Soybean (Glyine Max) a Globally Important Crop Plant That Originates From Asia

The seeds (called soybeans) are rich in protein (40% of dry weight) and contain a good mix of essential amino acids needed by humans (1). Not surprisingly, this makes soybeans and their products popular with vegetarians and vegans as a source of non-animal protein. However, soybean-protein is also widely used as the main protein source for intensive farming of animals including chickens, cows and pigs.

Concepts of QTL Analysis and Genomic Selection

The use of molecular genetic markers for selection and genetic improvement is based on genetic linkage between these markers and a quantitative trait locus (QTL) of interest. Thus, linkage analyses between markers and QTLs and between the proper multiple markers are essential for genetic selection from genomic information. It must be made clear that by definition, a QTL refers only to the statistical association between a genomic region and a trait.

Biometrics Applied to Molecular Analysis in Genetic Diversity

Studies about genetic diversity have been of great importance for the purposes of genetic improvement and to evaluate the impact of human activity on biodiversity. They are equally important in the understanding of the microevolutionary and macroevolutionary mechanisms that act in the diversification of the species, involving population studies, as well as in the optimization of the conservation of genetic diversity. They are also fundamental in understanding how natural populations are structured in time and space and the effects of anthropogenic activities on this structure and, consequently, on their chances of survival and/or extinction. This information provides an aid in finding the genetic losses generated by the isolation of the populations and of the individuals, which will be reflected in future generations, allowing for the establishment of better strategies to increase and preserve species diversity and diversity within the species.

How to Choice The Best Molecular Marker for Plant Breeding

The choice of the most appropriate molecular marker for genetic and plant breeding studies must be made on the basis of the ease of developing a useful technique coupled with the efficiency of data evaluation, interpretation, and analysis. The chosen marker must provide easy access and availability, rapid response and high reproducibility, and allow information exchange between laboratories and between populations and/or different species; it must also permit automation of data generation and subsequent analysis. Other desirable characteristics include a highly polymorphic nature, codominant inheritance (permitting the identification of homozygous and heterozygous individuals), frequent occurrence in the genome, and neutral selection (selection free from interference by management practices and environmental conditions). In addition to the characteristics of the marker, the goals of the project, the availability of financial, structural, and personal resources, convenience, and the availability of facilities for the development of the assay, as well as the genetic trait of the species under study, should all be considered.

Evolution of Genetics and Plant Breeding

Since the beginning of agriculture in approximately 10,000 BC, people have consciously or unconsciously selected plants with superior characteristics for the cultivation of future generations. However, there is controversy regarding the time when breeding became a science. Some believe that this occurred after Mendel’s findings, while others argue that it occurred even before the “era of genetics.”

Green Revolution to Gene Revolution

After World War II, as the world’s population spiraled out of control, many governments became concerned that they would not be able to feed everyone within their borders. The specter of mass starvation loomed. Mexico was one of the first countries to sound the alarm. In 1944, it imported half the wheat it needed but wanted to become self-sufficient. The government hired the agronomist Norman Borlaug, who had worked with the Civilian Conservation Corps during the Great Depression, the U.S. Forestry Service, and at the DuPont Chemical Company, to find a solution. Funded with grants from the Ford Foundation and the Rockefeller Foundation, Borlaug turned his attention to the problem, and by 1956 Mexico was producing enough wheat to feed its population. Furthermore, within a few short years it was exporting wheat to other countries. Mexico’s quick turnaround combined with that seen in other populous countries was dubbed the Green Revolution.

