Advances in cereal genomics and applications in crop breeding

Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits. Novel alleles, identified by functional genomics or haplotype analysis, can enrich the genetic basis of cultivated crops to improve productivity. Advances made in cereal genomics research in recent years thus offer the opportunities to enhance the prediction of phenotypes from genotypes for cereal breeding.     

Unique and conserved features of floral evocation in legumes

Legumes, with their unique ability to fix atmospheric nitrogen, play a vital role in ensuring future food security and mitigating the effects of climate change because they use less fossil energy and produce less greenhouse gases compared with N-fertilized systems. Grain legumes are second only to cereal crops as a source of human and animal food, and they contribute approximately one third of the protein consumed by the human population. The productivity of seed crops, such as grain legumes, is dependent on flowering. Despite the genetic variation and importance of flowering in legume production, studies of the molecular pathways that control flowering in legumes are limited.Recent advances in genomics have revealed that legume flowering pathways are divergent from those of such model species as Arabidopsis thaliana. Here, we discuss the current understanding of flowering time regulation in legumes and highlight the unique and conserved features of floral evocation in legumes.     

Genetic enrichment of cereal crops via alien gene transfer: New challenges

Genetic improvement of crops has traditionally been achieved through sexual hybridization between related species, which has resulted in numerous cultivars with high yields and superior agronomic performance. Conventional plant breeding, sometimes combined with classical cytogenetic techniques, continues to be the main method of cereal crop improvement. More recently, through the introduction of new tools of biotechnology, crossing barriers have been overcome, and genes from unrelated sources have become available to be introduced asexually into plants. Cereal crops were initially difficult to genetically engineer, mainly due to their recalcitrance to in vitro regeneration and their resistance to Agrobacterium infection. Systematic screening of cultivars and explant tissues for regeneration potential, development of various DNA delivery methods and optimization of gene expression cassettes have produced transformation protocols for the major cereals, although some elite cultivars still remain recalcitrant to transformation. Most of the transgenic cereals developed for commercial purpose exhibit herbicide and/or insect resistance; traits that are often controlled by a single gene. In recent years, more complex traits, such as dough functionality in wheat and nutritional quality of rice have been improved by the use of biotechnology. The current challenges for genetic engineering of plants will be to understand and control factors causing transgene silencing, instability and rearrangement, which are often seen in transgenic plants and highly undesirable in lines to be used for crop development. Further improvement of current cereal cultivars is expected to benefit greatly from information emerging from the areas of genomics, proteomics and bioinformatics.     

Mutation breeding of grain legumes

Summary Grain legumes are an important group of crop plants. They provide an essential source of protein food for many developing countries, but their production has gone down in favour of more profitable crops like cereals. Therefore, genetic improvement of grain legumes is urgently needed. The primary aim of grain legume breeding must be the increase of production through adaptation to more advanced cropping schemes and reduction of crop losses. Symbiotic nitrogen fixation as developed by natural evolution does not always seem to be compatible with the needed substantial increase in yield: It is not supplying sufficient nitrogen and supplementation by fertilizer is rather uneconomic. By genetic manipulation of the plant's regulatory system nitrogen fixation may become more effective and tolerant to high soil nitrogen levels. Through a number of mutation breeding projects in different countries involving all important grain legume species it has been proven that mutation induction is a good tool for supplementing the genetic variation available from natural evolution and from selection by man. High-yielding cultivars have been developed from induced mutants, which eventually also possess a more efficient nitrogen fixation capacity.     

Recent Progress in Development of Tnt1 Functional Genomics Platform for Medicago truncatula and Lotus japonicus in Bulgaria

Legumes, as protein-rich crops, are widely used for human food, animal feed and vegetable oil production. Over the past decade, two legume species, Medicago truncatula and Lotus japonicus, have been adopted as model legumes for genomics and physiological studies. The tobacco transposable element, Tnt1, is a powerful tool for insertional mutagenesis and gene inactivation in plants. A large collection of Tnt1-tagged lines of M. truncatula cv. Jemalong was generated during the course of the project 'GLIP': Grain Legumes Integrated Project, funded by the European Union (www.eugrainlegumes.org). In the project 'IFCOSMO': Integrated Functional and COmparative genomics Studies on the MOdel Legumes Medicago truncatula and Lotus japonicus, supported by a grant from the Ministry of Education, Youth and Science, Bulgaria, these lines are used for development of functional genomics platform of legumes in Bulgaria. This review presents recent advances in the evaluation of the M. truncatula Tnt1 mutant collection and outlines the steps that are taken in using the Tnt1-tagging for generation of a mutant collection of the second model legume L. japonicus. Both collections will provide a number of legume-specific mutants and serve as a resource for functional and comparative genomics research on legumes. Genomics technologies are expected to advance genetics and breeding of important legume crops (pea, faba bean, alfalfa and clover) in Bulgaria and worldwide.     

