Maize Research Department, Field Corps Inst., Agricultural Research Center, Giza, Egypt




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Conventional and modern breeding methods for disease resistance

Moshera S. E. Sadek (mosherasadek@yahoo.com)

Maize Research Department, Field Corps Inst., Agricultural Research Center, Giza, Egypt


Introduction

Plant diseases are one of the major limiting factors in crop production. Resistance to disease is a common component of plant defense systems in natural ecosystems and can be found in virtually all cultivated species. Agricultural production practices increase crop vulnerability to most diseases, so higher levels of resistance than occur in natural ecosystems may be needed. Virus diseases have long been a special problem area of crop protection. Virus diseases can be devastating in certain cops, reducing both their yield and their quality, yet control measures have been Scarce. The chemical control of plant virus diseases (Cassells, 1983) has been largely ineffective, infeasible or limited to indirect control of virus-transmitting insect vectors. Efficient control of plant virus diseases is difficult to achieve, and should combine use of healthy propagules, other phytosanitary measures, appropriate cultural practices and when available use of resistant cultivars. In general, prophylactic measures or cultural practices alone provide only partial virus control. In addition, these practices may be expensive, time consuming and applicable to only certain crops or situations. In comparison, provided that they also possess desirable yield and quality traits, use of virus-resistant cultivars can provide a simple and cheap approach to reducing the economic damage caused by plant viruses. However, breeding for resistance is a long and costly process and plant breeding companies and their customers need the resistance to be durable, i.e. to provide an efficient protection against the target virus, at least throughout the commercial life of cultivar. Breeding for virus resistance is often considered the most efficient and simplest way to avoid the losses due to plant virus diseases. Resistance mechanisms are very diverse and interact with various stages of the virus cycle in the host plant. Resistance may also differ in their specificity, stability and durability. Breeding for resistance is a long and costly process; therefore to be cost effective it should provide durable protection. Modern molecular biological techniques are allowing deeper insights into plant-pathogen interactions than ever before. Cell culture technology provides a powerful set of tools to produce disease-resistant plant genotypes. The unraveling of plant defence mechanisms and cloning of resistance genes are now opening new avenues for the genetic engineering of crop plants with enhanced resistance to diseases. Plant transformation has become a tool for crop improvement, and lines expressing genes conferring resistance to viruses, insects and herbicides have all found commercial application (Brich 1997).Also, the use of marker-assisted selection (MAS) for introgression of major quantitative trait loci (QTLs) for disease resistance is increasingly being used in crop improvement. In the last decade, MAS has been used in improvement of elite lines for disease resistance (Reyes-valdes, 2000; Bouchez et al., 2002; Frisch and Melchinger, 2005). In this article, conventional and modern breeding methods for disease resistance will be presented as follows

Nature of the resistance

Plant disease resistance can be classified into two categories: qualitative resistance conferred by a single resistance (R) gene and quantitative resistance (QR) mediated by multiple genes or quantitative trait loci (QTLs) with each providing a partial increase in resistance.

Usually, information is available on the nature of the virus resistance, including the genetic determinants and, where resistance studies were done accurately, the resistance mechanism. There is no clear correlation between resistance durability and its mode of inheritance (dominant or recessive genes), although Fraser (1992) noted a tendency for recessive resistances to be more durable. This might be because recessive resistances could fit a ‘negative’ functional model, where resistance is thought to result from loss of factor(s) essential for virus multiplication in the host plant (Fraser, 1992). If so, it would be difficult for the virus to fulfil the function of this missing factor. In contrast, Fraser (1992) postulated that dominant resistances were the result of active mechanisms (the ‘positive model’).Resistance-breaking could thus occur more easily by virus mutations that would suppress a specific recognition between the plant resistance factor and the virus avirulence factor.Polygenic resistances are generally quantitative and without clear strain-specific effects and so they are assumed to be more durable (Lindhout, 2002). However, the use of suchtypes of resistance in cultivated crops is far less frequent than the use of mono- or oligogenic resistances, so data on their durability are scarce. Moreover, evidence of quantitative resistance-breaking is difficult to obtain since the virus pathogenicity determinants can also be quantitative and difficult to measure. Assumptions about the durability of polygenic and/or quantitative resistances are based on the following:

•Quantitative resistance exerts a lower selective pressure on pathogens than qualitative resistance and decreases the risks of a virulent population emerging (Burdon, 1993).However, it can be argued that quantitative resistance allows a higher rate of virus multiplication than qualitative resistance, and consequently allows accumulation of mutations that may increase the probability of virulent variants appearing.


