loss of consciousness) and narcotic (reduces pain with drowsiness and loss of consciousness) in higher doses
Quinine tree (Cinchona spp.)QuinineAntipyretic (lowers body temperature) and antimalarial
Willow (Salix spp.)Salicylic acid (aspirin)Analgesic and antipyretic

Biodiversity of Plants

Biodiversity ensures a resource for new food crops and medicines. Plant life balances ecosystems, protects watersheds, mitigates erosion, moderates climate and provides shelter for many animal species. Threats to plant diversity, however, come from many angles. The explosion of the human population, especially in tropical countries where birth rates are highest and economic development is in full swing, is leading to human encroachment into forested areas. To feed the larger population, humans need to obtain arable land, so there is massive clearing of trees. The need for more energy to power larger cities and economic growth therein leads to the construction of dams, the consequent flooding of ecosystems, and increased emissions of pollutants. Other threats to tropical forests come from poachers, who log trees for their precious wood. Ebony and Brazilian rosewood, both on the endangered list, are examples of tree species driven almost to extinction by indiscriminate logging.

The number of plant species becoming extinct is increasing at an alarming rate. Because ecosystems are in a delicate balance, and seed plants maintain close symbiotic relationships with animals—whether predators or pollinators—the disappearance of a single plant can lead to the extinction of connected animal species. A real and pressing issue is that many plant species have not yet been catalogued, and so their place in the ecosystem is unknown. These unknown species are threatened by logging, habitat destruction, and loss of pollinators. They may become extinct before we have the chance to begin to understand the possible impacts from their disappearance. Efforts to preserve biodiversity take several lines of action, from preserving heirloom seeds to barcoding species. Heirloom seeds come from plants that were traditionally grown in human populations, as opposed to the seeds used for large-scale agricultural production. Barcoding is a technique in which one or more short gene sequences, taken from a well-characterized portion of the genome, are used to identify a species through DNA analysis.

Learning Objectives

Angiosperm diversity is due in part to multiple interactions with animals. Herbivory has favored the development of defense mechanisms in plants, and avoidance of those defense mechanism in animals. Pollination (the transfer of pollen to a carpel) is mainly carried out by wind and animals, and angiosperms have evolved numerous adaptations to capture the wind or attract specific classes of animals.

Plants play a key role in ecosystems. They are a source of food and medicinal compounds, and provide raw materials for many industries. Rapid deforestation and industrialization, however, threaten plant biodiversity. In turn, this threatens the ecosystem.


Kelps are ecologically important primary producers and ecosystem engineers, and play a central role in structuring nearshore temperate habitats. They play an important role in nutrient cycling, energy capture and transfer, and provide biogenic coastal defence. Kelps also provide extensive substrata for colonising organisms, ameliorate conditions for understorey assemblages, and provide three-dimensional habitat structure for a vast array of marine plants and animals, including a number of commercially important species. Here, we review and synthesize existing knowledge on the functioning of kelp species as biogenic habitat providers. We examine biodiversity patterns associated with kelp holdfasts, stipes and blades, as well as the wider understorey habitat, and search for generality between kelp species and biogeographic regions. Environmental factors influencing biogenic habitat provision and the structure of associated assemblages are considered, as are current threats to kelp-dominated ecosystems. Despite considerable variability between species and regions, kelps are key habitat-forming species that support elevated levels of biodiversity, diverse and abundant assemblages and facilitate trophic linkages. Enhanced appreciation and better management of kelp forests are vital for ensuring sustainability of ecological goods and services derived from temperate marine ecosystems.


Abscisic acid (ABA) is the hormone that is usually associated with major plant responses to stress. Pioneering studies by Hemberg found a water and ether soluble growth-inhibiting substance that is critical for the maintenance of bud dormancy in potato and Fraxinus ( Hemberg 1949a , 1949b ). This growth inhibitor was isolated in buds of Acer pseudoplatanus by Philip Wareing in 1963, and named dormin ( Eagles and Wareing 1963 ). During the same period, a substance that controlled the abscission of cotton fruits was discovered by Frederick Addicott and named abscisin II ( Ohkuma et al. 1963 ). The Addicott lab found that abscisin II also promotes leaf abscission in cotton seedlings and inhibits indoleacetic acid-induced growth of Avena coleoptiles. Later, dormin and abscisin II were found to be the same chemical compound and named abscisic acid ( Cornforth et al. 1965 Addicott et al. 1968 ). Although the abscission-promotion role of ABA was considered by many to be an indirect effect of the elevated level of ethylene ( Cracker and Abeles 1969 ), recent studies have demonstrated that ABA promotes leaf senescence and abscission independent of ethylene ( Ogawa et al. 2009 Zhao et al. 2016 ).

