Plant Biotech Blog

DNA banks or Gene banks are the ultimate facility for the ex situ conservationof genetic material to be sourced for a) genomic studies, b) to compile genomic libraries, and c) to isolate desired genes at will, for genetic engineering. However, currently they are not useful in regenerating whole plants, unlike the other forms of germplasm banking.

Any part of a plant yields DNA.  Plant material is dried using silica gel and stored at -800 C to extract DNA from it.  When fresh supplies not available, DNA can be obtained from dried plant material stored in botanical research institutions that house pressed and dried plant specimens called ‘herbarium’.  Though some fraction of the DNA from dried plants may be degraded, it would yield quality DNA in sufficient quantities.

DNA samples in the banks pass through extensive extraction procedures, minimizing cleaning process before using the sample.  However, the quality and concentration of DNA in a sample vary with species and so concentration procedures may be needed.  Even small quantities of DNA are adequate as they can be amplified a million fold using the technique of ‘polymerase chain reaction’ (PCR) that yields much larger quantities of DNA from minute quantities.

Samples in DNA banks are so well purified that they are stable at ambient temperatures for days in transit. While within the bank under controlled conditions, they are stable almost indefinitely. Ten-year old DNA samples were near perfect.

DNA banking is more economical than other forms of germplasm banking, as it occupies far lesser space, almost indefinitely viable and a small sample can be shared by many researchers through PCR amplification, without the need for repetitive extractions.

DNA BANKS

The following are some important examples among several DNA banks established in different parts of the world, which are networked for collaborative activity:

DNA Bank of the Royal Botanic Gardens, Kew

The DNA Bank at the Jodrell Laboratory, Royal Botanic Gardens, Kew, England,  contains over 22,000 samples of plant genomic DNA, all stored at -80°C. Information on the stored DNA is databased providing the names of the species, collectors, localities, etc. Each sample has a reference voucher of a herbarium specimen.  This database is linked to the Plant DNA C-values Database and the Database of the International Plant Names Index, which is quite useful.

DNA samples are provided to the collaborators all over world but can also be purchased by the others on a Material Transfer Agreement.

Plant DNA Bank in Korea (PDBK)

The PDBK website provides genomic lists of stored DNA and tissue samples, and their voucher information (label, specimen, and photo) held in PDBK and Korea University Herbarium (KUS), both located in the Graduate School of Biotechnology, Korea University, Seoul, Korea.

The Australian Plant DNA Bank (APDB)

The APDB located at Southern Cross University’s Centre for Plant Conservation Genetics at Lismore, is a comprehensive collection of DNA from both Australian native and important crop plant species. It also contains DNA of transgenic organisms developed through genetic engineering.  The APDB has invested heavily in advanced DNA storage facilities to ensure long term preservation of extracted DNA.

Missouri Botanical Garden’s DNA Bank (MBGDB)

Although the MBG describes its activity as ‘DNA Banking’, there is no evidence on its website that MBG banks extracted DNA samples.  It is a collection of samples of plant material stored at -20°C, suitable for DNA extraction.  Voucher specimens for these samples are deposited at the MBG or other institutions.  The material is provided to researchers against an agreement for molecular studies but not for commercial purposes such as bioprospecting, or screening for genes of interest in agricultural research.

DNA Bank Brazilian Flora Species

The Bank at the Rio de Janeiro Botanical Garden aims to preserve representative genetic material of the Brazilian flora, for plant conservation and biotechnology.

DNA Bank at Kirstenbosch

The Leslie Hill Molecular Systematics Laboratory at Kirstenbosch, in collaboration with the Royal Botanic Gardens, Kew, established a DNA bank to house genetic material of South African plants.  Extracted nuclear, mitochondrial and plastid DNA is stored at

-80ºC.  Each accession has a corresponding herbarium voucher.

NIAS DNA Bank

The NIAS, Ibanaki, Japan, is maintaining DNA samples and information gathered as a part of the genome projects of the Ministry of Agriculture, Forestry and Fisheries such as the Rice Genome Research Program (RGP).  cDNA clones, RFLP and other markers, PAC/BAC clones and YAC filters are available for distribution.

