Blast resistance in rice: a review of conventional breeding to molecular approaches

Blast disease caused by the fungal pathogen Magnaporthe oryzae is the most severe diseases of rice. Using classical plant breeding techniques, breeders have developed a number of blast resistant cultivars adapted to different rice growing regions worldwide. However, the rice industry remains threatened by blast disease due to the instability of blast fungus. Recent advances in rice genomics provide additional tools for plant breeders to improve rice production systems that would be environmentally friendly. This article outlines the application of conventional breeding, tissue culture and DNA-based markers that are used for accelerating the development of blast resistant rice cultivars. The best way for controlling the disease is to incorporate both qualitative and quantitative genes in resistant variety. Through conventional and molecular breeding many blast-resistant varieties have been developed. Conventional breeding for disease resistance is tedious, time consuming and mostly dependent on environment as compare to molecular breeding particularly marker assisted selection, which is easier, highly efficient and precise. For effective management of blast disease, breeding work should be focused on utilizing the broad spectrum of resistance genes and pyramiding genes and quantitative trait loci. Marker assisted selection provides potential solution to some of the problems that conventional breeding cannot resolve. In recent years, blast resistant genes have introgressed into Luhui 17, G46B, Zhenshan 97B, Jin 23B, CO39, IR50, Pusa1602 and Pusa1603 lines through marker assisted selection. Introduction of exotic genes for resistance induced the occurrence of new races of blast fungus, therefore breeding work should be concentrated in local resistance genes. This review focuses on the conventional breeding to the latest molecular progress in blast disease resistance in rice. This update information will be helpful guidance for rice breeders to develop durable blast resistant rice variety through marker assisted selection.     

Detection of chemically induced aneuploidy with plant test systems

The utility of plant test systems for detecting chemically induced aneuploidy was evaluated by using papers published in peer-reviewed journals. A total of 147 papers were provided to the group by the Environmental Mutagen Information Center. Based on the criteria established by the Gene-Tox Committee (Waters and Auletta, 1981), 22 papers were selected for in-depth review. Only those papers listing additional, missing, or lagging chromosomes in the meiotic or mitotic cells were included in this review. Although most plant test systems may be developed to utilize either mitotic or meiotic cells for cytogenetic analysis, only a few have been employed for this purpose. In this review, Allium cepa was found to be the most commonly used test system. Other species used less frequently were Vicia faba, Hordeum vulgare, Sorgham vulgare, and Pennisetum americanum. None of the plant test systems have been sufficiently utilized to warrant judgment for its sensitivity and specificity for detecting induced aneuploidy. A suggested protocol for detecting chromosomal malsegregation in meiotic or mitotic cells is presented. Further development and utilization of plant tissue culture techniques and morphological markers identifiable in the seedling stages is recommended for detecting chemically induced aneuploidy.     

Genetic Transformation of Crops for Insect Resistance: Potential and Limitations

Transgenic resistance to insects has been demonstrated in plants expressing insecticidal genes such as δ -endotoxins from Bacillus thuringiensis (Bt), protease inhibitors, enzymes, secondary plant metabolites, and plant lectins. While transgenic plants with introduced Bt genes have been deployed in several crops on a global scale, the alternative genes have received considerably less attention. The protease inhibitor and lectin genes largely affect insect growth and development and, in most instances, do not result in insect mortality. The effective concentrations of these proteins are much greater than the Bt toxin proteins. Therefore, the potential of some of the alternative genes can only be realized by deploying them in combination with conventional host plant resistance and Bt genes. Genes conferring resistance to insects can also be deployed as multilines or synthetic varieties. Initial indications from deployment of transgenics with insect resistance in diverse cropping systems in USA, Canada, Argentina, China, India, Australia, and South Africa suggest that single transgene products in standard cultivar backgrounds are not a recipe for sustainable pest management. Instead, a much more complex approach may be needed, one which may involve deployment of a combination of different transgenes in different backgrounds. Under diverse climatic conditions and cropping systems of tropics, the success in the utilization of transgenics for pest management may involve decentralized national breeding programs and several small-scale seed companies. While several transgenic crops with insecticidal genes have been introduced in the temperate regions, very little has been done to use this technology for improving crop productivity in the harsh environments of the tropics, where the need for increasing food production is most urgent. There is a need to develop appropriate strategies for deployment of transgenics for pest management, keeping in view the pest spectrum involved, and the effects on nontarget organisms in the ecosystem.     