Over the past 40 years, the core components of ABA biosynthesis and signaling have been identified through molecular-genetic, biochemical, and pharmacological approaches. Genetic screens for viviparous mutants in maize and Arabidopsis, and for mutants that are insensitive to sugar, salt, and ABA during germination lead to the identification of numerous components involved in ABA biosynthesis and signaling. Some of the first identified were the clade A PP2Cs such as ABA Insensitive (ABI) 1 and ABI2, and the key transcription factors ABI3, ABI4, and ABI5 ( Koornneef et al. 1984 Giraudat et al. 1992 Finkelstein 1994 Leung et al. 1994 , 1997 Meyer et al. 1994 McCarty 1995 Rodriguez et al. 1998 Finkelstein and Lynch 2000 Laby et al. 2000 Gonzalez-Guzman et al. 2002 ). Biochemical studies of the ABA activation of protein kinases resulted in the identification of AAPK, which is a homolog of the Arabidopsis core protein kinases, SnRK2s, in Vicia faba ( Li and Assmann 1996 ). Due to its high functional redundancy, the ABA receptor Pyrabactin resistance 1 (PYR1) and PYR1-like (PYL) proteins (hereafter referred to as PYLs) were not revealed until 2009 by Sean Cutler and co-workers through chemical genetic screens for mutants that are insensitive to the ABA analog pyrabactin ( Park et al. 2009 ). In the meantime, regulatory components of the ABA receptors (RCARs) were isolated through yeast two-hybrid screens in the Erwin Grill lab ( Ma et al. 2009 ). The function of the proteins of PYL/RCAR family was also demonstrated by in vitro reconstitution of the core ABA signaling pathway ( Fujii et al. 2009 ), and later further confirmed by substantial genetic and structural evidence ( Melcher et al. 2009 Miyazono et al. 2009 Nishimura et al. 2009 Yin et al. 2009 Santiago et al. 2009a , 2009b Gonzalez-Guzman et al. 2012 Zhang et al. 2015 Miao et al. 2018 Zhao et al. 2018 ). Here, we will summarize the latest updates on the dynamics of ABA level, ABA signaling and its stringent regulation as well as versatile functions in physiological processes.

Types of Seeds

A Seed is primarily of two types. The two types are:

Let us now study about these types of seeds in brief.

Structure of a Monocotyledonous Seed

A Monocotyledonous seed, as the name suggests, has only one cotyledon. There is only one outer layering of the seed coat. A seed has the following parts:

  • Seed Coat: In the seed of cereals such as maize, the seed coat is membranous and generally fused with the fruit wall, called Hull.
  • Endosperm: The endosperm is bulky and stores food. Generally, monocotyledonous seeds are endospermic but some as in orchids are non-endospermic.
  • Aleuron layer: The outer covering of endosperm separates the embryo by a proteinous layer called aleurone layer.
  • Embryo: The embryo is small and situated in a groove at one end of the endosperm.
  • Scutellum: This is one large and shield-shaped cotyledon.
  • Embryonal axis: Plumule and radicle are the two ends.
  • Coleoptile and coleorhiza: The plumule and radicle are enclosed in sheaths. They are coleoptile and coleorhiza.

Structure of a Dicotyledonous Seed

Unlike monocotyledonous seed, a dicotyledonous seed, as the name suggests, has two cotyledons. It has the following parts:

  • Seed coat: This is the outermost covering of a seed. The seed coat has two layers, the outer testa and the inner tegmen.
  • Hilum: The hilum is a scar on the seed coat through which the developing seed was attached to the fruit.
  • Micropyle: It is a small pore present above the hilum.
  • Embryo: It consists of an embryonal axis and two cotyledons.
  • Cotyledons: These are often fleshy and full of reserve food materials.
  • Radicle and plumule: They are present at the two ends of the embryonal axis.
  • Endosperm: In some seeds such as castor, the endosperm formed as a result of double fertilisation, is a food storing tissue. In plants such as bean, gram and pea, the endosperm is not present in the matured seed. They are known as non-endospermous.

Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security

Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered ‘omics’ approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.

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What are the receptors for brassinosteroids?

