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Soybean, (L.) Merr., has become the major source of edible vegetable oils and high protein feeds for livestocks in the world. A native of Eastern Asia, soybean was introduced into the USA and South America where it has become the most economically important agricultural crop and export commodity. In recent years, as demand for soybean increased due to the values of seed oil and protein, as well as industrial and nutriceutical uses, it has received more attention by scientists aiming to the development and employment of genomic technology for soybean improvement. Several DNA marker systems, such as restriction fragment length polymorphism (RFLP), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP), were integrated into the soybean genetic linkage map, which has been successfully utilized for mapping quantitative trait loci (QTL) linked to desirable traits and marker-assisted breeding of disease resistance and seed composition. The availability of a large number of expressed sequence tags (EST) and BAC sequences facilitated the discovery of new SNP and SSR markers in soybean toward the construction of high resolution genetic maps. Integrated genetic and physical maps will provide an invaluable resource for gene identification and positional cloning of important quantitative trait loci in soybean. Functional genomics has emerged as a new and rapidly evolved discipline to identify and understand gene functions via an integrated approach which includes transcriptomics, proteomics, metabolomics, translational genomics, and bioinformatics. The completion of whole soybean genome sequencing is anticipated in a few years. The availability of the soybean genome sequences in combination with the integrated genetic and physical maps will be invaluable resources providing soybean researchers powerful and efficient genomic tools to identify and characterize genes or QTLs for agronomic traits of soybean. As a result, it facilitates marker-assisted breeding and soybean improvement.

Forage quality depends on the digestibility of fodder, and can be directly measured by the intake and metabolic conversion in animal trials. However, animal trials are time-consuming, laborious, and thus expensive. It is not possible to study thousands of plant genotypes, as required in breeding programs. Therefore, several indirect methods including near-infrared reflectance spectroscopy (NIRS) have been established to overcome this limitation. However, the ideal indirect system for the prediction of forage performance would be based on gene-derived “functional” DNA markers, allowing early selection ultimately without need of field trials, and being environment independent. In addition, once identified relevant genes controlling forage quality are targets for transgenic approaches. Substantial progress has recently been achieved in the development and application of genomic tools both in model species and major forage crops such as ryegrass and alfalfa. Key genes involved in developmental and biochemical pathways affecting forage quality such as cell-wall, lignin, fructan, and tannin biosynthesis have been isolated and characterized. For some of these genes, allelic variation has been studied in detail and sequence motifs with likely effect on forage quality have been identified by association studies. Moreover, transgenic approaches substantiated the effect of several of these genes on forage quality. Perspectives and limitations of these findings for forage crop breeding are discussed given expected further progress in forage crop genomics, but also the complexity of the trait complex forage quality, since typically species mixtures of heterogeneous and heterozygous genotypes are grown in the field.

Significant progress has been made in molecular marker research in tomato, Mill., including generation of markers, development of maps, mapping of genes and QTLs, and fine-mapping, characterization and map-based cloning of genes and QTLs. Numerous types of molecular markers have been developed in tomato, including RFLPs, RAPDs, AFLPs, SSRs, CAPS, ESTs, COSs and SNPs. Several molecular maps of tomato have been developed based on different interspecific populations, including the saturated linkage map based on a × cross. Markers and maps have been utilized extensively to map genes and QTLs controlling agriculturally and biologically important traits and for marker-assisted improvement of many simple-inherited traits such as disease resistance. Marker information also has been used for fine mapping and map-based cloning of several major genes and QTLs. Comparatively, little progress has been made in improving complex traits via marker-assisted selection. However, rapid advances in developing more efficient and resolving markers and in refining QTL positions are expected to lead to a greater use of marker technology for crop improvement in tomato.

Genomic studies of Rosaceous fruit trees have concentrated on two species: peach (), which has served as a model for other species of the same genus, such as the stone fruits (apricot, cherry and plum) and almond; and apple ( x ), which itself is a model for other close species such as pear, quince and loquat. High density or saturated maps exist in both peach and apple, and sets of microsatellite markers spaced across the genome of both species are used for gene tagging and mapping in other populations. Efficient methods for mapping new markers and genes have been developed, such as “bin mapping” and the “genome scanning approach”. Tens of major genes and QTLs have been located on the maps of both species, and some of them are close to markers routinely used for selection in plant breeding. Comparative mapping has shown that all members of the genus share the same genome structure and that apple and pear genomes have a highly similar genetic organization. There are chromosomal rearrangements between the genomes of apple and , but extensive regions of synteny and collinearity are maintained. Several genes of apple and peach have been cloned using map-based techniques or are in the process of being cloned. A physical map is in an advanced stage of construction for peach and one has recently been started in apple. Large EST collections have been developed, particularly in apple and providing tens of thousands of new markers and gene sequences useful for functional analysis and map construction. Microarrays are proving to be valuable tools for identifying candidate genes for characters of interest. This information is stored in several databases with varying degrees of public access.