Exploring Complex Ornamental Genomes: The Rose as a Model Plant

Despite its high economic importance, little is known about rose genetics, genome structure, and the function of rose genes. Reasons for this lack of information are polyploidy in most cultivars, simple breeding strategies, high turnover rates for cultivars, and little public funding. Molecular and biotechnological tools developed during the genomics era now provide the means to fill this gap. This will be facilitated by a number of model traits as e.g., a small genome, a large genetic diversity including diploid genotypes, a comparatively short generation time and protocols for genetic engineering. A deeper understanding of genetic processes and the structure of the rose genome will serve several purposes: Applications to the breeding process including marker-assisted selection and direct manipulation of relevant traits via genetic engineering will lead to improved cultivars with new combinations of characters. In basic research, unique characters, e.g., the biosynthesis and emission of particular secondary metabolites will provide new information not available in model species. Furthermore comparative genomics will link information about the rose genome to ongoing projects on other rosaceous crops and will add to our knowledge about genome evolution and speciation. This review is intended as a presentation and is the compilation of the current knowledge on rose genetics and genomics, including functional genomics and genetic engineering. Furthermore, it is intended to show ways how knowledge on rose genetics and genomics can be linked to other species in the Rosaceae in order to utilize this information across genera.     

Pod shattering in grain legumes: emerging genetic and environment-related patterns

A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.

Recent genetic, genomic, and phenotypic studies of pod shattering in grain legumes lay the foundation for breeding crops suited for increasingly arid conditions.     

Sequence-related amplified polymorphism (SRAP) molecular marker system and its applications in crop improvement

Plant biotechnology has great potential for improving target traits in crops. This can be achieved by the production of transgenic crops and marker-assisted breeding. Marker-assisted breeding has gained momentum in recent times since it does not need biosafety regulations. Several kind of molecular markers are available for use in crop breeding, such as restriction fragment length polymorphism, microsatellites, sequence characterized amplified region, sequence-tagged site, inter-simple sequence repeat amplification, amplified fragment length polymorphism and single nucleotide polymorphism. Sequence-related amplified polymorphism is a novel molecular marker system which is based on open reading frames (ORFs) developed from genome sequence data of Arabidopsis. It provides a unique combination of forward and reverse primers which can be selected arbitrarily giving a large number of primer combinations. Since this is an ORF-based marker system, it targets functional genes and has potential for their application in crop breeding. This marker system was first used and demonstrated by Li and Quiros in Brassica oleracea in 2001, and since then there have been several reports in different plant species ranging from field crops to tree species for assessing genetic diversity, mapping and tagging of genes, hybrid identification and sex determination. This review provides an overview of SRAP markers and their applications in crop improvement.     

Advances in Arachis genomics for peanut improvement

Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.     

Genomics and molecular breeding in lesser explored pulse crops: Current trends and future opportunities

Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields.     

Genetic variation in biomass traits among 20 diverse rice varieties

Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops.     

Advances in development of transgenic pulse crops

It is three decades since the first transgenic pulse crop has been developed. Todate, genetic transformation has been reported in all the major pulse crops like Vigna species, Cicer arietinum, Cajanus cajan, Phaseolus spp, Lupinus spp, Vicia spp and Pisum sativum, but transgenic pulse crops have not yet been commercially released. Despite the crucial role played by pulse crops in tropical agriculture, transgenic pulse crops have not moved out from laboratories to large farm lands compared to their counterparts - 'cereals' and the closely related leguminous oil crop - 'soybean'. The reason for lack of commercialization of transgenic pulse crops can be attributed to the difficulty in developing transgenics with reproducibility, which in turn is due to lack of competent totipotent cells for transformation, long periods required for developing transgenics and lack of coordinated research efforts by the scientific community and long term funding. With optimization of various factors which influence genetic transformation of pulse crops, it will be possible to develop transgenic plants in this important group of crop species with more precision and reproducibility. A translation of knowledge from information available in genomics and functional genomics in model legumes like Medicago truncatula and Lotus japonicus relating to factors which contribute to enhancing crop yield and ameliorate the negative consequences of biotic and abiotic stress factors may provide novel insights for genetic manipulation to improve the productivity of pulse crops.     

Recent progress in livestock genomics and potential impact on breeding programs

Most of the major livestock breeding organizations in the world are actively involved in using the emerging tools for genome analysis to obtain a better understanding of the molecular architecture of their favourite production traits. This is bound to generate a considerable amount of novel biological information that will provide a competitive advantage to those that have access to it. At present, the preferred avenue to exploit this information is via marker-assisted selection (MAS), and several breeding organisations are starting to implement MAS in breeding programs. However, it seems unlikely that the exploitation of genomics information will be limited to MAS in the future. Even though it is difficult to anticipate the ultimate impact of genomics on animal production, it would be very surprising if it were not to revolutionize this industry as it is already revolutionizing the biomedical and plant breeding industries.