Studies from several laboratories contributed to the finding of the first BR receptor [19]. Clouse et al. identified the first BR-insensitive (BRI) mutant (named bri1) by observing the promotion of root elongation under inhibitory concentrations of BR compared to the wild type in Arabidopsis [20]. The bri1 mutant displayed dwarfism, reduced cell elongation, dark-green and thickened leaves, reduced apical dominance, delayed blooming and senescence, altered vascular patterning and male sterility. The positional cloning of BRI1 was performed by Jianming Li and J. Chory, who identified 18 alleles of bri1. Despite structural similarity between BRs and animal steroid hormones, BRI1 does not structurally resemble the nuclear steroid receptors of animals but encodes a leucine-rich repeat receptor-like kinase (LRR-RLK) with an extracellular leucine-rich repeat (LRR) domain and an intracellular serine/threonine kinase domain [21]. BRI1 is highly conserved across different plant species [19], consistent with the finding that BRs are widely present in plants. There are three BRI1 homologues in Arabidopsis, BRL1, BRL2 and BRL3. BRL1 and BRL3, but not BRL2, were shown to bind BRs with high affinity and rescue the phenotypes of the BRI1 mutation when expressed using the promoter of BRI1 [22]. Thus far, the ligands BRL2 might recognize still remain unknown. BRI1 is highly expressed in various tissues of plants and functions as the major receptor of BRs, whereas the expression of BRL1 and BRL3 is confined to vascular cells and display weak phenotypes when knocked out [22].

The strigolactones are rhizosphere signaling molecules as well as a new class of plant hormones with a still increasing number of biological functions being uncovered. Here, we review a recent major breakthrough in our understanding of strigolactone biosynthesis, which has revealed the unexpected simplicity of the originally postulated complex pathway. Moreover, the discovery and localization of a strigolactone exporter sheds new light on putative strigolactone fluxes to the rhizosphere as well as within the plant. The combination of these data with information on the expression and regulation of strigolactone biosynthetic and downstream signaling genes provides new insights into how strigolactones control the many different aspects of plant development and how their rhizosphere signaling role may have evolved.

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Global trade will accelerate plant invasions in emerging economies under climate change

Trade plays a key role in the spread of alien species and has arguably contributed to the recent enormous acceleration of biological invasions, thus homogenizing biotas worldwide. Combining data on 60-year trends of bilateral trade, as well as on biodiversity and climate, we modeled the global spread of plant species among 147 countries. The model results were compared with a recently compiled unique global data set on numbers of naturalized alien vascular plant species representing the most comprehensive collection of naturalized plant distributions currently available. The model identifies major source regions, introduction routes, and hot spots of plant invasions that agree well with observed naturalized plant numbers. In contrast to common knowledge, we show that the ‘imperialist dogma,’ stating that Europe has been a net exporter of naturalized plants since colonial times, does not hold for the past 60 years, when more naturalized plants were being imported to than exported from Europe. Our results highlight that the current distribution of naturalized plants is best predicted by socioeconomic activities 20 years ago. We took advantage of the observed time lag and used trade developments until recent times to predict naturalized plant trajectories for the next two decades. This shows that particularly strong increases in naturalized plant numbers are expected in the next 20 years for emerging economies in megadiverse regions. The interaction with predicted future climate change will increase invasions in northern temperate countries and reduce them in tropical and (sub)tropical regions, yet not by enough to cancel out the trade-related increase.

Text S1. Detailed description of model parameterization.

Text S2. Sensitivity analysis.

Text S3. List and discussion of major model assumptions.

Figure S1. Temporal development (1948–2009) of exchanged trade volumes.

Figure S2. Temporal development of the sizes of the two bilateral trade data sets.

Figure S3. Visualization of data used as predictor variables in model.

Figure S4. Predicted future increases in annual mean temperature and annual mean precipitation.

Figure S5. Intercorrelations of the probabilities P(Alien), P(Intro) and P(Estab).

Figure S6. Temporal development of goodness-of-fits for various model modifications.

Figure S7. Influence of changes of parameter values on model results.

Figure S8. Influence of the number of selected case studies (3–11 studies) on model accuracy.

Figure S9. Variation of model predictions for each country.

Figure S10. Predicted and reported number of naturalized plants of the 12 case studies used for parameterization.

Figure S11. Temporal development of the Pearson's correlation coefficient between the two bilateral annual trade data sets.

Table S1. The total number of naturalized plants transported from a donor region to a recipient region.

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Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species

In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a “sixth” mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.