Borlaug was a plant geneticist and microbiologist for DuPont when he accepted the position in Mexico. In the first few years, he experimented with 6,000 crossbreeds of wheat, producing varieties that were high yield and disease resistant. More important, he instituted two growing seasons per year, thereby doubling the amount of wheat the country produced. With Mexico as a template for success, Borlaug assisted other countries such as India and Pakistan in attaining food security. In 1970, Borlaug received the Nobel Peace Prize for his role in alleviating world hunger. He is often credited with saving more than 1 billion people from starvation through his work. Although Borlaug’s initial success predated the introduction of GM foods, as a plant geneticist he has always been a supporter of biotechnology as a solution to world hunger.
Among the critics of GM foods are those who do not object to them on principle but on the circumstances of their development. For instance, most GM crops have been developed to benefit the bottom line of large agricultural corporations. While GM seed may yield a greater harvest and prevent pest damage, it is also more expensive than non–GM seed, promotes environmentally damaging monoculture, cannot legally be reused by farmers, and sometimes requires the application of a corresponding herbicide (such as Monsanto’s Roundup). These conditions bode well for those who hold the patent on the seed but are not necessarily conducive to helping those who need help the most—subsistence farmers in the developing world who cannot afford the high-priced seed and herbicides. In fact, Vandana Shiva, a respected agriculture activist from India, believes that conditions surrounding the distribution of GM seed are destroying subsistence farmers’ ability to feed themselves.46 What smallholder farmers need, Shiva believes, is access to a variety of crops suitable for the land they cultivate and the promotion of time-honored traditions that protect the environment, such as crop rotation and natural pest control. What they do not need, she says, is GM seed that is grown specifically to become feed for livestock or as an ingredient in another product in which the farmer has no stake.
The Food and Agriculture Organization (FAO) of the United Nation’s 2004 annual report, The State of Food and Agriculture 2003–2004, called for a “gene revolution” on par with the Green Revolution of the 1960s that would bestow GM seed on those who would most benefit. In the next 30 years, the population of the poorest countries is forecasted to swell by 2 billion.
The gains of the Green Revolution have made continued population growth possible, and a new solution is needed. However, most GM seed planted worldwide is corn, along with lesser amounts of soybeans, canola, and cotton. The gene revolution needs to apply biotechnology to a wider range of crops. According to the FAO Director-General Dr. Jacques Diouf, “Neither the private nor the public sector has invested significantly in new genetic technologies for the so-called ‘orphan crops’ such as cowpea, millet, sorghum and tef that are critical for the food supply and livelihoods of the world’s poorest people.” Furthermore, according to the FAO: [GMOs] can provide farmers with disease-free planting materials and develop crops that resist pests and disease, reducing use of chemicals that harm the environment and human health. It can provide diagnostic tools and vaccines that help control devastating animal diseases. It can improve the nutritional quality of staple foods such as rice and cassava and create new products for health and industrial uses. India could also greatly benefit from a gene revolution. Predicted to overtake China as the world’s most populous country by 2050, India must attain food security by addressing the problems of soil erosion, water shortages, and rural poverty. According to C. S. Prakash, the director of the Center for Plant Biotechnology Research at Alabama’s Tuskegee University, “India also has serious problems of blast in rice, rust in wheat, leaf rust in coffee, viruses in tomato and chilies and leaf spot in groundnut across the country. These problems can be significantly minimised in an ecologically-friendly manner with the development of genetically reprogrammed seeds designed to resist these disease attacks, while minimising or even eliminating costly and hazardous pesticide sprays.” Even in the United States, some farmers are transitioning from traditional crops, such as wheat and corn (whose markets have fluctuated unfavorably) to transgenic crops that can benefit third world countries. Rice genetically modified
with proteins from human milk, saliva, and tears is being test-grown in Missouri in the hopes that it may be consumed by at-risk populations in countries that suffer from high death rates due to diarrhea.50 These GM crops could produce food that is medically beneficial in areas that have inadequate health care or sanitation systems. It could also help domestic farmers gain a better foothold in an industry that suffered an almost total collapse in the 1980s.
But would a gene revolution be overkill? Some believe the food problem requires a more simple solution. A low-tech agricultural practice called the system of rice intensification (SRI) could produce greater yields and require little in the way of scientific intervention. More than half of the world’s population depends on rice, and between 2007 and 2008 its price tripled, laying the groundwork for a possible humanitarian crisis in some of the world’s most fragile economies. Norman T. Uphoff, the former director of the Cornell International Institute for Food, Agriculture and Development (CIIFAD), developed the SRI as a way to help solve the global food crisis. No genetic engineering is necessary, according to Uphoff. Farmers simply plant rice early, give seedlings more room to grow, water them less, and rotate crops annually. Fewer seeds and deeper roots make for harvests roughly two to three times larger than traditional cultivation practices allow.51 If such processes are so easy, then why have farmers not adopted them sooner, ask critics of SRI. They believe the claims made for SRI are exaggerated and that the system cannot be replicated on a wide scale. While basic, it also requires much old-fashioned weeding by farmers. Some believe that this will negatively affect women in developing countries, who often undertake much of the heavy labor. Experts believe that GM food has yet to make an impact on securing the global food supply because it is not practiced on the crops that matter most to people in developing countries: potatoes, cassava, rice, wheat, millet, and sorghum.52 Ignoring these in favor of frost-resistant strawberries and stay-ripe bananas leaves GM food in the realm of a boutique industry rather than a marketplace necessity. There is no economic incentive for private companies to invest in research and development into the crops grown by subsistence farmers in the developing world, a phenomenon known as the “molecular divide.” Technology typically originates in the developed world but without economic incentives does not transfer to areas where it could help others most, particularly sub-Saharan Africa. That may be changing. In 2008, Monsanto announced plans to develop seeds that would double corn, soybean, and cotton yields by 2030 using less land and water. The effort is directed at “improv[ing] the lives of small and poor farmers by sharing [Monsanto’s] technology” without
charging royalties. As the journalist Andrew Pollack explained, the plan is “aimed at least in part at winning acceptance of genetically modified crops by showing that they can play a major role in feeding the world.”

Genetically Modified Crops in Developing Countries

By early 2003, genetically modified (genetically enhanced, as qualified by many scientists in developing countries) crops were already established in the third world: two-thirds of the 5.5 million farmers growing these crops are in developing countries, which demonstrates that small and poor farmers are also involved. In addition to maize, soybeans, rapeseed (canola) and a few horticultural crop varieties, genetically modified cotton is the fastest spreading non-food GM crop. It is currently cultivated in India, China, Indonesia, Thailand, Argentina and South Africa, and the prospects are very promising.

Illustrative regional examples of GM crops are given in later chapters. From the strategic viewpoint, the adoption of GM crops by an increasing number of developing countries, and particularly by the larger ones (e.g. China, India, Argentina), reflects the need to acquire the relevant technologies before they are completely in the hands of the industrialised countries. It also reflects the will to participate in the so-called biotechnology revolution and even to become formidable competitors in some areas, instead of just purchasing and adapting biotechnologies. China's huge commitment to plant biotechnology, through increasing five-fold the funds devoted to this area of endeavour (US $500 million annually by 2005) is illustrative of this trend.

