Conserving genetic resources whabplant breeders can do to address crop vulnerability

Conserving genetic resources

1. Conserving Genetic Resources

2. What is genetic vulnerability? “Genetic vulnerability is a term used to indicate the genetic homogeneity and uniformity of a group of plants that predisposes it to susceptibility to a pest, pathogen, or environmental hazard of large-scale proportions”. A case in point is the 1970 epidemic of southern leaf blight ( Helminthosporium maydis ) in the USA that devastated the corn industry. This genetic vulnerability in corn was attributed to uniformity in the genetic background in corn stemming from the widespread use of T-cytoplasm in corn hybrid seed production. The key factors that are responsible for the disastrous epidemics attributable to genetic vulnerability of crops are: The desire by breeders or consumers for uniformity in the trait that controls susceptibility to the biotic or abiotic environmental stress. The acreage devoted to the crop cultivar and the method of production.

3. What plant breeders can do to address crop vulnerability ? Reality check First and foremost, plant breeders need to be convinced that genetic vulnerability is a real and present danger. Without this first step, efforts to address the issue are not likely to be taken seriously. In soybean, it is estimated that only six cultivars constitute more than 50% of the genetic base of North American germplasm. Similarly, more than 50% of the acreage of many crops in the USA is planted to less than 10 cultivars per crop. Use of wild germplasm Many of the world’s major crops are grown extensively outside their centers of origin where they coevolved with pests and pathogens. Breeders should make deliberate efforts to expand the genetic base of their crops by exploiting genes from the wild progenitors of their species that are available in various germplasm repositories all over the world. Paradigm shift T here is a need for a paradigm shift regarding the use of germplasm resources. Traditionally, breeders screen accessions from exotic germplasm banks on a phenotypic basis for clearly defined and recognizable features of interest. Desirable genotypes are crossed with elite cultivars to introgress genes of interest. However, this approach is effective only for the utilization of simply inherited traits (conditioned by single dominant genes). The researchers proposed a shift from the old paradigm of looking for phenotypes to a new paradigm of looking for genes. To accomplish this, the modern techniques of genomics may be used to screen exotic germplasm using a genebased approach. They propose the use of molecular linkage maps and a new breeding technique called advanced backcross QTL (quantitative trait loci) that allows the breeder to examine a subset of alleles from the wild exotic plant in the genetic background of an elite cultivar.

4. What plant breeders can do to address crop vulnerability ? Use of biotechnology to create new variability The tools of modern biotechnology, such as rDNA, cell fusion, somaclonal variation, and others, may be used to create new variability for use in plant breeding. Genetic engineering technologies may be used to transfer desirable genes across natural biological barriers. Gene pyramiding Plant breeders may broaden the diversity of resistance genes as well as introduce multiple genes from different sources into cultivars using the technique of gene pyramiding , which allows the breeder to insert more than one resistance gene into one genotype. This approach will reduce the uniformity factor in crop vulnerability.

5. Conservation of plant genetic resources Plant breeders manipulate variability in various ways for example, they assemble, recombine, select, and discard. The preferential use of certain elite genetic stock in breeding programs has narrowed the overall genetic base of modern cultivars. As already noted, pedigree analysis indicates that many cultivars of certain major crops of world importance have common ancestry, making the industry vulnerable to disasters (e.g., disease epidemics, climate changes). National and international efforts have been mobilized to conserve plant genetic resources

6. Why conserve plant genetic resources? There are several reasons why plant genetic resources should be conserved: Plant germplasm is exploited for food, fiber, feed, fuel, and medicines by agriculture, industry, and forestry. As a natural resource, germplasm is a depletable resource. Without genetic diversity, plant breeding cannot be conducted. Genetic diversity determines the boundaries of crop productivity and survival. As previously indicated, variability is the life blood of plant breeding. As society evolves, its needs will keep changing. Similarly, new environmental challenges might arise (e.g., new diseases, abiotic stresses) for which new variability might be needed for plant improvement.