NATIONAL BUREAU OF PLANT GENETIC RESOURCES (NBPGR)

The NBPGR, New Delhi, India, has DNA fingerprinted about 2,200 crop varieties, and has expanding facilities for DNA banking.

GENE BANKS IN THE PRIVATE SECTOR

The private sector organizations, mostly multinational corporations, engaged in genetic engineering of crop plants have extensive collections of crop plant DNA.  Their extensive genomic libraries are an important source of useful genes for crop improvement.  However, this valuable material and information are not generally accessible to the public sector.

RESPONSIBILITIES OF DNA BANKS

The DNA banks have serious responsibilities in order to fulfill their mandates.  The more important of them are:

1. • Ensuring the authenticity of the scientific identity, source and geneology of the source species;
   • Adopting state of the art procedures of collection, recording, processing and preservation of DNA;
   • Maintaining quality DNA in adequate quantities;
   • Ensuring responsible use of the material supplied to others, assuring equitable benefit sharing by all parties;
   • Networking internationally, with other DNA banks, facilitating exchange of knowledge and material and to prevent duplication of efforts; and
   • Updating websites frequently and fulfilling the promises made.

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CONSERVATION OF PLANT GENETIC RESOURCES
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CONSERVATION OF PLANT SPECIES IN GERMPLASM BANKS

Tissue Culture and Micropropagation

Cells differentiated through natural life processes in several different specific ways form the tissues and organs in organisms.  The earlier undifferentiated cells can be made to develop along specific directed lines to develop into tissues, organs and even whole organisms in synthetic media in the laboratory, through process a called tissue culture.   While natural cells, tissues and organs can be made to respond in tissue culture, the technique can also be used to modify natural or tissue culture originated cells, tissues and organs in almost any manner.  On the medical side the stem cells are being explored and exploited to develop tissues and organs for transplantation to replace defunct parts.

The undifferentiated cells in the growing points of plants and animals are totipotent in the sense they can be made to develop into any type of cell of the organism and so the whole organism, through appropriate procedures in the laboratory.  Elegant tissue culture protocols are widely used in a variety of experimental and production phases both for plants and animals.  Since all this happens in the laboratory glassware, it is called in vitro (in glass), in contrast to in vivo that happens in the living systems.

In plants the growing points that contain undifferentiated are called meristems.  The meristematic cells can be tissue cultured to produce tissues, organs and whole plants.  Tissue culture produced tissues, organs and plantlets, that constitute germplasm, can be cryopreserved regenerated at a later date when needed using tissue culture protocols.  Pollen can be cultured to produce haploid plants (containing only one set of chromosomes instead of the usual two sets) and even fertilization and seed development can be achieved in vitro.  This facility provides for the conservation of plant germplasm in germplasm banks, variously called in vitro banks or tissue banks or gene banks.

When a piece of meristematic plant tissue (explant) of any part of a plant is subjected to culture protocols, it develops into an undifferentiated mass of cells (callus), from which numerous heart shaped structures (embryoids) arise.  Each one of these embryoids can be cultured into a whole plant in the laboratory.  The embryoids encapsulated in calcium alginate or other suitable material, called synthetic or artificial ‘seeds’, can be cryopreserved for long periods till required for use.

As a very large number of embryoids develop from cultured callus, it is possible to produce thousands of plantlets.  The plantlets are transferred to soil to acclimatize (hardened) and taken to the field to raise a crop.  This process is micropropagation, a way of cloning, which is used extensively to produce genetically uniform plants.  These plants are disease free at least till they are taken to the soil.   There are hundreds of success stories of mass cultivation of plants produced through micropropagation with such crops as banana, plantation tree species as eucalyptus and poplars, and ornamental species as orchids.

Cell and tissue culture techniques are also largely required in developing whole plants from transformed cells in genetic engineering.

In vitro Banks require expensive infrastructure and expertise in collecting, processing and culturing plant material and to preserve and regenerate the cultured material into plants.  The viability of the banked germplasm varies with the experimental finesse and the species, and hence it has to be periodically checked.  Germplasm banking is more reassuring than seed banks, where once the seed viability is lost, the collections become unusable.  Like the seeds in seed banks, banked in vitro germplasm can be a source of DNA, for use in genetic engineering even when it is unviable.