Novel approaches in plant breeding for rhizosphere-related traits

Selection of modern varieties has typically been performed in standardized, high fertility systems with a primary focus on yield. This could have contributed to the loss of plant genes associated with efficient nutrient acquisition strategies and adaptation to soil-related biotic and abiotic stresses if such adaptive strategies incurred a cost to the plant that compromised yield. Furthermore, beneficial interactions between plants and associated soil organisms may have been made obsolete by the provision of nutrients in high quantity and in readily plant available forms. A review of evidence from studies comparing older traditional varieties to modern high yielding varieties indeed showed that this has been the case. Given the necessity to use scarce and increasingly costly fertilizer inputs more efficiently while also raising productivity on poorer soils, it will be crucial to reintroduce desirable rhizosphere-related traits into elite cultivars. Traits that offer possibilities for improving nutrient acquisition capacity, plant–microbe interactions and tolerance to abiotic and biotic soil stresses in modern varieties were reviewed. Despite the considerable effort devoted to the identification of suitable donors and of genetic factors associated with these beneficial traits, progress in developing improved varieties has been slow and has so far largely been confined to modifications of traditional breeding procedures. Modern molecular tools have only very recently started to play a rather small role. The few successful cases reviewed in this paper have shown that novel breeding approaches using molecular tools do work in principle. When successful, they involved close collaboration between breeders and scientists conducting basic research, and confirmation of phenotypes in field tests as a ‘reality check’. We concluded that for novel molecular approaches to make a significant contribution to breeding for rhizosphere related traits it will be essential to narrow the gap between basic sciences and applied breeding through more interdisciplinary research that addresses rather than avoids the complexity of plant–soil interactions.     

培育具有安全选择标记或无选择标记的转基因植物

转基因植物中选择标记的安全性已成为植物基因工程研究的热点之一。从两个方面可以解决转基因植物中的选择标记问题。一是选用安全的正向选择标记,主要是与糖代谢和激素代谢相关的基因。二是构建能去除选择标记基因的转化系统,主要有共转化系统、双T-DNA边界载体系统、位点特异性重组系统和转座子系统等。这些植物基因工程的方法将有助于培育安全的转基因植物。 Abstract:The bio-safety of selective markers in transgenic plants has been a hot spot in the field of plant genetic engineering.To solve the problem of selective markers in the transgenic plants,two means of producing transgenic plants have been developed.One is the utilization of bio-safe positive selective markers which are genes mainly related to metabolism of auxins and carbohydrates.The other is the establishment of transformation systems allowing marker genes to be eliminated from the transgenic plants,which include co-ransformation,double T-DNA border vectors,site-specific recombination and transposition.All these approaches of plant genetic engineering will benefit breeding transgenic plants with bio-safety.     

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.     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

What Has Natural Variation Taught Us about Plant Development,Physiology, and Adaptation?

Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available.     

Development of Full-Length cDNAs from Chinese Cabbage (Brassica rapa Subsp. pekinensis) and Identification of Marker Genes for Defence Response

Arabidopsis belongs to the Brassicaceae family and plays an important role as a model plant for which researchers have developed fine-tuned genome resources. Genome sequencing projects have been initiated for other members of the Brassicaceae family. Among these projects, research on Chinese cabbage (Brassica rapa subsp. pekinensis) started early because of strong interest in this species. Here, we report the development of a library of Chinese cabbage full-length cDNA clones, the RIKEN BRC B. rapa full-length cDNA (BBRAF) resource, to accelerate research on Brassica species. We sequenced 10 000 BBRAF clones and confirmed 5476 independent clones. Most of these cDNAs showed high homology to Arabidopsis genes, but we also obtained more than 200 cDNA clones that lacked any sequence homology to Arabidopsis genes. We also successfully identified several possible candidate marker genes for plant defence responses from our analysis of the expression of the Brassica counterparts of Arabidopsis marker genes in response to salicylic acid and jasmonic acid. We compared gene expression of these markers in several Chinese cabbage cultivars. Our BBRAF cDNA resource will be publicly available from the RIKEN Bioresource Center and will help researchers to transfer Arabidopsis-related knowledge to Brassica crops.     

