Trait discovery and editing in tomato

Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.     

High-Throughput Genomics Enhances Tomato Breeding Efficiency

Tomato (Solanum lycopersicum) is considered a model plant species for a group of economically important crops, such as potato, pepper, eggplant, since it exhibits a reduced genomic size (950 Mb), a short generation time, and routine transformation technologies. Moreover, it shares with the other Solanaceous plants the same haploid chromosome number and a high level of conserved genomic organization. Finally, many genomic and genetic resources are actually available for tomato, and the sequencing of its genome is in progress. These features make tomato an ideal species for theoretical studies and practical applications in the genomics field. The present review describes how structural genomics assist the selection of new varieties resistant to pathogens that cause damage to this crop. Many molecular markers highly linked to resistance genes and cloned resistance genes are available and could be used for a high-throughput screening of multiresistant varieties. Moreover, a new genomics-assisted breeding approach for improving fruit quality is presented and discussed. It relies on the identification of genetic mechanisms controlling the trait of interest through functional genomics tools. Following this approach, polymorphisms in major gene sequences responsible for variability in the expression of the trait under study are then exploited for tracking simultaneously favourable allele combinations in breeding programs using high-throughput genomic technologies. This aims at pyramiding in the genetic background of commercial cultivars alleles that increase their performances. In conclusion, tomato breeding strategies supported by advanced technologies are expected to target increased productivity and lower costs of improved genotypes even for complex traits.Key Words: Solanum lycopersicum, genetic and genomic resources, molecular markers, microarray, resistance to pathogens, fruit quality.     

Map-based isolation of disease resistance genes from bread wheat: cloning in a supersize genome

The genome of bread wheat is hexaploid and contains 1.6 x 10 10 bp of DNA, of which more than 80% is repetitive sequences. Its size and complexity represent a challenge for the isolation of agronomically important genes, for which we frequently know only their position on the genetic map. Recently, new genomic resources and databases from genome projects have simplified the molecular analysis of the wheat genome. The first genes to be isolated from wheat by map-based cloning include three resistance genes against the fungal diseases powdery mildew and leaf rust. In this review, we will describe the approaches and resources that have contributed to this progress, and discuss genomic strategies that will simplify positional cloning in wheat in the near future.     

Novel Genomic Tools and Modern Genetic and Breeding Approaches for Crop Improvement

In recent past, genomic tools especially molecular markers have been extensively used for understanding genome dynamics as well for applied aspects in crop breeding. Several new genomics technologies such as next generation sequencing (NGS), high-throughput marker genotyping, -omics technologies have emerged as powerful tools for understanding genome variation in crop species at DNA, RNA as well as protein level. These technologies promise to provide an insight into the way gene(s) are expressed and regulated in cell and to unveil metabolic pathways involved in trait(s) of interest for breeders not only in model-/major- but even for under-resourced crop species which were once considered “orphan” crops. In parallel, genetic variation for a species present not only in cultivated genepool but even in landraces and wild species can be harnessed by using new genetic approaches such as advanced-backcross QTL (AB-QTL) analysis, introgression libraries (ILs), multi-parent advanced generation intercross (MAGIC) population and association genetics. The gene(s) or genomic regions, responsible for trait(s) of interest, identified either through conventional linkage mapping or above mentioned approaches can be introgressed or pyramided to develop superior genotypes through molecular breeding approaches such as marker-assisted back crossing (MABC), marker assisted recurrent selection (MARS) and genome wide selection (GWS). This article provides an overview on some recent genomic tools and novel genetic and breeding approaches as mentioned above with a final aim of crop improvement.     

Distribution,Etiology, Molecular Genetics and Management Perspectives of Northern Corn Leaf Blight of Maize (<i>Zea mays</i> L.)

Maize is cultivated extensively throughout the world and has the highest production among cereals. However, Northern corn leaf blight (NCLB) disease caused by Exherohilum turcicum, is the most devastating limiting factor of maize production. The disease causes immense losses to corn yield if it develops prior or during the tasseling and silking stages of crop development. It has a worldwide distribution and its development is favoured by cool to moderate temperatures with high relative humidity. The prevalence of the disease has increased in recent years and new races of the pathogen have been reported worldwide. The fungus E. turcicum is highly variable in nature. Though different management strategies have proved effective to reduce economic losses from NCLB, the development of varieties with resistance to E. turcicum is the most efficient and inexpensive way for disease management. Qualitative resistance for NCLB governed by Ht genes is a race-specific resistance which leads to a higher level of resistance. However, some Ht genes can easily become ineffective under the high pressure of virulent strains of the pathogen. Hence, it is imperative to understand and examine the consistency of the genomic locations of quantitative trait loci for resistance to NCLB in diverse maize populations. The breeding approaches for pyramiding resistant genes against E. turcicum in maize can impart NCLB resistance under high disease pressure environments. Furthermore, the genome editing approaches like CRISPR-cas9 and RNAi can also prove vital for developing NCLB resistant maize cultivars. As such this review delivers emphasis on the importance and current status of the disease, racial spectrum of the pathogen, genetic nature and breeding approaches for resistance and management strategies of the disease in a sustainable manner.     