Thousands of institutions have been engaged in plant tissue culture for over three decades and several succeeded in culturing a very large number of economically plant species, but only a few worked on crop plants.  While many institutions claim in vitro banks, only a few such as the Plant DNA Bank in Korea, are credible.   Some like the National Bureau of Plant Genetic Resources, New Delhi, India, bank only explant material.  Seed in the seed banks can also be used for tissue culture purposes.

Material in the in vitro banks suffers from some disadvantages.  Being much more sensitive to storage conditions, particularly temperature and humidity, than seeds and extracted DNA, the material requires very precisely controlled facilities to ensure longer viability periods.  Though plantlets produced through micropropagation can be transported rather easily, other kinds of in vitro banked material require special facilities for transit.  Tissue culturing requires high level of technical expertise and production costs are very high. 

Responsibilities of Germplasm Banks

The in vitro banks have serious responsibilities in order to fulfill their mandates.  The more important of them are:

1. • Ensuring the authenticity of the scientific identity, source and geneology of the explant source species;
   • Adopting state of the art procedures of collection, recording, processing, culturing  and preserving the cultured material;
   • Maintaining viability of the banked material and replenishing material of doubtful quality;
   • Ensuring responsible use of the material supplied to others, assuring equitable benefit sharing by all parties;
   • Networking internationally, with other in vitro banks, facilitating exchange of knowledge and material and to prevent duplication of efforts; and
   • Updating websites frequently and fulfilling the promises made.

RELATED ARTICLES:
CONSERVATION OF PLANT GENETIC RESOURCES
CONSERVATION OF PLANT SPECIES IN SEED BANKS
CONSERVATION OF PLANT SPECIES IN DNA BANKS

There is a pressing need is for the conservation of crop genetic resources, but it is largely impractical to conserve the very large number of crop species and their wild relatives in their natural habitats.  A viable alternative is to conserve whole seed in Seed Banks.  The seeds are germinated to raise plants from them for use in crop improvement.

The important role seed banks play in the conservation of crop genetic resources is now globally recognized.

Various techniques have been developed for preserving seed, retaining their viability for longer periods.  As temperature and humidity are very critical factors, cleaned seeds are stored at around -20o C, often using silica gel in the seed containers to reduce humidity.  Seeds may also be stored over liquid nitrogen around -186oC (cryopreservation), which maintains retains seed viability for very long periods.

Seeds in the seed banks need to be protected from pests and pathogens while in storage, but the risk from seed borne pests and pathogens persists.

THE INTERNATIONAL SEED TREATY (IST)

The International Treaty on Plant Genetic Resources for Food and Agriculture of the United Nations (the International Seed Treaty, IST), in force since June 2004, is a comprehensive international agreement in harmony with Convention on Biological Diversity. IST aims at guaranteeing food security through the conservation, exchange and sustainable use of the world’s plant genetic resources for food and agriculture.  It also ensures a fair and equitable benefit sharing arising from such use. Further, it recognizes Farmers’ Rights to a) free access to genetic resources, unrestricted by intellectual property rights; b) to be involved in relevant policy discussions and decision making; and c) to use, save, sell and exchange seeds, subject to national laws.

SEED BANKS

Seed banks can provide controlled plant material of high quality and genetic diversity for research, eliminating the need for expensive expeditions.

There are several seed banks in different countries, at the national, regional and local levels.  Some of the best seed banks in the world are in Peru, Colombia, Syria, India, Ethiopia, and the Philippines. Most botanical gardens also have seed collections.

A number of other seed banks, some of them called ‘community seed banks’ have been operating for decades with high decibel propaganda.  These have been amassing seed collections in a haphazard manner and without any semblance of science in matters of collection, characterization, identification and preservation.  With the evaporation of the initial enthusiasm or motivating factors, the collections are forgotten.  Such hodgepodge attempts are resources for lobbyists and hobbyists to gain political mileage, rather than tools to promote conservation.

To be of any use serving the objectives of conservation, seed banks with state of the art storage facilities should be established at the national and international levels  and all such banks should be networked so that material, knowledge and expertise on  particular crops is available on a global scale.