7. Genetic erosion “ Genetic erosion may be defined as the decline in genetic variation in cultivated or natural populations largely through the action of humans”. Loss of genetic variation may be caused by natural factors , and by the actions of crop producers , plant breeders , curators of germplasm repositories, and others in society at large. Natural factors Genetic diversity can be lost through natural disasters such as large-scale floods, wild fires, and severe and prolonged drought. These events are beyond the control of humans. Action of farmers Right from the beginnings of agriculture, farmers have engaged in activities that promote genetic erosion. These include clearing of virgin land in, especially, germplasm-rich tropical forests, and the choice of planting material (narrow genetic-based cultivars). Farmers, especially in developed economies, primarily grow improved seed , having replaced most or all landraces with these superior cultivars. Also, monoculture tends to narrow genetic diversity as large tracts of land are planted to uniform cultivars. Extending grazing lands into wild habitats by livestock farmers, destroys wild species and wild germplasm resources.

8. Action of breeders Farmers plant what breeders develop. Some methods used for breeding (e.g., pure lines, single cross, multilines ) promote uniformity and a narrower genetic base. When breeders find superior germplasm, the tendency is to use it as much as possible in cultivar development. In soybean, as previously indicated, most of the modern cultivars in the USA can be traced back to about half a dozen parents. This practice causes severe reduction in genetic diversity. Problems with germplasm conservation In spite of good efforts by curators of germplasm repositories to collect and conserve diversity, there are several ways in which diversity in their custody may be lost. The most obvious loss of diversity is attributed to human errors in the maintenance process (e.g., improper storage of materials leading to loss of variability). Also, when germplasm is planted in the field, natural selection pressure may eliminate some unadapted genotypes. Also, there could be spontaneous mutations that can alter the variability in natural populations. Hybridization as well as genetic drift incidences in small populations are also consequences of periodic multiplication of the germplasm holdings by curators. General public action As previously indicated, there is an increasing demand on land with increasing populations. Such demands include settlement of new lands , and the demand for alternative use of the land (e.g., for recreation, industry, roads) to meet the general needs of modern society. These actions tend to place wild germplasm in jeopardy. Such undertakings often entail clearing of virgin land where wild species occur.

9. Nature of cultivated plant genetic resources Currently five kinds of cultivated plant materials are conserved by concerted worldwide efforts – Landraces (folk or primitive varieties) , Obsolete Varieties , Commercial Varieties (Cultivars) , Plant Breeders’ Lines , Genetic stocks . Landraces are developed by indigenous farmers in various traditional agricultural systems or are products of nature. They are usually very variable in composition. Obsolete cultivars may be described as “ex-service” cultivars because they are no longer used for cultivation. Commercial cultivars are elite germplasm currently in use for crop production. These cultivars remain in production usually from 5 to 10 years before becoming obsolete and replaced. Breeders’ lines may include parents that are inbred for hybrid breeding, genotypes from advanced yield tests that were not released as commercial cultivars, and unique mutants. Genetic stocks are genetically characterized lines of various species. These are advanced genetic materials developed by breeders, and are very useful and readily accessible to other breeders. There are two basic approaches to germplasm conservation – in situ and ex situ . These are best considered as complementary rather than independent systems

10. Approaches for germplasm conservation In situ conservation This is the preservation of variability in its natural habitat in its natural state (i.e., on site). It is most applicable to conserving wild plants and entails the use of legal measures to protect the ecosystem from encroachment by humans. These protected areas are called by various names (e.g., nature reserves, wildlife refuges, natural parks ). Needless to say, there are various socioeconomic and political ramifications in such legal actions by governments. Environmentalists and commercial developers often clash on such restricted use or prohibited use of natural resources. This approach to germplasm conservation is indiscriminatory with respect to species conserved (i.e., all species in the affected area are conserved). Ex situ conservation In contrast to in situ conservation, ex situ conservation entails planned conservation of targeted species (not all species). Germplasm is conserved not in the natural places of origin but under supervision of professionals off site in locations called germplasm or gene banks . Plant materials may be in the form of seed or vegetative materials. The advantage of this approach is that small samples of the selected species are stored in a small space indoors or in a field outdoors , and under intensive management that facilitates their access to breeders. However, the approach is prone to some genetic erosion (as previously indicated) while the evolutionary process is halted. The special care needed is expensive to provide.