• polygenic resistances result from the action of different genes that can interact with different avirulence factors in the pathogen, thus limiting the probability of selecting

resistance-breaking populations through multiple virulence acquisition (Parlevliet, 1993, 2002). These different genes can also control resistance at different stages of the infection process, or resistance through different mechanisms which could also increase durability.


  • Types of resistance to viruses

The different types of resistance found are very diverse, and may interfere with virus development at the cell, organ, individual plant or population level. They are differentiated by comparing the behaviour of the different accessions with them to that of known susceptible cultivars. Phenotypically, resistance may interfere with different stages of the virus cycle in the host plant (Lecoq et al., 1982; Astier et al., 2001). The most common resistance types are:

• resistance to virus inoculation by vectors (Lecoq et al.,1979; Jones, 1998).

• tendency to escape infection. This ‘partial’ resistance may be characterised as a lower probability of infection becoming established than in susceptible plants, using the same level of inoculum (Caranta et al., 1997). ‘Mature plant resistance’ is a form of escaping infection that is expressed at the adult stage but not earlier.

• Immunity and extreme resistance. Here, replication does not occur (immunity) or is hardly detectable extreme resistance) in inoculated leaves or cells because of the lack of some factor necessary for virus pathogenesis (Köhmet al., 1993; Legnani et al., 1995).

• Resistance to virus movement between cells. The virus can multiply in the inoculated cells but generally cannot move out of them, or moves to only very few neighbouring cells.Sometimes, there is an hpersensitive reaction with the formation of necrotic local lesions. There may also be a sequestration of the virus to islands of cells without the induction of necrosis. Such resistances are the ones most commonly used by plant breeders, because they are easy to select (Fraser, 1992).

• Resistance to long distance movement of virus within the plant. Either the virus may become systemic more slowly than in the susceptible or invade only part of the plant.Sometimes a systemic hypersensitivity occurs. Specific tests are required to reveal this type of resistance (Dufour et al., 1989; Murphy and Kyle, 1995).

• resistance to virus multiplication or to virus accumulation.The virus may become systemic but remains at a low concentration in the plant tissues. Techniques such as DAS-ELISA which permits, under certain onditions, the quantification of virus concentrations in plant extracts, have greatly simplified screening for such resistances (Lecoq et al., 1982; Gray et al., 1986).

• resistance to virus acquisition by a vector. The last stage in the virus cycle within a host plant occurs when the virusis acquired by vectors for further spread. This type of resistance, which sometimes may be due to decreased virus multiplication and reduced virus availability to vectors, is useful in slowing down secondary virus spread within fields.

Other kinds of resistance have been described but poorly studied in regard to durability (e.g. systemic acquired resistance, virus-induced gene silencing). In addition, some forms of resistance may reduce symptom severity and therefore the losses caused by viruses without modifying the susceptibility of the plant to the virus itself. This is often referred to as ‘tolerance’. Although virus epidemics may be unaffected by such types of resistance, losses can be considerably decreased (Adlerz et al., 1985).