Another key element in the strategy of developing countries is to improve their competitiveness in international commodity and agricultural product markets. For those who are big exporters and whose agriculture is not subsidised, GM crops and agricultural biotechnology can contribute to decreasing production costs (e.g. through the reduction of use of biocides) and to increasing farmers' incomes. This aspect has been clearly demonstrated for GM soybeans in Argentina and GM cotton in South Africa and China.

This strategy also requires the design and update of biosafety regulations, the establishment or revision of intellectual property legislation and active participation in the negotiations on trade-related issues at the World Trade Organization.

Adopting GM crops is not synonymous with exclusion of other forms of agriculture, particularly the so-called biological or organic agriculture. A number of developing countries, e.g. Argentina and Chile, have an important and prosperous organic agriculture sector, which they wish to preserve and even extend because of its commercial benefits (e.g. Chile exports high volumes of ‘organic’ products to Japan and the European Union). Nevertheless, the advantages offered by GM crops enable developing countries to meet more rapidly the need to establish higher yielding, stress- and pest-resistant crop varieties, particularly when one has to deal with pathogens and pests against which there is no known natural resistance or tolerance.

Naturally, the developing countries are carefully following the controversy on GM crops in the European Union member countries as well as the disaccord between those countries and the USA in this respect. They are vigilant at the World Trade Organization, the Codex Alimentarius Commission on GM organisms and their impact on health and nutrition, in order to safeguard their interests. They generally consider that agricultural biotechnology and GM crops can help them to face the challenges of sustainable agricultural development. In this respect, their position is not far from that of the representatives of farmers in industrialised countries who welcome these technologies and maintain the highest standards of biosafety and biovigilance. They also consider, to a large extent, that the precautionary principle (now called the precautionary approach, since the 2002 Earth Summit in Johannesburg) should not become a dogma that hampers research, trials and large-scale cultivation. They agree on the need for biovigilance as in the case of medicines.

With regard to labelling and traceability of GM or biotechnology-derived products, developing countries tend to refer to substantial equivalence of these products compared to conventional ones, and to adopt labelling when there are substantial differences in composition. Thus, sugar, starch or vegetable oils derived from GM crops should not be labelled as GM. They are pragmatic in discussing the minimum percentage of GMOs in foodstuffs and agricultural products, the threshold of 0.9% (proposed by the European Union's Council of Ministers) being considered as unrealistic.

Finally, developing countries support the strengthening of regulatory institutions and biosafety measures, but they wish to avoid over-regulation, which will hinder their competitiveness. There is also a growing trend of improving public perception and social acceptance of agricultural biotechnology in developing countries, involving the participation of all sectors of society.
Confronted by the urgent need to feed their people and make their agriculture more competitive on international commodity markets, the developing countries, be they food exporters or not, have resisted the adoption of a moratorium on the cultivation of GM crops like that in Europe. In contrast, they wish to draw benefits from modern agricultural biotechnology and seize the opportunities offered to them.

In addition to the competitive edge provided to the commodity-exporting developing countries, agricultural biotechnology must reach resource-poor farmers—a large majority in developing countries. For such a purpose, it is necessary to carry out the social analysis of these technologies, when they are transferred to the farming communities. It is also necessary to pay great attention to the so-called orphan crops such as sorghum, millet, cassava, yams, sweet potato, etc., which do not attract the big seed corporations, but which play a vital role in local and national economies.

While favouring a sustainable diversified agriculture, including agricultural biotechnology, and making special efforts to help the resource-poor farmers, developing countries can protect their biological diversity (e.g. through the conservation of potentially useful varieties), clone crops on a large scale and participate in the selection of new varieties with the appropriate traits. Many projects being carried out in developing countries reflect these goals, while at the same time key issues, such as biosafety regulation, risk assessment and management, intellectual property rights and training of human resources are dealt with.

There are undoubtedly, in this vast area of research and development, opportunities for collaboration among the developing countries but also between them and industrialised countries' public research centres, enterprises and professional associations. In this regard, we are dealing not only with solidarity, but also with mutually beneficial cooperation in important international markets.

Agricultural Biotechnology for Developing Countries

Since the early 1970s, when the exploitation of biotechnology started to soar in the industrialised countries, developing countries—representing about 80% of the world's population—have progressively adopted and adapted biotechnology as a contribution to solving their social and economic development problems. At the beginning of the 21st century, most developing countries use biotechnology in one form or another, at scales and complexities that depend on their economic, scientific and technological status. In particular, they often rely on agricultural biotechnology, such as in vitro micropropagation of plant tissues or organs, followed by clonal multiplication of herbaceous or tree crops to produce virus and pathogen-free plants. They also use a wide range of food fermentations.