1. Introduction

Anthropogenic activities have changed the global environment, reducing the biodiversity through extinction and also reducing the population size of already surviving species. Due to man-made activities and interruptions, the current rate of species extinction is 1,000 times higher than natural background rates of extinction and future rates are likely to be 10,000 times higher [1]. According to IUCN 2015 report, currently 79,837 species were assessed, of which 23,250 are threatened with extinction. Only one-third of the world’s freshwater fishes are at risk from hydropower dam expansion [2]. According to various estimates, each year few thousands to 100,000 species extinct, most without ever having been scientifically described [3]. Due to these tremendous anthropogenic activities, the notion has been emerged that earth biota is entering a “sixth” mass extinction [4] which is based on the facts that recent rates of species extinction are very high than prehuman background rates [5, 6]. Only in the Island of Tropical Oceana, 1800 bird species were reported to extinct in approximately 2000 years, since human colonization [7]. Even in the scientifically advanced 19th and 20th centuries, numerous species of birds, mammals, reptiles, fresh water fishes, amphibians, and other organisms extinction have been documented [5, 8, 9]. If species extinction persists at such a tremendous speed, future generation will occupy a planet with significantly reduce biodiversity, diminished ecosystem services, reduced evolutionary potential, and ultimately higher extinction rate and collapse ecosystem [3, 10].

It is a major challenge for biologists and ecologists to protect endangered species. Several measures have been taken and efforts done in this regard which is extensively described in literature such as population viability analysis, formulation of metapopulation theory, species conservation, contribution of molecular biology, development of global position system, geographical information system, and remote sensing [11]. In the recent era, genomics is a key part of all the biological sciences and a quickly changing approach to conservation biology. The genomes of many thousands of organisms including plants, vertebrates, and invertebrates have been sequenced and the results augmented, are annotated, and are refined through the use of new approaches in metabolomics, proteomics, and transcriptomics that enhance the characterization of metabolites, messenger RNA, and protein [12]. The genomic approaches can provide detail information about the present and past demographic parameters, phylogenetic issues, the molecular basis for inbreeding, understanding genetic diseases, and detecting hybridization/introgression in organisms [13]. It can also provide information to understand the mechanisms that relate low fitness to low genetic variation, for integrating genetic and environmental methodologies to conservation biology and for designing latest, fast monitoring tools. The rapid financial and technical progress in genomics currently makes conservation genomics feasible and will improve the feasibility in the very near future even [14]. The objective of this review is to describe recently advanced molecular technologies and their role in species conservation. We have described the effectiveness and possibility of conservation technology using the advance genomic approaches along with their limitations and future development. We hope that this review will provide fundamentals and new insights to both new readers and experienced biologists and ecologists in formulating new tools and establishing technologies to prevent endangered species.

2. Biodiversity and Conservation

Biodiversity refers to the variety of all forms of life on this planet, including various microorganisms, plants, animals, the ecosystem they form, and the genes they contain. Biodiversity within an area, biome, or planet is therefore considered at three levels including species diversity, genetic diversity, and ecosystem diversity [15]. As the names indicate, species diversity refers to the variety of species genetic diversity is the variation of genes within species and populations and ecosystem diversity relates to the variety of habitats, ecological processes, and biotic communities in the biosphere [15]. Today’s biodiversity about 9.0 to 52 million species is the result of billions of years of evolution, shaped by natural phenomena, and forms the web of life of which we are an integral part and upon which we are so fully [15, 16]. For species adaptation and survival, genetic diversity is the basic element and all the evolutionary achievement and to some degree survival depend on it. Though both adaptation and survival can be viewed in terms of space, time, and fitness but fitness further includes adaptation, genetic variability, and stability. The phenomenon of extinction can be the result of either abiotic or biotic stresses, caused by various factors such as disease, parasitism, predation, and competition or due to habitat alteration or isolation due to human activities, natural catastrophes, and slow climatic and geological changes. Considering these persistent threats, it is very crucial that genetic diversity in species should be appropriately understood and efficiently conserved and used [17].

At present, several species are in retreat, losing localities, and increasingly threatened with extinction by various factors mainly human intervention, and thus conservation biology has become a major file in recent times. A “threatened” designation generally recognizes a significant risk of becoming endangered throughout all or a portion of a species’ range. Although extinction is a natural process, the human understanding of the value of the endangered species and its realization to intervene the stability of the environment is rapidly increasing. Human interferes in the natural environment of species in different ways, such as destruction of natural habitat, the introduction of nonnative organisms, and direct killing of natural components of a population [18]. Maintaining natural variation of species is beneficial from an economical, ecological, and social perspective. Several combinations of benefit occur for any particular species, and some species are obviously more valuable than the others.