Crop genomics: advances and applications

The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the history of plant domestication and to accelerate crop improvement. Crop plant comparative genomics is being transformed by these data and a new generation of experimental and computational approaches. The future of crop improvement will be centred on comparisons of individual plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here we review such strategies and insights that are emerging.     

Resistance and Susceptibility of Plants to Fungal Pathogens

Plants are under continuous threat of infection by pathogens endowed with diverse strategies to colonize their host. Comprehensive biochemical and genetic approaches are now starting to reveal the complex signaling pathways that mediate plant disease resistance. Initiation of defense signaling often involves specific recognition of invading pathogens by the products of specialized host resistance (R) genes. Potential resistance signaling components have been identified by mutational analyses to be required for specific resistance in the model Arabidopsis and some crop species. Strikingly, many of the components share similarity to that of innate immune systems in animals. Evidence is also accumulating that plant pathogens have a number of ways to evade host defenses during the early stages of infection, similar to animal pathogens. These strategies are becoming much better understood in a number of plant–pathogen interactions. In this review, we focus on the current knowledge of host factors that control plant resistance and susceptibility to fungal pathogens. The knowledge accumulated in these studies will serve a fundamental basis for combating diseases in strategic molecular agriculture.     

On the trail of a cereal killer: recent advances in Fusarium graminearum pathogenomics and host resistance

The ascomycete fungal pathogen Fusarium graminearum (sexual stage: Gibberella zeae) causes the devastating head blight or scab disease on wheat and barley, and cob or ear rot disease on maize. Fusarium graminearum infection causes significant crop and quality losses. In addition to roles as virulence factors during pathogenesis, trichothecene mycotoxins (e.g. deoxynivalenol) produced by this pathogen constitute a significant threat to human and animal health if consumed in respective food or feed products. In the last few years, significant progress has been made towards a better understanding of the processes involved in F. graminearum pathogenesis, toxin biosynthesis and host resistance mechanisms through the use of high-throughput genomic and phenomic technologies. In this article, we briefly review these new advances and also discuss how future research can contribute to the development of sustainable plant protection strategies against this important plant pathogen.     

Arabidopsis paves the way: genomic and network analyses in crops

Arabidopsis genomic and network analyses have facilitated crop research towards the understanding of many biological processes of fundamental importance for agriculture. Genes that were identified through genomic analyses in Arabidopsis have been used to manipulate crop traits such as pathogen resistance, yield, water-use efficiency, and drought tolerance, with the effects being tested in field conditions. The integration of diverse Arabidopsis genome-wide datasets in probabilistic functional networks has been demonstrated as a feasible strategy to associate novel genes with traits of interest, and novel genomic methods continue to be developed. The combination of genome-wide location studies, using ChIP-Seq, with gene expression profiling data is affording a genome-wide view of regulatory networks previously delineated through genetic and molecular analyses, leading to the identification of novel components and of new connections within these networks.     

From plant immunity to crop disease resistance

Plant diseases caused by diverse pathogens lead to a serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases. In the last decade, our understanding of plant immunity at both molecular and genomic levels has improved greatly. Combined with advances in biotechnologies, particularly clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based genome editing, we can now rapidly identify new resistance genes and engineer disease-resistance crop plants like never before. In this review, we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants. We also discuss existing challenges in this field and suggest directions for future studies.     

From plant genomics to breeding practice

New alleles are constantly accumulated during intentional crop selection. The molecular understanding of these alleles has stimulated new genomic approaches to mapping quantitative trait loci (QTL) and haplotype multiplicity of the genes concerned. A limited number of quantitative trait nucleotides responsible for QTL variation have been described, but an acceleration in their rate of discovery is expected with the adoption of linkage disequilibrium and candidate gene strategies for QTL fine mapping and cloning. Additional layers of regulatory variation have been studied that could also contribute to the molecular basis of quantitative genetics of crop traits. Despite this progress, the role of marker-assisted selection in plant breeding will ultimately depend on the genetic model underlying quantitative variation.     

Engineering plants with increased disease resistance: what are we going to express?

