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The completion of the genome sequence of the small weed plant (The Arabidopsis genome initiative 2000), and more recently of rice (Goff et al. 2002; Yu et al. 2002, 2005), has greatly changed the face of plant biology. Knowing the exact sequence and location of all the genes of a given organism is the first step towards understanding how all parts of a biological system work together. Information about the hypothesized function of an unknown gene may be deduced from its sequence homology to other genes of known function. However, genome sequencing projects have revealed the existence of a tremendous amount of biological diversity, with large proportion of genes sharing no homology to genes with known or hypothesized functions. In this respect functional genomics is the key approach to transforming quantity into quality (Borevitz and Ecker 2004; Holtfort et al. 2002). Functional genomics is a general approach toward understanding how the genes of an organism work together by assigning new functions to unknown genes.

Crop yield is fundamentally related to the (a) amount of solar radiation absorbed; (b) efficiency of solar energy use in photosynthesis; (c) translocation of photosynthate to sinks, especially sinks later harvested; (d) capacity for growth in sinks; (e) efficiency of converting photosynthate to new biomass; and (f) metabolic cost of maintenance. has been defined as the yield of a cultivar grown in an environment to which it is suited, with ample nutrients and water, and with pests, diseases, weeds, lodging, and other stresses effectively controlled (Evans and Fischer 1999). In principle, it integrates the genetic limitations on (a)–(f) as expressed in yield. It is an upper limit to on-farm yield of a cultivar, based on empirical study of that cultivar. As distinct from yield potential, is the yield theoretically possible from a given amount of absorbed solar energy and a specified crop biochemical composition. It is a theoretical construct based on known stoichiometries of biochemical reactions.

Though by far less popularly publicized than the 50 jubilee of the determination of DNA structure, celebrated three years ago, 2006 will be the 40 anniversary of the introduction of molecular markers in the genetic analysis, by Richard Lewontin in 1966. From the earliest, labour intensive and time-consuming applications to the study of the natural populations, to the massive exploitation in genome mapping of important plant species, it took therefore less than half a century for molecular markers to become a fundamental tool of theoretical and applied genetics. The oldest method for the analysis of the animal and plants' genomes is their mapping, i.e. the ordered positioning of a number of tags, acting as markers, along the entire length of the genome itself or, in the case of the eukaryotic genomes, of each of the chromosomes in which it is fragmented. The concept that two phenotypic traits can be inherited more often together rather than separately, probably dates back to the early breeding experiences. In the early decades of last century, the developments of genetic analysis led to the construction of the first genetic maps, consisting of a few tens of markers — mostly phenotypic, visible or easily scorable traits (Sturtevant 1913). It took about 50 years for a new breakthrough in the linkage mapping technologies and strategies to occur, as it was recognized that molecular tags, for example the isoenzymatic variants coded by different alleles at the same genetic locus, could be treated as markers as well (Lewontin and Hubby 1966), and their association with other traits, or between them, could be studied by standard genetic means.

Agronomy, the science ruling the fields, has the privilege and the task of dealing with many aspects and related disciplines, covering the biological and the physical sphere. Harmonizing the complex of interactions arising form the organisms, factors and conditions involved in the process of plant growth is not an easy task, as general. Optimising plant growth and crop production, while safeguarding the environment, often proves a harder challenge. In this light, the crops for industrial end-uses may intrinsically be seen as crops of potential large scale, thus exerting a significant influence - both positive and negative — on the environment.

For centuries plant fibres have been used in a number of commercial areas including textiles, construction, paper and pulp, reinforced composites, and as biomass for energy production. These fibres come from a whole host of crops ranging from cotton, jute and flax for textiles; wood crops such as poplar, eucalyptus and conifers for paper and pulp; and cereal crops such as maize, sorghum and barley to provide straw, bedding and animal fodder. In more recent years the popularity of fibre crops in some of these areas has been superseded by synthetic fibres such as those made from plastic or glass. Environmentally, these synthetic fibres are non-renewable and continue to accumulate as sources of pollution. The impact of this pollution has led to a renewed interest in the use of plant fibres as a sustainable commodity for the future.

Plant fibres have decisive advantages compared with synthetic fibres. One great advantage of plant fibres is their optimized strength to weight ratio. Others are their better workability as a result of optimum fibre length and cell wall thickness, their high anisotropic qualities and their good ion exchange capacity. The natural products are readily biodegradable and renewable.

Starch is the most abundant reserve carbohydrate present in higher plants, where it is predominantly found in the amyloplasts of storage organs such as roots, tubers and seeds. The green leaves have the unique ability to harvest light energy in the presence of carbon dioxide and water to synthesize sugars, which are transported to storage organs such as roots, tubers or seeds, where storage starch is synthesized for utilization by the plants at a later stage. Approximately 2050 and 679 million tonnes of storage starch is produced annually by the cereal and tuber crops, respectively, (Tester and Karkalas 2002) and harvested by humans for food, feed and industrial ap- carbohydrates, which are converted into starch. Starch present in the plications. leaves is known as transitory starch, because it is broken down into simple

Bioethanol (CHCHOH) is a liquid biofuel which can be produced from several different biomass feedstocks and conversion technologies. Its main physical and chemical characteristics, compared to diesel and gasoline fuels, are given in the Table 8.1.

In all living organisms lipids play several roles and, according to their structures, can be divided into two main groups: the non-polar lipids (acylglycerols, sterols, free fatty acids, wax and steryl esters) and polar lipids (phosphoglycerides, glycosylglycerides, and sphingolipids). Triacylglycerols act as compact, easily metabolised and non-hydrated energy stores. They are important storage products especially in plants producing oilseeds and in oily fruits such as avocado, olive and oil palm. Waxes are commonly extracellular components such as surface coverings, which function both to reduce water loss and to protect plants from noxious environmental conditions. They also act as an energy store in jojoba.

Biodiesel is a fuel for diesel engines that consists of the mono-alkyl esters of fatty acids from vegetable oils and animal fats. It can be used either pure, or in blends with petroleum-based diesel fuel. It does not require that engines or fueling infrastructure be modified although checking elastomers for compatibility is recommended when pure biodiesel (B100) is used. Biodiesel allows diesel engines to produce lower exhaust emissions of smoke, particulate, carbon monoxide, and unburned hydrocarbons. Oxides of nitrogen may increase slightly under some operating conditions but the difference for biodiesel blends up to 20% is difficult to measure.