Many developing countries, for example India, China, Thailand, Brazil, Mexico, Egypt and South Africa, utilise the so-called modern biotechnology, based on genetic engineering and genomics. Agricultural biotechnology is the most widespread biotechnology in developing countries, but only a few of them are able to carry out all of the research and development activities leading to the commercialisation of genetically modified seeds. These include basic research in molecular and cell biology and genetics; greenhouse and field trials according to internationally agreed biosafety standards; risk assessment and management; respect for intellectual property rights relating to the transferred genes and to the creation of new crop varieties; production of genetically modified (GM) seeds by private corporations or working in cooperation with the public agricultural research sector; extension activities aiming at delivering the new seeds to the farmers and biovigilance in the fields of GM crops so as to detect any abnormalities or any hazards caused to the environment and to conventional crops. It is therefore important to follow the strategy of the countries capable of going through all these steps in order to understand how agricultural biotechnology supply meets economic and social demand (Sasson, 2000). A number of these countries are considered in more detail in later chapters in this section. Unfortunately, due to time constraints, it was not possible to include all of the key countries, so that the geographical coverage of this section is not complete. In particular China, where agricultural biotechnology has a rapidly growing role, is not covered in a separate chapter. The editors believe that the current coverage presents the reader with a detailed discussion of the major issues and opportunities of agricultural biotechnology in developing countries but they plan to extend the coverage in future editions of the Handbook.

It should be emphasised that the developing countries whose economies still largely depend on their food supply, exports and employment on agriculture that is not (or very little) subsidised by the government, must face the following challenges:

*
increase in production and productivity, and in competitiveness at national, regional and international levels (within the framework of the rules being established or revised by the World Trade Organization);
* protection of the environment and biological diversity, while reducing agricultural inputs (water, fertilizers and biocides), improving soil fertility and conservation (e.g. biological nitrogen fixation), increasing nitrogen and phosphorus absorption by crops, without significantly decreasing yields;
* diversification of agro-food production so as to meet the evolving needs of consumers and the food industry.

These challenges are similar to those faced by industrialised countries whose intensive agriculture employs, nevertheless, a very small proportion of the active population and is generally heavily subsidised (which leads to unfair competition with food-exporting developing countries).

Although food self-sufficiency is not an intangible rule anymore, and countries can devote land to high value-added export products and buy cereals or legumes on international markets at rather low prices, it is important to keep in mind the strategic role of efficient agriculture.

Population Growth and the Food-Production Challenge

Norman Borlaug (2002, 2004) has analysed the ways in which the birth of agriculture some 10 000–12 000 years ago, led to a stable food supply and enabled humankind to increase its population from some 15 million at that time to about 250 million by the start of the Christian era. Borlaug (2004) noted that that population doubled by 1650, then doubled again (to one billion) by 1850, redoubled by 1930 and doubled again by 1975, when the global population reached four billion. The next doubling is projected by 2020 and this will represent a 530-fold increase since the origin of crop improvement by selection of seeds from the best plants for sowing to deliver the next generation. Although the rate of increase of the world's population is now decreasing, the current rate in much of the developing world is still so high that the world's population is likely to increase to at least 10 billion people over the next 50 years, with 90–95% of them living in low-income developing countries and under conditions of poverty. Although it is hoped that the world's population will stabilise at 11–12 billion by the end of the 21st century, we have to confront a situation today where more than two billion people have no food security and 840 million of them are chronically malnourished. Six million children under the age of five die each year as a result of hunger and malnutrition. Of these millions, relatively few are the victims of famines. Most die unnoticed, killed by the effects of chronic hunger and malnutrition that leaves them weak, underweight and vulnerable. Health and mortality indicators are closely correlated with the prevalence of hunger. Common childhood diseases are far more likely to be fatal in children who are even mildly undernourished, and the risk increases sharply with the severity of malnutrition. Eliminating hunger and malnutrition could save millions of lives each year (FAO, 2002).

There are two major challenges that mankind must confront. The first is to produce enough food to satisfy the needs of the huge population. The second, even more complex problem is to ensure that the food is equitably distributed. The chief impediment to equitable food distribution is poverty (lack of purchasing power). Some 42% (2.6 billion people) of the world's population live on the land and rely on their own efforts to feed themselves. Only increases in agricultural productivity in food-deficient areas can enable the millions of rural poor to become food-secure.

The possibility of expansion of arable land area is limited for most regions of the world and the International Food Policy Research Institute (IFPRI) has estimated that more than 85% of the essential increase in cereal production (which represents two-thirds of human calorific intake) must come from increasing yields on land that is already in production. These productivity increases must come from varieties with higher genetic yield potential and greater tolerance of drought, insects and diseases. Crop management must emphasise soil and water conservation, reduced tillage, fertilization, weed and pest control and post-harvest handling.

Irrigated crops, which account for 70% of global water withdrawals, cover some 17% of cultivated land and yet provide nearly 40% of the world's food production. The rapid increase in land irrigation and in urban and industrial water usage has resulted in growing water shortages. It seems likely that two-thirds of the world's population will be suffering from water stress by 2025 (Borlaug, 2004).

The efficiency of water use in agriculture can be improved by several technologies. Wastewater treatment enables use for irrigation, especially for peri-urban agriculture. New improved varieties which require less water can achieve significant savings, especially if they are used in systems with more efficient crop rotation and more timely planting. Technologies are now available for saving water by increasing water productivity (yield per unit of water used). Reduction of soil salinity is now a matter of the highest priority. Borlaug (2004) has emphasised the need to bring about a ‘blue revolution’ by marrying water-use productivity to land-use productivity.