11. Germplasm collection Planned collections (germplasm explorations or expeditions) are conducted by experts to regions of plant origin. These trips are often multidisciplinary, comprising members with expertise in botany, ecology, pathology, population genetics, and plant breeding. Familiarity with the species of interest and the culture of the regions to be explored are advantageous. Most of the materials collected are seeds, even though whole plants and vegetative parts (e.g., bulbs, tubers, cuttings, etc.) and even pollen may be collected. Because only a small amount of material is collected, sampling for representativeness of the population’s natural variability is critical in the collection process, in order to obtain the maximum possible amount of genetic diversity. For some species whose seed is prone to rapid deterioration, or are bulky to transport, in vitro techniques may be available to extract small samples from the parent source. Collectors should bear in mind that the value of the germplasm may not be immediately discernible. Materials should not be avoided for lack of obvious agronomically desirable properties. It takes time to discover the full potential of germplasm. Seed materials vary in viability characteristics. These have to be taken into account during germplasm collection, transportation, and maintenance in repositories. Based on viability, seed may be classified into two main groups – orthodox and recalcitrant seed: 1 Orthodox seeds . These are seeds that can prolong their viability under reduced moisture content and low temperature in storage. Examples include cereals, pulses, and oil seed. Of these, some have superior (e.g., okra) while others have poor (e.g., soybean) viability under reduced moisture cold storage. 2 Recalcitrant seeds . Low temperature and decreased moisture content are intolerable to these seeds (e.g., coconut, coffee, cocoa). In vitro techniques might be beneficial to these species for long-term maintenance. The conditions of storage differ depending on the mode of reproduction of the species: 1 Seed propagated species . These seeds are first dried to about 5% moisture content and then usually placed in hermetically sealed moisture-proof containers before storage. 2 Vegetatively propagated species . These materials may be maintained as full plants for long periods of time in field gene banks, nature reserves, or botanical gardens. Alternatively, cuttings and other vegetative parts may be conserved for a short period of time under moderately low temperature and humidity. For long-term storage, in vitro technology is used

12. Types of plant germplasm collections There are four types of plant genetic resources maintained by germplasm repositories – base collections , backup collections , active collections , and breeders’ or working collections . These categorizations are only approximate since one group can fulfill multiple functions. Base collections These collections are not intended for distribution to researchers, but are maintained in long-term storage systems. They are the most comprehensive collections of the genetic variability of species. Entries are maintained in the original form. Storage conditions are low humidity at subfreezing temperatures ( - 10 to - 18°C) or cryogenic ( - 150 to - 196°C), depending on the species. Materials may be stored for many decades under proper conditions. Backup collections The purpose of backup collections is to supplement the base selection. In case of a disaster at a center responsible for a base collection, a duplicate collection is available as insurance. In the USA, the National Seed Storage Laboratory at Fort Collins, Colorado, is a backup collection center for portions of the accessions of the Centro Internationale de Mejoramiento de Maiz y Trigo (CIMMYT) and the International Rice Research Institute (IRRI). Active collections Base and backup collections of germplasm are designed for long-term unperturbed storage. Active collections usually comprise the same materials as in base collections, however, the materials in active collections are available for distribution to plant breeders or other patrons upon request. They are stored at 0°C and about 8% moisture content, and remain viable for about 10–15 years. To meet this obligation, curators of active collections at germplasm banks must increase the amount of germplasm available to fill requests expeditiously. Because the accessions are more frequently increased through field multiplication, the genetic integrity of the accession may be jeopardized. Working or breeders’ collections Breeders’ collections are primarily composed of elite germplasm that is adapted. They also include enhanced breeding stocks with unique alleles for introgression into these adapted materials. In these times of genetic engineering, breeders’ collections include products of rDNA research that can be used as parents in breeding programs