Conventional breeding methods

Plant breeding is defined as identifying and selecting desirable traits in plants and combining these into one individual plant. Since 1900, Mendel's laws of genetics provided the scientific basis for plant breeding. As all traits of a plant are controlled by genes located on chromosomes, conventional plant breeding can be considered as the manipulation of the combination of chromosomes. In general, there are three main procedures to manipulate plant chromosome combination. First, plants of a given population which show desired traits can be selected and used for further breeding and cultivation, a process called (pure line-) selection. Second, desired traits found in different plant lines can be combined together to obtain plants which exhibit both traits simultaneously, a method termed hybridization. Heterosis, a phenomenon of increased vigor, is obtained by hybridization of inbred lines. Third, polyploidy (increased number of chromosome sets) can contribute to crop improvement. Finally, new genetic variability can be introduced through spontaneous or artificially induced mutation

In this article we will mention the breeding methods which depend on selection and hybridization.

Selection

Selection is the most ancient and basic procedure in plant breeding. It generally involves three distinct steps. First, a large number of selections are made from the genetically variable original population. Second, progeny rows are grown from the individual plant selections for observational purposes. After obvious elimination, the selections are grown over several years to permit observations of performance under different environmental conditions for making further eliminations. Finally, the selected and inbred lines are compared to existing commercial varieties in their yielding performance and other aspects.

Hybridization

The most frequently employed plant breeding technique is hybridization. The aim of hybridization is to bring together desired traits found in different plant lines into one plant line via cross- pollination. The first step is to generate homozygous inbred lines. This is normally done by using self-pollinating plants where pollen from male flowers pollinates female flowers from the same plants. Once a pure line is generated, it is outcrossed, i. e. combined with another inbred line. Then the resulting progeny is selected for combination of the desired traits. If a trait from a wild relative of a crop species, e.g. resistance against a disease is to be brought into the genome of the crop, a large quantity of undesired traits (like low yield, bad taste, low nutritional value) are transferred to the crop as well. These unfavorable traits must be removed by time-consuming back-crossing, i. e. repeated crossing with the crop parent.

Pedigree method

Pedigree method consists of selecting individual F2 plants for desirable features, including resistance to diseases. Progenies of these selections are reselected in each succeeding generation until homozygosity is obtained. Artificial epiphytotic conditions are created in early segregating generations for the selection for disease resistance. Advantages: This method is quite suited for breeding for horizontal (polygenic) resistance. Occasionlly, transgressive segregation of quantitative characters including disease resistance is encountered.

figure4crop

Fig (1) Steps of Pedigree selection

Plant breeder made some modifications in pedigree selection method

Backcross methods. The most important modifications included

  • Recurrent pedigree selection

  • Backcross pedigree selection

  • Single seed descent


Back cross method


When resistance is dominant, F1 is back crossed to the susceptible parent. The progeny of first backcross generation is tested for resistance. The resistant plants are again backcrossed to the susceptible (recurrent) parent. After several generations of backcrossing (5-6), plants with characters almost identical to the original susceptible variety are obtained with an added advantage of resistance in them. When resistance is recessive, the progeny of each back cross generation is selfed. At the end of backcross programme, the progeny are selfed & resistant plants are selected. Progenies derived from different resistant plants that are identical in agronomic characteristics are usually bulked to produce the new disease resistant variety. The new variety is almost identical to the recurrent parent, except for disease resistance.

The Advantages of this method: 1) when resistant variety is unadapted & agronomically undesirable, backcross method is an obvious choice. 2) Useful to transfer one or few major genes (vertical resistance). 3) Extensive yield trials are usually not required before its release for commercial cultivation. 4) Multiple resistance breeding is possible. Disadvantage: No advancement in yield potential is possible.


Modified bulk method

The bulk-population method of breeding differs from the pedigree method primarily in the handling of generations following hybridization. The F2 generation is sown at normal commercial planting rates in a large plot. At maturity the crop is harvested in mass, and the seeds are used to establish the next generation in a similar plot. In this method hybridization between susceptible and resistant plants. Plants of F1 generation planted in bulks in the second year. Selection in F2 generation of resistant plants under artificial infection. Bulk selected plants in the other generation and so on until fifth generation where bulk and plant at commercial seeding rate. Select and establish family rows according to resistance and yield. Propagation of the most superior one. Success of this method depends on nature of the selected trait and number of genes which controlled it.