Coffee tree belongs to the genus , comprising of two main cultivated species L. (the only tetraploid species with 2n = 4x = 44) and Pierre ex A. Forehner (diploid, 2n = 2x = 22), yielding arabica and robusta types of coffee, respectively. In addition, there are ~100 diploid, wild, coffee species many of which hybridize readily with each other. These provide a rich and valuable source of desirable genetic variability for improvement of cultivated coffee germplasm. Arabica coffee is known for excellent cup quality but suffers from a narrow genetic base due to its domestication history and susceptibility for diseases and pests. In contrast, robusta coffee though poor in quality has better adaptability to various biotic/abiotic stresses. To meet the ever-changing demands of the environment and also of the sensibilities of market, there is a continuous need for genetic improvement of coffee, which unfortunately is severely constrained owing to inherently slow pace of tree breeding using conventional methods compounded with a general lack of genetic markers, screening and selection tools. The overall experience in India and worldwide from onerous conventional breeding efforts to develop new evolved coffee varieties has been rather frustrating with only few successes. The situation warrants recourse to newer, easy and efficient practical alternatives/technologies that can surmount the above problems and provide acceleration, reliability and directionality to the breeding efforts. In this context, development/utilization of: genomic variations based DNA markers, molecular linkage maps and markers-assisted breeding approaches that provide high-genetic resolution and new hopes and possibilities for genetic improvement of difficult species like coffee has become essential, a realization dawned on coffee research community rather recently. This chapter gives a brief overview of the worldwide efforts undertaken in recent years to develop, use and integrate DNA marker tools/technologies in coffee genetics research. It also provides few thoughts about future needs and perspectives to fully harness the potential of DNA marker based applications in managing and utilizing the available germplasm resources, construction of linkage maps, QTL mapping and genetic improvement of coffee.

Soybean is a suitable crop material for studying root nodulation and full genome sequencing because of its economic value. This review introduces the “nodulation” phenomenon that occurs in legume root systems such as the soybean. In addition, the paper identifies and discusses nodulation mutants (e.g., non-nodulation, ineffective nodulation, and super-/hypernodulation) and the genetic loci that control nodulation. The advent of genomics, proteomics, metabolomics, etc., has greatly contributed in improving our understanding of the symbiotic interactions between legume plants and Rhizobia, particularly for the identification of nodulation-related genes. Furthermore, molecular gene identification should be combined with biochemical pathways for nodulation in order to better understand the symbiotic interactions between legume and Rhizobia.

The review covers several issues concerning the state of molecular knowledge of the effects induced by domestication and breeding on the wheat crop. Genes at the root of the domestication syndrome are currently the focus of an active research which frequently uses comparative genomics approaches. Conclusions drawn on available data indicate that the domestication syndrome is originated by “sudden” genetic events, controlled by few major pleiotropic genes. These events were followed by the accumulation of a larger set of minor mutations, having a multifactorial mode of inheritance. Moreover the organization of nucleotide variability enables the detection of domestication-related molecular footprints, suggesting that the genomic regions more responsible for genetic variation and more related to domestication are reduced when compared to the whole genome size. The polyploidy history of the domesticated wheats is presented, making a specific mention to the origin of the wheat A, B, D and G genomes and to the molecular control of chromosome pairing in polyploids. A general presentation is also provided on the genomic changes which have accompanied the emergence of domesticated wheats. What follows is a molecular information on: i) the wheat adaptation to the environment (genomics of photoperiod, vernalization, heading date, plant height, and erect plant type); ii) the effect of domestication on seed-related yield components (genomics of seed size, grain hardness, and tillering); iii) modification of traits affecting harvestability (emergence of free-threshing seeds, rachis toughness, and presence of ear awns). Genetic bottlenecks which have been associated to wheat domestication and breeding are considered in a final section. The relatively young history of the wheat crop, the presumably small founder population of this gene pool, and the intensive long-term selection for agronomic traits did set the basis for a reduced genetic variability of the genus.

Sugarcane is being considered one the most important crops to meet the demand of the world bionergy needs. However the productivity in commercial plantations around the world is far way from its potential of about 300 tons/ha. Sugarcane breeding did not take advantage yet of the best plant breeding technologies, mainly because constrains imposed by the high polyploid nature of its genome. Even transgenic technologies would face difficulties because of the complex behaviour of introduced genes regarding the chromosome where the gene is inserted. One important resource to overcome at least part of these difficulties is the availability of a large collection of sugarcane Expressed Sequence Tags. The transcriptome information has allowed the identification of genes involved in biotic and abiotic stress response, disease resistance and sucrose accumulation. In additioncomparative mapping has allowed the identification in sugarcane disease resistance genes already mapped in sorghum and maize. In this chapter we discuss the use of transcriptome resources for sugarcane improvement.