13. Managing plant genetic resources The key activities of curators of germplasm banks include regeneration of accessions, characterization, evaluation, monitoring seed viability and genetic integrity during storage, and maintaining redundancy among collections. Germplasm banks receive new materials on a regular basis. These materials must be properly managed so as to encourage and facilitate their use by plant breeders and other researchers. Regeneration Germplasm needs to be periodically rejuvenated and multiplied. The regeneration of seed depends on the life cycle and breeding system of the species as well as cost of the activity. To keep costs to a minimum and to reduce loss of genetic integrity, it is best to keep regeneration and multiplication to a bare minimum. It is a good strategy to make the first multiplication extensive so that ample original seed is available for depositing in the base and duplicate or active collections. The methods of regeneration vary for self-pollinated, cross-pollinated , and apomictic species. A major threat to genetic integrity of accessions during regeneration is contamination (from outcrossing or accidental migration), which can change the genetic structure. Other factors include differential survival of alleles or genotypes within the accession, and random drift. The isolation of accessions during regeneration is critical, especially in cross-pollinated species, to maintaining genetic integrity. This is achieved through proper spacing, caging, covering with bags, hand pollination, and other techniques. Regeneration of wild species is problematic because of high seed dormancy, seed shattering, high variability in flowering time, and low seed production . Some species have special environmental requirements (e.g., photoperiod, vernalization) and hence it is best to rejuvenate plants under conditions similar to those in the places of their origin, to prevent selection effect, which can eliminate certain alleles. Characterization Users of germplasm need some basic information about the plant materials to aid them in effectively using these resources. Curators of germplasm banks characterize their accessions, an activity that entails a systematic recording of selected traits of an accession . Traditionally, these data are limited to highly heritable morphological and agronomic traits. However, with the availability of molecular techniques, some germplasm banks have embarked upon molecular characterization of their holdings. For example, CIMMYT has used the simple sequence repeat (SSR) marker system for characterizing the maize germplasm in their holding. Passport data are included in germplasm characterization. These data include an accession number, scientific name, collection site (country, village), source (wild, market), geography of the location, and any disease and insect pests. To facilitate data entry and retrieval, characterization includes the use of descriptors . These are specific pieces of information on plant or geographic factors that pertain to the plant collection. The International Plant Genetic Resources Institute (IPGRI) has prescribed guidelines for the categories of these descriptors. Descriptors have been standardized for some species such as rice .

14. Evaluation Genetic diversity is not usable without proper evaluation. Preliminary evaluation consists of readily observable traits. Full evaluations are more involved and may include obtaining data on cytogenetics, evolution, physiology, and agronomy . More detailed evaluation is often done outside of the domain of the germplasm bank by various breeders and researchers using the specific plants. Traits such as disease resistance, productivity, and quality of product are important pieces of information for plant breeders. Without some basic information of the value of the accession, users will not be able to make proper requests and receive the most useful materials for their work. Monitoring seed viability and genetic integrity During storage, vigor tests should be conducted at appropriate intervals to ensure that seed viability remains high. During these tests, abnormal seedlings may indicate the presence of mutations. Exchange The ultimate goal of germplasm collection, rejuvenation, characterization, and evaluation is to make available and facilitate the use of germplasm. There are various computer-based genetic-resource documentation systems worldwide, some of which are crop-specific. These systems allow breeders to rapidly search and request germplasm information. There are various laws regarding, especially, international exchange of germplasm. Apart from quarantine laws, various inspections and testing facilities are needed at the point of germplasm.

