关联分析及其在植物遗传学研究中的应用

植物的很多重要经济性状均属于复杂性状。基于连锁分析的QTL作图是研究复杂性状的有效手段, 但其尚存在一定的局限性。随着现代生物学的发展, 一种基于连锁不平衡的新剖分复杂性状方法--关联分析法, 开始应用于植物遗传学研究。与QTL作图法相比, 应用关联分析法具有不需要构建特殊的群体, 可同时对多个等位基因进行分析, 定位QTL精度可达到单基因水平等优势。该文介绍了关联分析方法学的基础和特性, 简述了其在植物遗传学研究中的进展情况, 并对其未来发展和在植物遗传学研究中的应用进行了展望。     

Association mapping and meta-analysis: two complementary approaches for the detection of reliable Septoria tritici blotch quantitative resistance in bread wheat (Triticum aestivum L.)

Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola, is one of the most ubiquitous and important diseases of bread wheat worldwide. The aim of this study was to identify markers linked to loci conferring resistance to STB from seven biparental populations. Linkage analysis, meta-analysis and association mapping were combined to identify robust quantitative trait loci (QTLs) for resistance. Linkage analysis led to the detection of 115 QTLs for resistance to STB and 66 QTLs linked to plant height and/or earliness. Meta-analysis clustered these 115 QTLs into 27 Meta-QTLs (MQTLs) of pathogen resistance, of which 14 were found to be linked to plant height and/or earliness. Both the relationship between dwarfing and susceptibility to STB and the significant negative correlation between earliness and STB symptoms were confirmed. Eleven loci were linked to STB resistance by association mapping using a general linear model and/or a mixed linear model, of which eight co-located with STB MQTLs and two co-located with individual QTLs. Associated markers located in MQTL regions enhanced the relevance of the results and validated the potential of an association mapping approach. With several biparental populations, meta-analysis is the most relevant form of genetic analysis study, but association mapping can be used as a validation method. Regions linked to resistance in both methods should be relevant for use in breeding programs for improving resistance to STB in wheat varieties. The main interest in comparing both approaches is to detect robust loci that will be functional in many genetic backgrounds rather than just in one or a few specific backgrounds.     

Development, genetic mapping of candidate gene-based markers and their significant association with the shoot fly resistance quantitative trait loci in sorghum [Sorghum bicolor (L.) Moench]

The associations of candidate genes with quantitative trait loci (QTL) for insect resistance provide primary insight into the molecular mechanisms of resistance. The objectives of the present study were to genetically map the candidate genes and identify their association with shoot fly resistance, and update the genetic map with new markers to locate additional QTL. In this study, 80 candidate gene (CG)-based markers were developed, targeting the seven most important shoot fly resistance genomic regions reported in our previous study. Of the 17 polymorphic CGs, the allelic polymorphisms of seven genes were significantly associated with 18 major QTL for component traits of resistance in multiple QTL mapping (MQM), and two genes in the single-marker analysis. MQM with an updated map revealed 20 new QTL with LOD and R ² (%) values ranging from 2.6 to 15.6 and 5.5 to 34.5?%, respectively. The susceptible parent 296B contributed resistance at 10 QTL. Interestingly, an orthologous insect resistance gene Cysteine protease-Mir1 (XnhsbmSFC34/SBI-10), previously presumed to be a CG based on synteny with maize, was significantly associated with major QTL for all traits (except seedling vigor) explaining 22.1?% of the phenotypic variation for deadhearts%, a direct measure of shoot fly resistance. Similarly, a NBS?CLRR gene (XnhsbmSFCILP2/SBI-10), involved in rice brown planthopper resistance, was associated with deadhearts% and number of eggs per plant. Beta-1,3-glucanase (XnhsbmSFC4/SBI-10), involved in aphid and brown planthopper resistance, was associated with deadhearts% and leaf glossiness. Comparative QTL analysis revealed the existence of common QTL for shoot fly and other important sorghum insect pests such as greenbug, head bug, and midge. Finally, the associated CGs should aid in elucidating the molecular basis of resistance, high-resolution mapping, and map-based cloning of major QTL, besides providing powerful gene tags for marker-assisted selection of shoot fly resistance.     

关联分析及其在植物遗传学研究中的应用

植物的很多重要经济性状均属于复杂性状。基于连锁分析的QTL作图是研究复杂性状的有效手段,但其尚存在一定的局限性。随着现代生物学的发展,一种基于连锁不平衡的新剖分复杂性状方法——关联分析法,开始应用于植物遗传学研究。与QTL作图法相比,应用关联分析法具有不需要构建特殊的群体,可同时对多个等位基因进行分析,定位QTL精度可达到单基因水平等优势。该文介绍了关联分析方法学的基础和特性,简述了其在植物遗传学研究中的进展情况,并对其未来发展和在植物遗传学研究中的应用进行了展望。     

Evolving ideas about genetics underlying insect virulence to plant resistance in rice-brown planthopper interactions

Many plant-parasite interactions that include major plant resistance genes have subsequently been shown to exhibit features of gene-for-gene interactions between plant Resistance genes and parasite Avirulence genes. The brown planthopper (BPH) Nilaparvata lugens is an important pest of rice (Oryza sativa). Historically, major Resistance genes have played an important role in agriculture. As is common in gene-for-gene interactions, evolution of BPH virulence compromises the effectiveness of singly-deployed resistance genes. It is therefore surprising that laboratory studies of BPH have supported the conclusion that virulence is conferred by changes in many genes rather than a change in a single gene, as is proposed by the gene-for-gene model. Here we review the behaviour, physiology and genetics of the BPH in the context of host plant resistance. A problem for genetic understanding has been the use of various insect populations that differ in frequencies of virulent genotypes. We show that the previously proposed polygenic inheritance of BPH virulence can be explained by the heterogeneity of parental populations. Genetic mapping of Avirulence genes indicates that virulence is a monogenic trait. These evolving concepts, which have brought the gene-for-gene model back into the picture, are accelerating our understanding of rice-BPH interactions at the molecular level.     