The conclusion that cereal yields must be increased on lands currently farmed, using less water and biocides means that in addition to conventional agricultural techniques, other techniques relating to protection of the environment and preservation of natural resources, drastic reduction of postharvest losses and control of biotic and abiotic stresses should be utilised (Borlaug, 2002). This is where agricultural biotechnology will help; it is not a panacea, nor a substitute for established agronomic techniques, but it represents another tool for increasing productivity and improving food quality.

During the World Food Summit, organised in 2002 in Rome by the Food and Agriculture Organization of the United Nations (FAO), it was again emphasised that developing countries should rely on agricultural biotechnology along with other agricultural technologies, while respecting internationally agreed biosafety standards. One year earlier, in its Report on Human Development, the United Nations Development Programme (UNDP) recommended the widest application of biotechnology (and other advanced technologies) in developing countries.

There is indeed an overall consensus on the utility of in vitro production of plantlets, derived from plant tissue or organ micropropagation, that are free of viruses and other pathogens and can contribute to increasing agricultural production, provided that small and poor farmers can purchase them at a low cost. In vitro production, which also concerns ornamental and forest species, is widespread in developing countries. It has become an important element of agro-food production, as it is applied to potato and several other tuber and root crops, high value-added horticultural varieties, oil palms and date palms, banana and plantain, which are the staple food of several hundred million people worldwide (Sasson, 2000).

How to Produce Haploid Plant ?

Haploids are defined as saprophytes with gametophytic chromosome number and have been produced in a variety of plant species using a variety of methods.

Although, the significance of haploids in genetics and plant breeding has been recognized for long time, with the advent of new biotechnology it has received renewed emphasis, so that the production of haploids has become an important component of biotechnology programmes in different countries.
Although, haploids could be produced following delayed pollination, irradiation of pollen, temperature shocks, colchicine treatment and distant hybridization, the most important methods currently being utilized under biotechnology programmes include

(i) anther or pollen culture and ovule culture and
(ii) chromosome elimination following interspecific hybridization (bulbosum technique).
Factors Affecting Haploid Production

- A number of factors influence androgenesis in vitro. The genotype of the donor plant plays a significant role in determining the frequency of pollen plant production. Anther wall factors also support pollen embryo development.

Histological studies support this view. As induction of the pollen into embryoids occurs most easily within the confines of an anther, the anther wall seems to provide a nursing effect. There are two schools of thought regarding the role of the anther wall. One is that it may have a stimulatory effect on the growth of pollen embryos (probably due to the presence of enhanced levels of some amino acids such as glutamine and serine); the other view holds that it may emanate some inhibitory substances into the culture medium thereby blocking the growth of more pollen into embryos.
The culture medium also plays a vital role since the requirements vary with the genotype and probably the age of the anther as well as conditions under which donor plants are grown. The medium should contain the correct amount and proportion of inorganic nutrients to satisfy the nutritional as well as physiological needs of the many plant cells in culture.

In addition to basal salts and vitamins, hormones in the medium are critical factors for embryo or callus formation. Cytokinins (e.g. kinetin) are necessary for induction of pollen embryos in many species of Solanaceae except tobacco. Auxins, in particular 2,4-0, greatly promote the formation of pollen callus in cereals. For regeneration of plants from pollen calli, a cytokinin and lower concentration of auxin are often necessary.

Sucrose has been considered the most effective carbohydrate source which cannot be substituted by other disaccharides. Glucose can be used in anther culture in some cases but fructose is far less effective. The concentration of sucrose also plays an important role in induction of pollen plants. Activated charcoal is also added to the culture medium.
It helps in the removal of inhibitors from the agar used for gelling the medium. Another role assigned to activated charcoal is the adsorption of 5¬hydroxymethylfurfural, a product of sucrose dehydration during autoclaving, assumed to bean inhibitor of growth in anther cultures.

Certain organic supplements added to the culture medium often enhance the growth of anther cultures. Some of these include the hydrolyzed products of proteins such as casein (found in milk), nucleic acids, and others. Coconut milk obtained from tender coconuts is often added to tissue culture media. It contains a complex mixture of nucleic acids, sugars, growth hormones and some vitamins.

The physiological state of the parent plant plays a role in haploid production. Success in haploid induction is in part dependent on knowledge of the physiology of the pollen yielding plant. In various plant species it has been shown that the frequency of androgenesis is higher in anthers harvested at the beginning of the flowering period and declines with plant age.
This may be due to deterioration in the general condition of the plants, especially during seed set. The lower frequency of induction of haploids in anthers taken from older plants may also be associated with a decline in pollen viability. Seasonal variations, physical treatment, and application of hormones and salts to the plant also alter its physiological status, which is reflected in a change in anther response.

Temperature and light are two physical factors which play an important role in culture of anthers. Higher temperatures (30°C) yield better results. Temperature shocks also enhance the induction frequency of microspore androgenesis. Frequency of haploid formation and growth of plantlets are generally better in light.
Certain physical and chemical treatments given to flower, buds or anthers prior to culture, can be highly conducive to the development of pollen into plants. The most significant is cold treatment.
The developmental stage of pollen greatly influences the fate of the microspore, Androgenesis occurs when a microspore or pollen is induced to shift from a gametophytic pathway to a sporophytic pathway of embryo formation.