15. Germplasm storage technologies Once collected, germplasm is maintained in the most appropriate form by the gene bank with storage responsibilities for the materials. Plant germplasm may be stored in the form of pollen, seed, or plant tissue. Woody ornamental species may be maintained as living plants, as occurs in arboreta. Indoor maintenance is done under cold storage conditions, with temperatures ranging from - 18 to - 196°C. Seed storage Seeds are dried to the appropriate moisture content before being placing in seed envelopes. These envelopes are then arranged in trays that are placed on shelves in the storage room. The storage room is maintained a - 18°C, a temperature that will keep most seeds viable for up to 20 years or more. The curator of the laboratory and the staff periodically sample seeds of each accession to conduct a germination test. When germination falls below a certain predetermined level, the accession is regrown to obtain fresh seed. Field growing Accessions are regrown to obtain fresh seed or to increase existing supplies (after filling orders by scientists and other clients). To keep the genetic purity, the accessions are grown in isolation, each plant covered with a cotton bag to keep foreign sources of pollen out and also to ensure self-pollination. Cryopreservation Cryopreservation or freeze-preservation is the storage of materials at extremely low temperatures of between - 150 to - 196°C in liquid nitrogen. Plant cells, tissue, or other vegetative material may be stored this way for a long time without loosing regenerative capacity. Whereas seed may also be stored by this method, cryopreservation is reserved especially for vegetatively propagated species that need to be maintained as living plants. Shoot tip cultures are obtained from the material to be stored and protected by dipping in a cryoprotectant (e.g., a mixture of sugar and polyethylene glycol plus dimethylsulfoxide ). In vitro storage Germplasm of vegetatively propagated crops is normally stored and distributed to users in vegetative forms such as tubers, corms, rhizomes, and cuttings. However, it is laborious and expensive to maintain plants in these forms. In vitro germplasm storage usually involves tissue culture. There are several types of tissue culture systems (suspension cells, callus, meristematic tissues). To use suspension cells and callus materials, there must be an established system of regeneration of full plants from these systems, something that is not available for all plant species yet. Consequently, meristem cultures are favored for in vitro storage because they are more stable. The tissue culture material may be stored using the method of slow growth (chemicals are applied to retard the culture temperature) or cryopreservation. Molecular conservation The advent of biotechnology has made it possible for researchers to sequence DNA of organisms. These sequences can be searched for genes at the molecular level. Specific genes can be isolated by cloning and used in developing transgenic products.

16. Germplasm enhancement or prebreeding The process of the initial introgression of a trait from an undomesticated source (wild) or agronomically inferior source, to a domesticated or adapted genotype is called prebreeding or germplasm enhancement . Plant breeders usually make elite × elite crosses in a breeding program. This practice coupled with the fact that modern crop production is restricted to the use of highly favored cultivars, has reduced crop genetic diversity and predisposed crop plants to disease and pest epidemics. To reverse this trend, plant breeders need to make deliberate efforts to diversify the gene pools of their crops to reduce genetic vulnerability. Furthermore, there are occasions when breeders are compelled to look beyond the advanced germplasm pool to find desirable genes. The desired genes may reside in unadapted gene pools. As previously discussed, breeders are frequently reluctant to use such materials because the desired genes are often associated with undesirable effects ( unadapted , unreproductive, yield reducing factors). Hence, these exotic materials often cannot be used directly in cultivar development. Instead, the materials are gradually introduced into the cultivar development program through crossing and selecting for intermediates with new traits, while maintaining a great amount of the adapted traits. To use wild germplasm, the unadapted material is put through a preliminary breeding program to transfer the desirable genes into adapted genetic backgrounds. It may be argued that prebreeding is not an entirely new undertaking, considering the fact that all modern crops were domesticated through this process. The traditional techniques used are hybridization followed by backcrossing to the elite parent, or the use of cyclical population improvement techniques. The issues associated with wide crossing are applicable (e.g., infertility, negative linkage drag, incompatibility), requiring techniques such as embryo rescue to be successful. The modern tools of molecular genetics and other biotechnological procedures are enabling radical gene transfer to be made into elite lines without linkage drag ( e.g.,transfer of genes from bacteria into plants).

17. Major uses of germplasm enhancement The major uses of germplasm enhancement may be summarized as follows: Preventions of genetic uniformity and the consequences of genetic vulnerability. Potential crop yield augmentation. History teaches us that some of the dramatic yield increases in major world food crops, such as rice, wheat, and sorghum, were accomplished through introgression of unadapted genes (e.g., dwarf genes). Introduction of new quality traits (e.g., starch, protein). Introduction of disease- and insect-resistance genes. Introduction of environment-resistance genes (e.g., drought resistance).

18. A population is a group of sexually interbreeding individuals. The capacity to interbreed implies that every gene within the group is accessible to all members through the sexual process. A gene pool is the total number and variety of genes and alleles in a sexually reproducing population that are available for transmission to the next generation. Rather than the inheritance of traits, population genetics is concerned with how the frequencies of alleles in a gene pool change over time.