Currently, the maintenance of rare and endangered species is a main focus of interest of biologists and geneticists. The impact of extinction is not always apparent and difficult to predict, and thus several parameters have been set and different technologies are being developed. For example, population viability analysis (PVA) quantitatively predicts the probability of extinction and prioritizes the conservation needs. It takes into account the combined impact of both stochastic (including the demography, environment, and genetics) and terministic (including habitat loss and overexploitation) factors [11]. Mandujano and Escobedo-Morales using PVA method for howler monkeys (Alouatta palliata mexicana) to simulate a group trend and local extinction and to investigate the role of demographic parameters to population growth under two landscape scenarios isolated populations and metapopulation [19]. They found that the rate of relative reproductive success and fecundity is directly linked with the number of adult females per fragment. As a result, the finite growth rate depended mainly on the survival of adult females while in both isolated populations and metapopulation the probability of extinction was exponentially dependent on fragment size. Further, it establishes a minimum viable population, predicts population dynamics, establishes conservation management programs, and evaluates its strategies. However, it is limited by several factors for example, it is often very difficult to measure small-population parameters which need to be used in PVA models. This necessitates the development of more comprehensive and well-established approaches that can not only predict the extinction but also predict rather at a very early stage.

3. Role of Genomics Analysis Tools in Species Conservation

The term genome is about 75 years old and refers to the total set of genes on chromosomes or refers to the organism complete genetic material [20]. Together with the effect of an environment, it forms the phenotype of an individual. Thomas Roderick in 1986 coined the term genomics as a scientific discipline which refers to the mapping, sequencing, and analysis of the genome [21]. Now due to universal acceptance of genomics, it expands and is generally divided into functional and structural genomics. Structural genomics refers to the evolution, structure, and organization of the genome while functional genomics deals with the expression and function of the genome. Functional genomics needs assistance from structural genomics, mathematics, computer sciences, computational biology, and all areas of biology [22].

Genome analysis was once limited to model organisms [23] but now the genomes of thousands of organisms including plants, invertebrates, and vertebrates have been sequenced and the results annotated are further refined and augmented by using new approaches in metabolomics, proteomics, and transcriptomics [12]. Nowadays, it is quite easier to investigate the population structure, genetic variations, and recent demographic events in threatened species, using population genomic approaches. With recent developments, hints for becoming endangered species can be found in their genome sequences. For example, any deleterious mutations in the genes for brain function, metabolism, immunity, and so forth can be easily detected by advanced genomic approaches. Conversely, these can also detect any changes in their genome which may result in enhanced functions of some genes, for example, related to enhanced brain function and metabolism that may lead to the abnormal accumulation of toxins [24–26]. Specific genetic tools and analytical techniques are used to assess the genome of various species to detect genetic variations associated with specific conservation and population structure. Currently, most commonly used genetic tools for detection of genetic variations in both plant and animal species include random fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), random amplification of polymorphic DNA (RAPD), single strand conformation polymorphism (SSCP), minisatellites, microsatellites, single nucleotide polymorphisms (SNPs), DNA and RNA sequence analysis, and DNA finger printing. Analysis of genetic variation in species or population using these tools is carried out either using current DNA of individuals or historic DNA [27]. These tools target different variables within the genome of target species and selection of the specific tools and gnome part to be analyzed is carried out based on the available information. For example, mitochondrial DNA in animals possessing a high substitution rate is a useful marker for the determination of genetic variations in individuals of the same species. However, these techniques have several limitations associated with them. For instance, genetic high substitution rate in animal mitochondrial DNA is only inherited in female lines. Similarly, the mitochondrial DNA in plants has a very high rate of structural mutations and thus can rarely be used as genetic marker for detection of genetic variation. Various genomic tools used for the detection of genetic variations in species and limitations associated with them are summarized in Figure 1. Genome-wide association studies (GWAS), development of genome-wide genetic markers for DNA profiling and marker assisted breeding, and quantitative trait loci (QTL) analysis in endangered and threatened species can give us information about the role of natural selection at the genome level and identification of loci linked with the disease susceptibility, inbreeding depression, and local adaptations. For example, most of the QTLs have been detected using linkage mapping and cover large segments of the genome in different species. Currently, due to the availability of high-density SNP chips and genome-wide analysis techniques, GWAS has proven to be effective in identification of important genomic regions more precisely within the genome of species, for example, those associated with genetic variations and important qualitative and quantitative traits [28]. Further, use of population genetics and phylogenomics can help us in identifying conservation units for recovery, management, and protections [23]. As the genome of more species is sequenced, the rescue of more endangered species will become easier. The applications of advance genomics in the conservation of threatened biota are illustrated in Figure 2.

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