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Bread wheat ( L.) is one of the most important crop plants. Due to its hexaploid nature consisting of three different genomes (A, B and D) and its large genome size of approximately 15 billion base pairs, it is also one of the most complex crop genomes. This has rendered the use of molecular markers in wheat genome analysis and breeding slow and difficult. Mainly, through the use of microsatellite or SSR (simple sequence repeat) markers, wheat molecular marker analysis has gained momentum during the last ten years. The advantage of microsatellite markers is that they detect an unsurpassed level of polymorphism in this recently polyploidised organism with a generally low level of sequence variation. Furthermore, a large proportion of the microsatellite markers is genome-specific, thus amplifying a defined single product from one of the three wheat genomes. Currently, 2.000 to 2.500 mapped microsatellite markers are available for the wheat genome. With microsatellite markers, the chromosomal position of many relevant breeding traits such as disease resistance genes and quality traits has been identified and they are increasingly used in marker-assisted selection during wheat breeding. For the future, high expectations are being put into another marker type that is called single nucleotide polymorphisms (SNPs) since their number in the wheat genome should be much higher and cost-efficient, highly multiplexed technologies are available for the analysis of SNP markers in plants. SNP marker development and use are, however, still in their infancy. Based on recent results, we discuss here the advantages and disadvantages of SNPs compared to microsatellite markers for future wheat breeding.

Molecular marker technology is playing an increasingly important role in the selection of wheat lines with improved quality attributes. This is due to the identification of molecular markers tightly linked to chromosome regions involved in the control of important quality characteristics such as dough properties, grain hardness, semolina and flour colour, grain protein content and starch composition, which strongly influence wheat end use, and its nutritional and market value. Marker assisted selection (MAS) will increase the efficiency of the breeding process, particularly when phenotyping requires laborious and time-consuming analyses, performed in advanced generations because of the relatively large amount of grain required. Moreover, the implementation of MAS allows the selection of individuals carrying the favourable alleles at the target loci, and also the pyramiding of favourable QTL alleles from different sources and for different traits. This not withstanding, the progress obtained until now in applying MAS to quality characteristics has been slow compared to other traits.

Barley genotypes, in particular landraces and wild species, represent an important source of variation for adaptive traits that may contribute to increase yield and yield stability under drought conditions, and that could be introgressed into improved varieties. Traits that have been investigated include physiological/biochemical and developmental/ morphological traits. Yield performance under drought is particularly a complex phenomenon, and plants exhibit a diverse range of genetically complex mechanisms for drought resistance. Quantitative trait loci (QTL) studies with and without have shown that developmental genes, notably those involved in flowering time and plant stature show pleiotropic effects on abiotic stress tolerance and ultimately determine yield. Problems associated with the hybridization of such as alleles with deleterious effects on field performance could be best addressed in the advanced backcross (AB-) QTL analysis. It was interesting to see that in AB-QTL populations like in balanced populations major QTL overshadowed minor QTL-alleles. Nevertheless, crosses with , AB-QTL populations and association studies with have also identified new alleles and genes that are related to abiotic stress tolerance. In order to identify genes that are related to drought tolerance microarrays analysis to monitor gene expression profiles for plants exposed to limited water environment is performed. Several studies with rapid dehydration treatment have shown that osmotic-stress-inducible genes could explain the response to drought stress in plants. Another development is the identification and use of nucleotide polymorphisms (SNP) in genes related to abiotic stress tolerance. An understanding of the combined function and expression of genes involved in various abiotic stresses, could help identify candidate genes underlying QTL of interest.