The following are among the important international seed banking facilities:

a) The National Bureau of Plant Genetic Resources (NBGPR), New Delhi, India: NBGPR has over 3.43 lakh samples of 2.47 lakh varieties of 1,256 species, which include about 28,000 accessions of wild relatives of various crops.

b) Seed Banks of Global Network of Agricultural Research Institutions:

Ten international agricultural research institutions, co-ordinated by the Consultative Group on International Agricultural Research (CGIAR), Washington, are focused on crops and have extensive seed collections for such crops as rice, maize, wheat, barley, millets, pulses, oil seeds, tuber crops, banana, tropical forage and fruits.  The collections in these seed banks are well documented and the institutions are networked among themselves and with several other institutions.

c) The Millennium Seed Bank Project:

The Millennium Seed Bank Project (MSBP) at the Royal Botanic Garden, Kew, England, is one of the largest conservation projects.  MSBP’s 47 partner organizations in 17 countries intend to store 25 per cent of the world’s plant species by 2020. The Seed Information Database (SID) at Kew is an ongoing compilation of seed characteristics and traits world wide, targeted at >24,000 species.

d) The Svalbard Global Seed Vault:

0n February 26, 2008, the Svalbard Global Seed Vault (SGSV) opened near Longyearbyen (Norway), 600 miles from the North Pole.  SGSV is designed to hold 4.5 billion batches of seeds of the world’s main crops.

The SGSV is a glazed cave-like structure, drilled 500 ft below permafrost, in the middle of a frozen Arctic mountain topped with snow, with the goal to store and protect samples from every seed collection in the world, which will stay frozen.   An automated digital monitoring system controls temperature and humidity and provides high security.

The SGSV is an insurance against natural disasters such as earthquakes and tsunamis, or deliberate attacks like bomb blasts or human errors such as nuclear disasters or failure of refrigeration that may erase the seeds of any important species in the other seed banks or in the wild, in the other countries.  Such seed can be re-established using seeds from SGSV.

LONGEVITY OF SEED IN SEED BANKS

Any seed can imbibe water and swell, which is a mere physical process.  It may even germinate, and produce a short root, but longevity, the potential to develop into a plant is the most crucial factor in seed banking.

The claims that 10,000 year old seed of sacred lotus, arctic lupine and date palm germinated and produced plants were challenged.  Systematic scientific dating of seed and production of plants from them has shown that the germinated date palm seed is about 2,000 yr old and the lotus is 1,200 yr old.  The other authenticated reports on seed longevity are Canna (600 yr), and species of Liparia, Leucospermum and Acacia (200 yr).   Samples of 110 yr old cereal and weed seeds, stored in sealed glass vials in Vienna, germinated.  These are very exceptional examples of long seed viability.

Contemporary data indicate that willow seeds are viable for only a week.  The seeds of tropical rain forest trees have low viability.  Seeds of sugarcane, tea, and coco palm, have a life-span of up to a year. Rush seed was viable for seven years.

Data gathered from 13 worldwide seed-storage stations indicate that seeds of crops such as barley, corn, oats, potato, rice, soybean, and wheat, have half-lives between 3–13 yr, which means that in the period specific for each crop, seed viability comes down by 50 per cent.  Seeds with hard seed coats such as beans and soybean would be viable much longer than the cereals.

Seed banks should periodically check for pests and pathogens and test for seed viability, collect fresh samples from the plants obtained by germinating the old deteriorating samples.  Seed longevity can be maximized only in scientifically managed seed banks.  If the seed loses its longevity, seed banks become seed musea, though the DNA from the seed can be used in genetic engineering of crops.

All life that constitutes Biodiversity depends on plants, the most crucial components of ecosystems in which all microorganisms, animals and humans, live.  Direct threats to plant survival are a combination of habitat loss, aggressive alien species, over exploitation and climate change.  The fundamental causes of these threats are rooted more in uncontrolled population growth, short sighted policies, ignorance or greed.  The consequent socio-economic factors are difficult to control.

Loss of plants leads to worsening food insecurity, increasing vulnerability to disease, lower material wealth, deteriorating social relations and restricted freedom of choice and action.  Despite such deep reliance on plants, continued misuse of ecosystems has taken us to a crisis point.