Anthers of some species (Datura, tobacco) give the best response if pollen is cultured at first. mitosis or later stages (postmitotic), whereas in most others (barley, wheat, rice) anthers are most productive when cultured at the uninucleate microspore stage (premitotic). Anthers at a very young stage (containing microspore mother cells m tetrads) or a late stage (containing binucleate, starch filled pollen) of development are generally ineffective, albeit some exceptions are known.

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Types of Seed Dormancy

This review will focus on the process of primary seed dormancy. As noted above, primary dormancy is characterised by a transient inability of mature dispersed seeds to germinate under conditions that are normally conducive to germination (Grappin et al., 2000); the inception of primary dormancy occurs during seed development (reviewed in Bewley, 1997) . Dormancy can also be induced in mature, already dispersed, nondormant seeds (known as induced or secondary dormancy) by environmental conditions that are unfavourable for germination, e.g. anoxia, unsuitable temperatures or illumination (Bewley, 1997). In induced dormancy, the seed loses its sensitivity to dormancy-breaking factors (e.g. light, nitrate, etc., depending on the species) (Bewley and Black, 1994).

Primary dormancy is generally classed into two major types: embryo dormancy and coat-imposed dormancy (more accurately termed coat-enhanced dormancy) (Bewley and Black, 1994). In embryo dormancy, it is the embryo that is dormant and the embryonic axis will not elongate even if the embryo is excised from its enclosing seed tissues and placed on water. In coat-enhanced dormancy, the embryo, when isolated is capable of germination, but the intact seed is dormant; thus, it is the surrounding seed tissues that impose the block to germination. The inhibitory nature of the enclosing seed tissues may be attributed to one or a combination of the following effects: (1) interference with water uptake; (2) mechanical restraint; (3) interference with gas exchange; (4) supply of inhibitors to the embryo or promotion of the synthesis of inhibitors within the embryo and (5) prevention of the exit of inhibitors from the embryo (Bewley and Black, 1994). For many seeds, more than one of these factors operates to maintain coat-enhanced dormancy.

A variety of germination inhibitors have been identified within the seed tissues that enclose the embryo. While their presence does not necessarily imply a causal role in preventing germination, in many cases, where repeated washing (leaching) of seeds relieves dormancy, inhibitors are known to be removed (Bewley and Black, 1994). The inhibitor that has received the most attention with respect to dormancy imposition and maintenance is ABA .

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Seeds control the survival and reproductive capacity of plants

Seeds control the survival and reproductive capacity of plants and therefore occupy a critical position in the life history of higher plants. The successful establishment of the new plant, both temporally and spatially, as well as the vigour of the young seedling, is largely determined by physiological and biochemical processes that occurred earlier, i.e. during seed development. At dispersal, the quiescent mature seed, upon encountering favourable environmental conditions (that can include light of a given wavelength, sufficient water, optimal temperatures and adequate oxygen), commences germination.

Germination, sensu stricto includes those events commencing with imbibition or uptake of water by the quiescent dry seed and culminates with the elongation of the radicle (Bewley and Black, 1994; Bewley, 1997). It is accompanied by a reactivation of metabolic systems, a process that depends in part on components that were preserved during seed desiccation as well as on components that are de novo synthesised. Ultimately, there is renewed cell expansion (elongation of the radicle) and cell division as the seedling becomes established (Figure 33.1). Visible evidence of the completion of germination is usually protrusion of the radicle through the seed structures surrounding the embryo (such as the testa and endosperm, or megagametophyte).

Subsequent events, including activation of the shoot apical meristem and the mobilization of the major storage reserves are associated with the growth of the seedling. Some seeds fail to complete germination under seemingly favourable conditions, even though they are viable. These dormant seeds must be exposed to environmental cues such as periods of warm-dry conditions (after-ripening), moist chilling, or even smoke for dormancy to be terminated (Adkins et al., 1986; Egerton-Warburton, 1998).

Although generally considered an undesirable trait by the agricultural and forest industries, dormancy in nature is clearly an adaptive trait, since it improves survival by optimising the distribution of germination over time. For example, a seed that germinates in spring after remaining dormant throughout the winter has a greater chance of successful seedling establishment than that which germinates immediately after its dispersal in the fall. Seed dormancy can also lead to a distribution of germination in space (Bewley and Black, 1994). Consider those seeds whose dormancy is terminated by light, the most effective wavelengths being 660 nm (the red region of the spectrum).

This mechanism prevents these seeds from germinating and attempting seedling establishment under competitive situations (e.g. in light transmitted through green leaves, since it is poor in the red component) or when the seeds are buried at depths in the soil to which suitable light cannot penetrate. These seeds readily germinate when close to the soil surface and when unrestricted by leaf canopies. Since seedling emergence from the soil is supported solely by mobilisation of the seed's reserves, some of these mechanisms for preventing germination occur in small seeds that contain a limited amount of stored reserves (Bewley and Black, 1994).

Once a seed has initiated cell division and becomes a seedling, it passes from its most stress-resistant state to its most stress-susceptible state, during which it is highly vulnerable to environmental conditions, and there is no reversal to a resistant state. However, as will be discussed, under conditions that are not optimal for a transition from germination to seedling growth, seeds express genes that impose a transient ‘quiescence’ until those conditions become optimal. Thus, control of seed germination and growth is crucial to the survival of seeds and there are critical checkpoints at the transitions from dormancy to germination and from germination to growth.