Barley ( L.) is one of the oldest crop plants and among the most important cereals worldwide which is cultivated from the polar circle to the tropics. Barley crops can be infected and severely damaged by many fungal, viral and bacterial pathogens as well as insect pests. Therefore, breeding for disease and pest resistance is of special importance in barley in order to prevent or reduce yield losses. Furthermore, genetic resistance allows the reduction of agrochemical applications and thereby greatly contributes to environment and consumer protection. Resistance breeding has already been very successful in the past and provided many resistant or tolerant barley varieties highly adapted to adverse growing conditions. The genetic basis of such resistance depends on the respective pathogen or pest: Many cases of monogenic (major gene) resistance have been described but oligo- or polygenic types of resistance are also widespread and appreciated by breeders and growers due to their superior durability. Today, molecular markers are available for many major resistance genes and resistance QTL (quantitative trait loci) against a wide range of pathogens in barley. Such markers are the basis for an efficient marker assisted selection (MAS) in scientific breeding research and commercial barley breeding. Furthermore, marker assisted backcrossing procedures allow an enhanced incorporation of resistance genes derived from non-adapted germplasm (e.g. ). Beyond this, pyramiding of resistance genes by marker-assisted combination breeding may lead to longer lasting resistance and enable the further use of resistance genes already overcome by single strains or isolates of the respective pathogen. This chapter reviews the present state of the art concerning markers available for major resistance genes and resistance QTL in barley and exemplifies marker assisted backcrossing and pyramiding strategies in the pathosystem barley – barley yellow mosaic virus disease caused by BaYMV and BaMMV.

A number of resistance genes against biotrophic pathogens recently have been cloned from wheat and barley. These include the barley stem rust resistance gene Rpg1, the leaf rust resistance genes Lr10 and Lr21 in wheat and several alleles from the highly diverse powdery mildew resistance loci Mla in barley and Pm3 in wheat. In addition, the durable and recessive mlo gene also conferring powdery mildew resistance as well as the viral resistance genes rym4 / rym5 were isolated from barley. There are many advanced projects in a number of research groups aimed at the isolation of additional resistance genes, including some quantitative trait loci with major effects on resistance against biotrophic and necrotrophic pathogens. The availability of these genes for transgenic approaches as well as the development of highly diagnostic markers to test for the presence of the gene in plants will allow new breeding strategies. Resistance breeding, possibly more than breeding for any other major trait, will benefit enormously and rapidly from this new molecular information: a rapid diagnosis of resistance genes as well as a rational combination of qualitative and quantitative resistance factors based on molecular knowledge will become feasible in the next decade.

The 1909 publication of G. H. Shull was the dawn of the modern era of maize breeding. Since that time maize has been unique as a major crop of the world and a very important species for basic research. Most of the knowledge from that research has been either worthless or inaccessible to maize breeding programs and actual improvement of maize. Recently, this relationship has changed and the connections between basic research and breeding have improved. The previous 10-15 years have been especially eventful with the advent of transgenic maize and DNA sequence information for maize germplasm. There is much to learn about the maize genome. Only a small fraction of the 30,000 to 60,000 genes and other sequences have functions assigned to them on the basis of direct experimentation. The advent of the genomics era of maize breeding, even at such an early stage, has clearly underlined our abilities to empirically assess all of the promising genetic options and questions that are raised by new sources of information. Field-based phenotyping and the prioritization of phenotyping have become much more important in the genomics era of maize breeding. The gains and pains of the initial decades of maize breeding have been well documented for some traits and production environments. But, with the exception of improved resistance to biotic and abiotic stress as a basis for genetic gains in grain yield, very little fundamental information and few validated mechanisms have been identified from that era. The next era of maize breeding should be fundamentally different in the sense that the strategies will rely more on a scientific method; consequently, some of the reasons for success or failure will be known and considered for devising more efficient methods of maize improvement.

The status of rice as a model crop and the sequencing of the and genomes have provided breeders with the necessary tools for marker assisted breeding. Simple Sequence Repeat (SSR) markers are easily available for any region of the genome, and candidate gene markers are being developed rapidly. The likely targets of MAS include yield and agronomic traits, cooking and nutritional quality, and resistances to abiotic and biotic stresses. MAS for gene pyramiding for disease and insect resistances is being widely used. For major genes and QTLs of larger effect, marker assisted backcrossing (MAB) is an effective method for developing improved versions of widely-grown “mega” varieties. Developing submergence tolerant mega varieties is a good example of how the MAB approach can result in significantly improved mega varieties within two to three years. The use of markers in more conventional breeding nurseries has been limited by cost, but is beginning to be applied for some traits like grain quality. Lower-cost marker methods combined with large-scale gene discovery will increase the use of MAS over the next decade.