Exploitation of induced 2n-gametes for plant breeding

Key Message

Efficient induction of unreduced gamete in different crops and its genetic consequences will open new avenues for plant breeding.

Abstract

Unreduced gamete formation derived via abnormal meiotic cell division is an important approach to polyploidy breeding. This process is considered the main driving force in spontaneous polyploids formation in nature, but the potential application of these gametes to plant breeding has not been fully exploited. An effective mechanism for their artificial induction is needed to attain greater genetic variation and enable efficient use of unreduced gametes in breeding programs. Different approaches have been employed for 2n-pollen production including interspecific hybridization, manipulation of environmental factors and treatment with nitrous oxide, trifluralin, colchicine, oryzalin and other chemicals. These chemicals can act as a stimulus to produce viable 2n pollen; however, their exact mode of action, optimum concentration and developmental stages are still not known. Identification of efficient methods of inducing 2n-gamete formation will help increase pollen germination of sterile interspecific hybrids for inter-genomic recombination and introgression breeding to develop new polyploid cultivars and increase heterozygosity among plant populations. Additionally, the application of genomic tools and identification and isolation of genes and mechanisms involved in the induction of 2n-gamete will enable increased exploitation in different plant species, which will open new avenues for plant breeding.     

Powdery Mildew Resistance in Tomato by Impairment of SlPMR4 and SlDMR1

Genetic dissection of disease susceptibility in Arabidopsis to powdery and downy mildew has identified multiple susceptibility (S) genes whose impairment results in disease resistance. Although several of these S-genes have been cloned and characterized in more detail it is unknown to which degree their function in disease susceptibility is conserved among different plant species. Moreover, it is unclear whether impairment of such genes has potential in disease resistance breeding due to possible fitness costs associated with impaired alleles. Here we show that the Arabidopsis PMR4 and DMR1, genes encoding a callose synthase and homoserine kinase respectively, have functional orthologs in tomato with respect to their S-gene function. Silencing of both genes using RNAi resulted in resistance to the tomato powdery mildew fungus Oidium neolycopersici. Resistance to O. neolycopersici by SlDMR1 silencing was associated with severely reduced plant growth whereas SlPMR4 silencing was not. SlPMR4 is therefore a suitable candidate gene as target for mutagenesis to obtain alleles that can be deployed in disease resistance breeding of tomato.     

抗条锈病小麦品种9365在抗病育种中的利用与评价

9365是陕西省小麦研究中心创制的抗条锈病小麦品种.经多年观察、利用发现,9365对条锈病表现高抗,其穗大、成穗率高、落黄好、高产、综合农艺性状好,是陕西省小麦抗条锈病育种可资利用的抗条锈小麦品种.其缺点是植株偏高、成熟偏晚、抗性受隐性基因控制.     

Expanding the plant genome editing toolbox with recently developed CRISPR–Cas systems

Since its first appearance, CRISPR–Cas9 has been developed extensively as a programmable genome-editing tool, opening a new era in plant genome engineering. However, CRISPR–Cas9 still has some drawbacks, such as limitations of the protospacer-adjacent motif (PAM) sequence, target specificity, and the large size of the cas9 gene. To combat invading bacterial phages and plasmid DNAs, bacteria and archaea have diverse and unexplored CRISPR–Cas systems, which have the potential to be developed as a useful genome editing tools. Recently, discovery and characterization of additional CRISPR–Cas systems have been reported. Among them, several CRISPR–Cas systems have been applied successfully to plant and human genome editing. For example, several groups have achieved genome editing using CRISPR–Cas type I-D and type I-E systems, which had never been applied for genome editing previously. In addition to higher specificity and recognition of different PAM sequences, recently developed CRISPR–Cas systems often provide unique characteristics that differ from well-known Cas proteins such as Cas9 and Cas12a. For example, type I CRISPR–Cas10 induces small indels and bi-directional long-range deletions ranging up to 7.2 kb in tomatoes (Solanum lycopersicum L.). Type IV CRISPR–Cas13 targets RNA, not double-strand DNA, enabling highly specific knockdown of target genes. In this article, we review the development of CRISPR–Cas systems, focusing especially on their application to plant genome engineering. Recent CRISPR–Cas tools are helping expand our plant genome engineering toolbox.

Recently discovered and characterized clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR–Cas) systems allow additional applications to plant genome editing.     