Conservationof species, particularly the agriculturally important ones which have an impact on human well being, has now attained paramount importance, in our efforts to provide for the sustainable utilization of biological resources, by preventing further loss.

In plants and animals, the DNA is the genetic material that maintains the organism’s continuity from generation to generation.  While a genome is one set of all genes of an organism, a gene pool is all the genes in a population of that species.

The genetic material of many organisms is of immense value and needs to be preserved for the benefit of the future generations.  Plant genetic resources should be available for use in research and breeding in agriculture and forestry.  These are a) actual currently cultivated varieties (cultivars), b) once favoured but now discontinued old cultivars, c) locally developed and preferred varieties called landraces that are or were grown and c) wild relatives of crop species.

The cells (including pollen), tissues, organs, whole single or few celled organisms, seeds or other propagules that serve as a means of regenerating the whole organism, constitute the germplasm which is preserved by various means in controlled storage facilities called biobanks or germplasm banks.  These are variously called as seedbanks, in vitro banks, gene banks and DNA banks, depending upon the material that is conserved in them.    Currently, extracted and preserved DNA cannot be used to regenerate the whole organism, but any chosen gene can be isolated for use in genetic engineering.

Several pressing considerations necessitate biobanking, of which the following are more significant:

1. It is estimated that 60,000 to 1,00,000 plant species, with diverse economic uses,  are under threat of extinction and need to be protected.
2. About three-quarters of crop biodiversity has been lost in the last century.  Eighty per cent of maize varieties known in the 1930s in Mexico no longer exist and in the USA 94 per cent of varieties of peas are no longer grown.
3. During the past 50 years many high yielding and/or otherwise better varieties particularly those with higher pest and disease tolerance, have continuously replaced the once favoured cultivars and landraces.  .
4. The dropped varieties may contain genes affording advantages to future agriculture.  For example, the genes for resistance against the late blight fungus that caused the Irish potato famine in 1845 were taken from South American potato varieties, not in active cultivation.
5. Wild relatives of crop species may contain genes useful in crop improvement. The genes for resistance against red rot of sugarcane that causes heavy losses were introduced from a wild relative (Saccharum spontaneum).
6. The Centres of Origin of the species that gave rise to crops and the original Centres of Domestication of crop varieties are a reservoir of crop genetic resources, most of which have already been lost and the rest need to be conserved.
7. Economics encourage farmers to drop crops and many farms now grow just one or two crops, with very high efficiency.  But on account of genetic uniformity, these crops may become vulnerable to the changes in the habitat, and pests and diseases.  Conservation of crop genetic resources is an insurance against such risks to food security.
8. Farmers have long stopped conserving seed for any reason.

Germplasm banking is a system to conserve crop varieties and their wild relatives, protecting them from the vagaries of climate, politics and human error.

APPROACHES TO SPECIES CONSERVATION

There are two main approaches to conservation wild or cultivated species:

In situ conservation: Conservation in the natural habitats, where evolutionary progression continues.  Over a period of time and several generations, the species/variety may change its genetic and morphological composition and even the desired traits may be lost, if they do not have any advantage to the species in that environment.  While whole populations of wild plant species can be conserved in bioreserves, cultivated species have to be cultivated and so are not amenable for in situ conservation.

Ex situ conservation: Conservation away from the natural habitats, which requires appropriate techniques for long term preservation of the seed or other material in biobanks.   On account of removal from the natural habitat, there is cessation of evolutionary progression, but the desired genes would be preserved.  The seed and other propagules may lose their viability sooner or later, but tissue culture methods may help in the revival of the material, if preservation techniques are appropriate.  Genetic engineering techniques would help in the recovery of the desired genes and their use in developing transgenics of the same or another crop.  While small populations of wild plant species can be grown in botanic gardens, cultivated species offer problems.  Ex situ conservation requires continuous professional attention, elaborate infrastructure and heavy financial inputs.

Since each has some disadvantages and some special advantages, a judicious combination of both in situ and ex situ approaches is needed for successful conservation of species.

RELATED ARTICLES:
CONSERVATION OF PLANT SPECIES IN SEED BANKS
CONSERVATION OF PLANT SPECIES IN GERMPLASM BANKS
CONSERVATION OF PLANT SPECIES IN DNA BANKS