To engineer plants with increased and durable disease resistance using transgenic technologies we must address two questions. First, what gene or genes do we want to express to improve disease resistance, and second, how are we going to express these genes so that crop yields are actually increased? Emerging technologies are providing us with a plethora of candidate genes that might lead to enhanced crop protection through genetic engineering. These genes can come from plants, from pathogens or from other organisms and several strategies for their manipulation show promise. Here, we discuss recent advances and consider future perspectives for producing plants with durable disease resistance.     

Genetic markers between Biomphalaria glabrata snails susceptible and resistant to Schistosoma mansoni infection

The analysis of the genetic variability related to susceptibility to Schistosoma mansoni infection in the vector of the genus Biomphalaria is important in terms of a better understanding of the epidemiology of schistosomiasis itself, the possible pathological implications of this interaction in vertebrate hosts, and the formulation of new strategies and approaches for disease control. In the present study, the genetic variability of B. glabrata strains found to be resistant or susceptible to S. mansoni infection was investigated using DNA amplification by random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). The amplification products were analyzed on 8% polyacrylamide gel and stained with silver. We selected 10 primers, since they have previously been useful to detect polymorphism among B. glabrata and/or B. tenagophila. The results showed polymorphisms with 5 primers. Polymorphic bands observed only in the susceptible strain. The RAPD-PCR methodology represents an adequate approach for the analysis of genetic polymorphisms. The understanding of the genetic polymorphisms associated to resistance may contribute to the future identification of genomic sequences related to the resistance/susceptibility of Biomphalaria to the larval forms of S. mansoni and to the development of new strategies for the control of schistosomiasis.     

Pathogen‐informed breeding for crop disease resistance

The development of durable and broad‐spectrum resistance is an economical and eco‐friendly approach to control crop diseases for sustainable agricultural production. Emerging knowledge of the molecular basis of pathogenesis and plant–pathogen interactions has contributed to the development of novel pathogen‐informed breeding strategies beyond the limits imposed by conventional breeding. Here, we review the current status of pathogen‐assisted resistance‐related gene cloning. We also describe how pathogen effector proteins can be used to identify resistance resources and to inform cultivar deployment. Finally, we summarize the main approaches for pathogen‐directed plant improvement, including transgenesis and genome editing. Thus, we describe the emerging role of pathogen‐related studies in the breeding of disease‐resistant varieties, and propose innovative pathogen‐informed strategies for future applications.     

Ecological genomics: understanding gene and genome function in the natural environment

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic variation. Likewise, genomic approaches are beginning to offer new insights into higher-level biological phenomena that previously occupied the realm of ecological investigation only. We discuss various approaches that are likely to be useful in ecological genomic studies and offer thoughts on where this field is headed in the future.     

Genomic approaches in Xanthomonas campestris pv. vesicatoria allow fishing for virulence genes

Xanthomonas campestris pv. vesicatoria is an economically important pathogen of pepper and tomato and has been established as a model organism to study bacterial infection strategies. In the last two decades, intensive genetic and molecular analyses led to the isolation of many genes that play a role in the intimate molecular relationship with the host plant. Essential for pathogenicity is a type III protein secretion system, which delivers bacterial effector proteins into the host cell. Currently, the genome of X. campestris pv. vesicatoria is being sequenced. The availability of genomic sequence information will pave the way for the identification of new bacterial virulence factors by bioinformatic approaches. In this article, we will present preliminary data from the genomic sequence analysis and describe recent and novel studies to identify bacterial type III effector genes.     

植物抗虫基因工程研究进展

植物抗虫基因工程为防治农业害虫提供了一条崭新途径。本文对植物抗虫基因工程近年来所取得的某些研究进展,包括目前已发现和利用的抗虫基因、提高抗虫基因在植物体内表达的方法以及防止或延缓害虫产生抗性的策略等方面进行了综合评述,并对植物抗虫基因工程中有待解决的问题和发展前提提出了自己的看法。     

植物抗虫基因工程研究进展

植物抗虫基因工程为防治农业害虫提供了一条崭新途径。本文对植物抗虫基因工程近年来所取得的某些研究进展,包括目前已发现和利用的抗虫基因、提高抗虫基因在植物体内表达的方法以及防止或延缓害虫产生抗性的策略等方面进行了综合评述,并对植物抗虫基因工程中有待解决的问题和发展前景提出了自己的看法。     

Meiotic genes and proteins in cereals

We review the current status of our understanding and knowledge of the genes and proteins controlling meiosis in five major cereals, rye, wheat, barley, rice and maize. For each crop, we describe the genetic and genomic infrastructure available to investigators, before considering the inventory of genes and proteins that have roles to play in this process. Emphasis is given throughout as to how translational genomic and proteomic approaches have enabled us to circumvent some of the intractable features of this important group of plants.