Molecular genetics and functional genomics of abiotic stress-responsive genes in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.): a review of recent advances and future

Abiotic stresses are the key factors which negatively influence plant development and productivity and are the main cause of extensive agricultural production losses worldwide. Brassica napus is an oilseed crop of global economic significance and major contributor to the total oilseed production, quite often encounters abiotic stresses, resulting in reduced agricultural productivity. Hence, there is an immediate need being felt to raise B. napus cultivars which would be more suitable for various abiotic stress conditions presently and in the years to come. Biotechnology and molecular plant breeding has emerged as an important tool for molecular understanding of plant response to various abiotic stresses. Currently, various stress-responsive genes and mechanisms have been identified and functionally characterized in model plant Arabidopsis and other major crop plants such as Oryza sativa and Zea mays. However, very inadequate success has been achieved in this direction in a major oilseed crop such as B. napus. In this review, we present the latest methods and approaches of studying abiotic stress in B. napus. In this review, we describe the genes functioning as markers for crop breeding and discuss the recent progress and advances in genome editing by break through CRISPR/Cas9 multigene–multiplex approaches for developing multiple abiotic stress tolerance with our on-going research as a scheme. We also throw some light on molecular genetics, plant breeding and abiotic stress biotechnology of B. napus which offer a new prospective on the research directions for the practical plant breeding and functional genomics of B. napus in response to different abiotic stress conditions.     

Use of Arabidopsis thaliana and Pseudomonas syringae in the Study of Plant Disease Resistance and Tolerance

The interaction between Arabidopsis thaliana and the bacterium Pseudomonas syringae is being developed as a model experimental system for plant pathology research. Race-specific ("gene-for-gene") resistance has been demonstrated for this interaction, and pathogen genes that determine avirulence have been isolated and characterized. Because certain lines of both Arabidopsis and soybean are resistant to bacteria carrying the avirulence genes avrRpt2 and avrB, extremely similar pathogen recognition mechanisms are apparently present in these two plant species. Isogenic bacterial strains that differ by the presence of single avirulence genes are being used to analyze plant resistance. Plant resistance genes have been identified in crosses between resistant and susceptible lines. The extensive map-based cloning tools available in Arabidopsis are being used to isolate these resistance genes. In a related project, ethylene-insensitive Arabidopsis mutants are being used to examine the role of ethylene in disease development. Ethylene apparently mediates symptom formation in susceptible plants and is not required for resistance, suggesting possible strategies for enhancement of disease tolerance in crops.     

抗病转基因育种中基因资源的应用与研究进展

植物病害的防治是农业生产的主要环节,抗病育种是一个关键而有效的解决方法.随着转基因育种的兴起,抗病转基因育种也得到了很大的发展.本文就近年来抗病转基因育种过程中所利用的基因资源进行综述,试图从抗菌物质、植物的抗性基因、代谢途径中的关键酶、各类激活蛋白和调控基因等方面阐述所利用基因资源的挖掘思路,总结各类抗病基因资源挖掘策略,探索性地提出一些今后可能应用的基因资源,拓宽可供挖掘的基因资源种类,提出合理有效的抗病基因资源克隆策略.     

Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis

Depletion of non-renewable rock phosphate reserves and phosphorus (P) fertilizer price increases has renewed interest in breeding P-efficient varieties. Internal P utilization efficiency (PUE) is of prime interest because there has been no progress to date in breeding for high PUE. We characterized the genotypic variation for PUE present within the rice gene pool by using a hydroponic system that assured equal plant P uptake, followed by mapping of loci controlling PUE via Genome-Wide Association Studies (GWAS). Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12. The highest PUE was associated with a minor indica-specific haplotype on chromosome 1 and a rare aus-specific haplotype on chromosome 11. Comparative variant and expression analysis for genes contained within the chromosome 1 haplotype identified high priority candidate genes. Differences in coding regions and expression patterns between genotypes of contrasting haplotypes, suggested functional alterations for two predicted nucleic acid-interacting proteins that are likely causative for the observed differences in PUE. The loci reported here are the first identified for PUE in any crop that is not confounded by differential P uptake among genotypes. Importantly, modern rice varieties lacked haplotypes associated with superior PUE, and would thus benefit from targeted introgressions of these loci from traditional donors to improve plant growth in phosphorus-limited cropping systems.