16-05

Fig (2) Steps of modified bulk method

Induced mutation

Instead of relying only on the introduction of genetic variability from the wild species gene pool or from other cultivars, an alternative is the introduction of mutations induced by chemicals or radiation. The mutants obtained are tested and further selected for desired traits. The site of the mutation cannot be controlled when chemicals or radiation are used as agents of mutagenesis. Because the great majority of mutants carry undesirable traits, this method has not been widely used in breeding programs.

Modern breeding method

Cell and Tissue culture techniques

Somaclonal variation and selection in vitro

In the past 20 years great advances have been made in the culturing of isolated plant cells and tissues under controlled conditions in vitro. When plants are regenerated from cultured cells, they may exhibit new phenotypes, sometimes at surprisingly high frequencies. If these are heritable and affecting desirable agronomic traits, such 'somaclonal variation' (Larkin and Scowcroft, 1981) can be incorporated into regular breeding programmes and be used in crop improvement. However, the finding of specific valuable traits by this method is largely left to chance and hence inefficient. Rather than relying on this undirected process, selection in vitro targets specific traits (Wenzel, 1985) by subjecting large populations of cultured cells to the action of a selective agent in the Petri dish. For purpose of disease resistance this selection can be provided by pathogens, culture filtrates of pathogens, or isolated pathotoxins that are known to have a role in pathogenesis (Daub, 1986).The selection will allow only those cells to survive and proliferate that are resistant to the challenge. Plants regenerated from resistant cells often display a resistant phenotype when evaluated with either the toxin or the pathogen itself. Owing to efforts in many laboratories, the list of disease-resistant plants obtained through somaclonal variation and selection in vitro has been growing steadily. Although this approach has obviously yielded some impressive results, it also has its limitations: first, many pathogens do not produce pathogenesis-specific toxins useful for selection; second, culture filtrates are rather artificial and neither pathogens nor plant cells grown together in vitro behave quite as they would in a natural environment; lastly, the selection approach can only detect mutations in plant genes that are expressed at the time that selection is applied. In order to be useful, new resistance traits, whether selected or not, must be heritable sexually or, in the case of vegetatively propagated crops, must be transmitted through vegetative propagules. Heritability has been demonstrated in a number of cases (Daub, 1986) but was absent in others (Wenzel and Foroughi-Wehr1990, ) Breeding programmes are beginning to make use of disease-resistant germplasm derived from culture in vitro: for example, somaclonal sugar-cane cultivars with improved resistance to Fiji virus (Krishnamurthi and Tlaskal, 1974) were introduced on a commercial scale more than a decade ago.

Methods of tissue culture

  • Somatic cell hybridization and anther culture

  • Meristem Tip Culture ( for virus free planting material)

Genetic engineering for disease resistance

No other technology has changed biological research in the

No other technology has changed biological research in the past ten years as much as has what is collectively called molecular biology. There are, indeed, few aspects of biology that have not benefited from these new tools and progress has been truly dramatic. Plant pathology is just one field that is rapidly expanding beyond its former limits owing to the molecular approaches that have become available. Boundaries between basic and applied research have become fluid and meaningless. Positive formal proof for a causal relationship between a gene action and a particular phenotype comes from the expression of the isolated gene in a transgenic host. More often than not, this will create a genetically altered organism with new, clearly defined, and sometimes valuable properties. In the area of phytopathology, such testing of genes by scientists primarily interested in basic biological processes has yielded disease-resistant plants that are intrinsically and eminently interesting from an applied point of view as well. Molecular phytopathological research has produced startling insights into plant-pathogen interactions, such as the characterization of virulence and resistance genes and the analysis of plant defence mechanisms, as well as the molecular fine-structure of viruses. This research, while still in its first decade, is progressing at an astonishing rate. Some of its impact on future crop-protection practices can already be projected if one assumes that findings made with experimental systems will soon be extended to additional host-pathogen systems and that research progress derived from model plants (such as tobacco) will be applied to major crops in due course.