Rice is arguably the most important food crop of the world and due to its small genome size compared to other major cereals, rice was selected as model crop species for decoding of its full genome. The international rice genome sequencing project (IRGSP), a consortium of laboratories from ten different countries, has generated a very high quality map based sequence of the 12 chromosomes of rice cultivar ‘Nipponbare’ and made it available in the public domain. A whole genome draft sequence of type rice variety ‘93-11’ has also been reported by the Beijing Genomics Institute. Annotation and comparative analysis of these and other partial genomic sequences has provided a wealth of information to the rice geneticists and breeders. Simple Sequence Repeat (SSR) markers are now easily available for any region of the rice genome. SSR markers have also been derived from the expressed sequence tags (ESTs) and unigene sequences, which correspond to the expressed component of the genome and thus have greater potential in comparative genome analysis. Furthermore, millions of single nucleotide polymorphism (SNP) and insertion-deletion (InDel) markers have already been identified in rice. Saturation of the genome with such sequence based SSR and SNP markers is accelerating fine mapping and map-based cloning of genes, and thus, development of gene-based allele-specific markers. Rice improvement programs are expected to benefit greatly from the use of these markers in near future.

Sorghum [ (L.) Moench] is an important food and feed crop in many parts of the world, and has potential uses in the biofuels industry. Compared to most other cereals, sorghum is more tolerant to many abiotic stresses, including heat, drought, and flooding, making it an ideal crop for growing on marginal lands as demands for food, feed, and energy increase. Though it is generally stress-tolerant, the true potential of sorghum can only be realized through concerted genetic improvement programs. The use of DNA-based markers for the genetic analysis and manipulation of important agronomic and stress-tolerance traits is becoming an increasingly useful tool in sorghum improvement. The known germplasm of sorghum is incredibly diverse, and molecular markers are being used to assess this diversity to help manage large germplasm collections, and to make these collections more useful to breeders. Molecular markers have been used in sorghum to identify quantitative trait loci (QTL) for many complex traits, including pre-flowering and post-flowering drought tolerance, early-season cold tolerance, and resistance to the parasitic weed . However, progress in utilizing these QTL had been limited by the lack of a standard genetic map and a common nomenclature for the various linkage groups of sorghum. Fortunately, the genetic map of sorghum has recently become standardized, and has also been linked to physical chromosomes. The use of a common map will facilitate the exchange of marker and QTL information between sorghum research groups. This will allow independent validation of QTL and should expedite efforts to use these QTL for the development of improved sorghum cultivars through marker-assisted selection and trait introgression. Newer, faster marker technologies based on single nucleotide polymorphisms (SNPs), and mapping methods based on linkage disequilibrium (association mapping), will soon become useful tools for future efforts to improve this important crop.

Grain legumes are important crops for providing key components in the diets of resource-poor people of the semi-arid tropic (SAT) regions of the world. Although there are several grain legume crops grown in SAT, the present chapter deals with three important legumes i.e. groundnut or peanut (), chickpea () and pigeonpea (). Production of these legume crops are challenged by serious abiotic stresses e.g. drought, salinity as well as several fungal, viral and nematode diseases. To tackle these constraints through molecular breeding, some efforts have been initiated to develop genomic resources e.g. molecular markers, molecular genetic maps, expressed sequence tags (ESTs), macro-/micro- arrays, bacterial artificial chromosomes (BACs), etc. These genomic resources together with recently developed genetic and genomics strategies e.g. functional molecular markers, linkage-disequilibrium (LD) based association mapping, functional and comparative genomics offer the possibility of accelerating molecular breeding for abiotic and biotic stress tolerances in the legume crops. However, low level of polymorphism present in the cultivated genepools of these legume crops, imprecise phenotyping of the germplasm and the higher costs of development and application of genomic tools are critical factors in utilizing genomics in breeding of these legume crops.