The agricultural and forest industries rely upon seeds that exhibit high germinability and vigorous, synchronous growth after germination; hence dormancy is generally considered an undesirable trait. In agriculture, extensive breeding programmes have reduced the degree of dormancy as well as improving other traits of crops, particularly yield. In the forest industry, tree orchards have been established in order to meet the planting demands for several conifer species. Here breeding programmes are complicated by the fact that the generation time for trees are untimely long and many species are characterised by a deeply manifested dormancy. Moreover, maintaining genetic diversity is a key endeavour. Some of the problems unique to the forest industry in relation to the deep dormancy of conifer species will be discussed.

Functional genomics approaches hold promise for elucidating genes and proteins that control seed dormancy and germination. The understanding of molecular and physiological mechanisms underlying seed dormancy, particularly of angiosperms, has been accelerated through the analysis of mutants that are disrupted in their development (including dormancy inception and maintenance) as a result of a deficiency in hormone biosynthesis or response. Cloning of the genes that are defective in these mutants has opened up avenues to reduce dormancy by altering specific traits (genes) through the technology of gene transfer. The recent cloning of the genes encoding key enzymes for the metabolism of abscisic acid (ABA) (i.e. ABA 8′-hydroxylase and ABA glucosyltransferase) may also lead to unique approaches for germination control. These and other biotechnological approaches for manipulating germination will be discussed.

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Anew building to accommodate growth of federally funded research in plant sciences.

Plant Science Expansion

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Plant Science Expansion - Presentation Transcript

1. Plant Science Expansion
   
2. Anew building to accommodate growth of federally funded research in plant sciences.
   
3. Provide increased plant growth facilities
   
4. Provide increased use of computation in plant science research
   
5. Allow MSU to recruitand retain the world’s best plant scientists to solve complex problems relatedto energy, food and health.
   
6. Located at the corner of Bogue St. and Wilson Rd.
   
7. It will connect to the
   Plant Biology
   Building
   and
   Plant and Soil Science Building.
   
8. A research home for faculty in…
   Biochemistry & Molecular Biology, DOE Plant Research Lab,Forestry, Horticulture, Plant Biology, Plant Pathology, andCrop & Soil Sciences.
   
9. This building will support faculty conducting the latest plant science research at MSU.
   
10. Research funding for plant science in the College of Natural Science alone has doubled to $12M/yr in the last 5 years.
    
11. This includes projects involving the Great Lakes Bioenergy Research Center ($50M), DOE Plant Research Lab ($4.5 M), NIH Grand Opportunity Grant for medicinal plants ($2.8M), and other NSF, NIH and DOE grants.
    
12. The building will have four floors and 40,000 square feet.
    
13. Three floors will be research laboratories with space for 15 research groups and…
    
14. 144 graduate students,
    post-docs, technicians
    and undergraduates
    
15. The open lab design will maximize interaction, collaboration, and
    space utilization.
    
16. The basement provides MSU scientists a 30% increase in plant growth chambers.
    
17. Connections to the other buildings allows transportation of plants between growth chambers, labs and green houses without exposure to weather, disease, and insects.
    
18. The first floor provides an entrance to the horticulture gardens.
    
19. The first floor features a 225-seat lecture hall and interaction space.
    
20. Budget: $43MConstruction: May 2010 - December 2011
    
21. Architect/Engineers: SmithGroup, Detroit, Mich.Construction Managers: The Christman Company, Lansing, Mich.
    
22. College of Natural Science
    College of Agriculture and Natural Resources
    Michigan Agriculture Experiment Station

The Criollo genome has uncovered the genetic basis of pathways leading to the most important quality traits of chocolate

The production of high quality chocolate, and the farmers who grow it, will benefit from the recent sequencing and assembly of the chocolate tree genome, as per an international team led by Claire Lanaud of CIRAD, France, with Mark Guiltinan of Penn State, and including researchers from 18 other institutions.

The team sequenced the DNA of a variety of Theobroma cacao, considered to produce the world's finest chocolate. The Maya domesticated this variety of Theobroma cacao, Criollo, about 3,000 years ago in Central America, and it is one of the oldest domesticated tree crops. Today, a number of growers prefer to grow hybrid cacao trees that produce chocolate of lower quality but are more resistant to disease.

"Fine cocoa production is estimated to be less than 5 percent of the world cocoa production because of low productivity and disease susceptibility," said Guiltinan, professor of plant molecular biology.

The scientists report in the current issue of Nature Genetics "consumers have shown an increased interest for high-quality chocolate made with cocoa of good quality and for dark chocolate, containing a higher percentage of cocoa, while also taking into account environmental and ethical criteria for cocoa production".

Currently, most cacao farmers earn about $2 per day, but producers of fine cacao earn more. Increasing the productivity and ease of growing cacao can help to develop a sustainable cacao economy. The trees are now also seen as an environmentally beneficial crop because they grow best under forest shade, allowing for land rehabilitation and enriched biodiversity.

The team's work identified a variety of gene families that may have future impact on improving cacao trees and fruit either by enhancing their attributes or providing protection from fungal diseases and insects that effect cacao trees.

"Our analysis of the Criollo genome has uncovered the genetic basis of pathways leading to the most important quality traits of chocolate -- oil, flavonoid and terpene biosynthesis," said Siela Maximova, associate professor of horticulture, Penn State, and a member of the research team. "It has also led to the discovery of hundreds of genes potentially involved in pathogen resistance, all of which can be used to accelerate the development of elite varieties of cacao in the future".