Over the past 8 years a variety of methods have been developed for the introduction and expression of foreign genes in plants that include some of the major crop species


Methods of Genetic engineering

Agrobacterium-mediated Gene Transfer

Particle Bombardment


Marker Marker-assisted selection (MAS)

Marker assisted selection (MAS) is indirect selection process where a trait of interest is selected not based on the trait itself but on a marker linked to it. For example if MAS is being used to select individuals with a disease, the level of disease is not quantified but rather a marker allele which is linked with disease is used to determine disease presence. The assumption is that linked allele associates with the gene and/or quantitative trait locus (QTL) of interest. MAS can be useful for traits that are difficult to measure, exhibit low heritability, and/or are expressed late in development.

Gene pyramiding has been proposed and applied to enhance resistance to disease and insects by selecting for two or more than two genes at a time. For example in rice such pyramids have been developed against bacterial blight and blast. The advantage of use of markers in this case allows selecting for QTL-allele-linked markers that have same phenotypic effect.

Marker Marker-assisted selection has been widely applied in breeding programs for targeted transferring and pyramiding resistance loci in different crops MAS will provide an important approach for breeding Broad-spectrum resistance (BSR) and durable resistance (DR) corps, although in the past QR has been used in crop improvement by conventional breeding without the knowledge of resistance loci (Parlevliet and Ommeren, 1988). With the knowledge of genes underlying resistance loci, MAS can improve the efficiency by using gene-specific or closely linked markers to avoid bringing undesired traits into an improved cultivar owing to linkage drag .MAS may be more effective for the selection of the first and second groups of resistant loci mentioned above, whose functions depend on the specificities of encoding proteins. MAS may be less effective for selection of the third group of resistant loci, whose functions are initiated by upstream signaling thus depend on the genetic background. This prediction is supported by the reports that MAS is less effective for selection of some quantitative traits other than disease resistance (Hu et al., 2008)

Types of markers

Table 1 Molecular Markers Used in Plant Breeding and Their Important Features

Marker

Description

Suitability for Employment in MAS

RFLPs

Restriction fragment length polymorphism

Despite the high reproducibility and the co-dominant nature, RFLPs are not suitable for MAS due to their complex analysis protocols, high cost per sample and low amenability to automation

RAPDs

Rapid amplification of genomic DNA with random primers

RAPDs are markers easy to analyse and with a low cost for reaction. Nevertheless their use in MAS programmes is unreliable due to a low reproducibility

AFLPs

Amplified fragment length polymorphism following DNA digestion and adapter ligation

AFLPs detect a good level of polymorphism (up to 100 loci per reaction); nevertheless AFLPs are dominant markers, not fully suitable for automation and high-throughput analysis at low cost

SSRs

Simple sequence repeat polymorphism

Also known as microsatellite markers, they are based on a single PCR reaction. SSRs detect a good polymorphism level and are suitable for automation and high-throughput analysis at low cost. Together with the co-dominant behaviour, these features make SSRs highly recommended markers for MAS programmes

SNPs

Single nucleotide polymorphism

SNP markers can be dominant or co-dominant depending on the analysis protocol. Development costs are generally high, but once developed, the marker can be used in high-throughput analysis at low cost per sample, being therefore highly recommended for MAS programmes

DArT

Diversity array technology markers, based on microarray hybridisation of genomic DNA

The use of these markers is linked to the work of laboratories that supply the analysis on samples of a number of species in short time and at low cost (www.triticarte.com). Despite their dominant behaviour, DArT markers have been used in some MAS protocols developed for key agronomic traits in wheat at Triticarte lab

TRAP

Target region amplification polymorphism, based on amplification of genomic DNA with a random primer and a gene specific primer

Similar to AFLPs and RAPDs, these markers allow analyzing a high number of loci per reaction, with a single PCR reaction and with high reproducibility. The low cost and the suitability to automation make them good candidate for MAS, despite their being mainly co-dominant


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