Because the Criollo trees are self-pollinating, they are generally highly homozygous, possessing two identical forms of each gene, making this particular variety a good choice for accurate genome assembly.

The scientists assembled 84 percent of the genome identifying 28,798 genes that code for proteins. They assigned 88 percent or 23,529 of these protein-coding genes to one of the 10 chromosomes in the Criollo cacao tree. They also looked at microRNAs, short noncoding RNAs that regulate genes, and observed that microRNAs in Criollo are probably major regulators of gene expression.

"Interestingly, only 20 percent of the genome was made up of transposable elements, one of the natural pathways through which genetic sequences change," said Guiltinan "They do this by moving around the chromosomes, changing the order of the genetic material. Smaller amounts of transposons than found in other plant species could lead to slower evolution of the chocolate plant, which was shown to have a relatively simple evolutionary history in terms of genome structure".

Guiltinan and colleagues are interested in specific gene families that could link to specific cocoa qualities or disease resistance. They hope that mapping these gene families will lead to a source of genes directly involved in variations in the plant that are useful for acceleration of plant breeding programs.

The scientists identified two types of disease resistance genes in the Criollo genome. They compared these to previously identified regions on the chromosomes that correlate with disease resistance -- QTLs -- and observed that there was a connection between a number of the resistance genes' QTL locations. The team suggests that a functional genomics approach, one that looks at what the genes do, is needed to confirm potential disease resistant genes in the Criollo genome.

Hidden in the genome the scientists also found genes that code for the production of cocoa butter, a substance highly prized in chocolate making, confectionary, pharmaceuticals and cosmetics. Most cocoa beans are already about 50 percent fat, but these 84 genes control not only the amounts but also quality of the cocoa butter.

Other genes were observed that influence the production of flavonoids, natural antioxidants and terpenoids, hormones, pigments and aromas. Altering the genes for these chemicals might produce chocolate with better flavors, aromas and even healthier chocolate.

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Rapid Advancements in Plant Breeding

University of Illinois research has resulted in the development of a novel and widely applicable molecular tool that can serve as a road map for making plant breeding easier to understand. Scientists developed a unified nomenclature for male fertility restorer (RF) proteins in higher plants that can make rapid advancements in plant breeding.

"Understanding the mechanism by which RF genes suppress the male sterile phenotype and restore fertility to plants is critical for continued improvements in hybrid technology," said Manfredo J. Seufferheld, U of I assistant professor of crop sciences.

To reach this goal, Seufferheld teamed up with post-doctoral scientists Simeon O. Kotchoni and Emma W. Gachomo of Purdue University, and Jose C. Jimenez-Lopez of the Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas (CSIC) in Granada, Spain, to develop a simplified genetic-based nomenclature that automatically catalogues the entire RF gene products into families and subfamilies.

"Up to now, there has been no unified nomenclature for naming the RF proteins," Seufferheld said. "As the systematic sequencing of new plant species has increased in recent years, naming has been simply arbitrary. We have had 'chaos' in the databases. The RF information in the databases could not be adequately handled in the context of comparative functional genomics".

This new tool will help plant breeders and researchers make decisions more quickly. Breeders can now easily match sterility in plants to male restorer mechanisms. Ultimately, growers appears to benefit sooner from new developments in plant breeding since breeders will be able to generate new hybrids at a faster pace, Jimenez-Lopez said.

"Genomic sequencing, coupled with protein modeling, allowed us to begin dismantling this complexity that has held us back in the field of science," Kotchoni said. "Now we can easily compare unknown gene functions to known and well characterized genes in order to determine their functions and family hood".

With a number of teams of scientists competing to finish this task first, Kotchoni said it has been an honor to have this model accepted as the new standard for RF protein nomenclature. This system has been developed as a building block for plant genomics.

"The nomenclature, which is designed to include new RF genes as they become available in the future, is not based on one species or another, but rather on the function of the gene itself," Seufferheld said. "This allows researchers to work with a wide range of plants and take a gene with known function(s) from one plant and transfer it into another plant to restore male fertility".

Corn growers only need to look back to the southern corn leaf blight epidemic in 1972 to see the importance of this scientific development.

In 1972, Texas-Cytoplasm Male Sterility (T-CMS) corn was heavily used in hybrid seed production because it eliminated the costly practice of hand detasseling. Nearly 85 percent of the U.S. corn crop was produced using T-CMS, which was highly susceptible to Helminthosporium maydis, the fungus that causes southern corn leaf blight.

Since then, understanding the function of RF genes in higher plants has been a priority of a number of researchers. "The first male sterility restorer ever characterized in plants was maize ALDH," Kotchoni said. "When this gene is altered, it causes male sterility".

Seufferheld said this will also be a great tool for studying plant evolution.

"We can follow how plants became domesticated," Seufferheld said. "It is easier now because we have all the structures of the RF proteins organized and can look at the evolution of these proteins in a systematic manner. If we just look at the sequence of the gene, part of the phylogenetic scene has been lost through evolution. However, the structure of protein provides more information that can go well into the past."

This public gene database will allow researchers to search using the old or new names of RF proteins, Seufferheld said.

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