Detached leaf assay to screen for host plant resistance to Helicoverpa armigera

The noctuid Helicoverpa armigera (Hübner) is a major insect pest of chickpea Cicer arietinum L., pigeonpea Cajanus cajan (L.) Millsp., peanut Arachis hypogaea L., and cotton Gossypium spp., and host plant resistance is an important component for managing this pest in different crops. Because of variations in insect density and staggered flowering of the test material, it is difficult to identify cultivars with stable resistance to H. armigera across seasons and locations. To overcome these problems, we standardized the detached leaf assay to screen for resistance to this pest in chickpea, pigeonpea, peanut, and cotton under uniform insect pressure under laboratory conditions. Terminal branch (three to four fully expanded leaves) of chickpea, first fully expanded leaf of cotton, trifoliate of pigeonpea, or quadrifoliate of peanut, embedded in 3% agar-agar in a plastic cup/jar of appropriate size (250-500-ml capacity) infested with 10-20 neonate larvae can be used to screen for resistance to H. armigera. This technique keeps the leaves in a turgid condition for approximately 1 wk. The experiments can be terminated when the larvae have caused > 80% leaf damage in the susceptible check or when differences in leaf feeding between the resistant and susceptible checks are maximum. Detached leaf assay can be used as a rapid screening technique to evaluate germplasm, segregating breeding materials, and mapping populations for resistance to H. armigera in a short span of time with minimal cost, and under uniform insect infestation. It also provides useful information on antibiosis component of resistance to the target insect pest.     

Role of tyrosine, DOPA and decarboxylase enzymes in the synthesis of monoamines in the brain of the locust

The metabolic transformation of tyrosine (TYR) by the decarboxylase and hydroxylase enzymes was investigated in the central nervous system of the locust, Locusta migratoria. It has been demonstrated that the key amino acids, 3,4-dihydroxyphenylalanine (DOPA), 5-hydroxytryptophan (5HTP) and tyrosine are decarboxylated in all part of central nervous system. DOPA and 5HTP decarboxylase activities show parallel changes in the different ganglia, but the rank order of the activity of TYR decarboxylase is different. Enzyme purification has revealed that the molecular weights of TYR decarboxylase and DOPA/5HTP decarboxylase are 370,000 and 112,000, respectively. The decarboxylation of DOPA by DOPA/5HTP decarboxylase is stimulated, whereas the decarboxylation of DOPA by TYR decarboxylase is inhibited in the presence of the cofactor pyridoxal-5'-phosphate. TYR hydroxylase could not be detected and 3H-TYR is found to be metabolised to tyramine (TA), but not to DOPA. The haemolymph contains a significant concentration of DOPA (120 pmol/100 microl haemolymph), and the ganglia incorporates DOPA from the haemolymph by a high affinity uptake process (K(M)=12 microM and V(max)=24 pmol per ganglion/10 min). Our results suggest that no tyrosine hydroxylase is present in the locust CNS and the DOPA uptake into the ganglia by a high affinity uptake process as well as the DOPA decarboxylase enzyme may be responsible for the regulation of the ganglionic dopamine (DA) level. Two types of decarboxylases exist, one of them decarboxylating DOPA and 5HTP (DOPA/5HTP decarboxylase), other decarboxylating TYR (TYR decarboxylase). The DOPA/5HTP decarboxylase enzyme present in the insect brain may correspond to the 5HTP/DOPA decarboxylase in vertebrate brain, whereas TYR decarboxylase is characteristic only for the insect brain.     

Physical education - new technologies for mapping plant genomes

Locating DNA sequences to specific chromosomal segments is essential for associating genes with phenotypes. It is routinely achieved by segregation analysis using meiotic mapping populations that have also been used to collect phenotypic information. However, meiotic mapping is struggling to cope with the shear volume of sequences emerging from high-throughput (HTP) gene-discovery programs. We describe two approaches, Radiation Hybrid and ‘HAPPY’ mapping, which, in conjunction with meiotic mapping, represent valuable HTP tools in the quest to link genes to phenotypes.     

Silicon-augmented resistance of plants to herbivorous insects: a review

Silicon (Si) is one of the most abundant elements in the earth's crust, although its essentiality in plant growth is not clearly established. However, the importance of Si as an element that is particularly beneficial for plants under a range of abiotic and biotic stresses is now beyond doubt. This paper reviews progress in exploring the benefits at two‐ and three‐trophic levels and the underlying mechanism of Si in enhancing the resistance of host plants to herbivorous insects. Numerous studies have shown an enhanced resistance of plants to insect herbivores including folivores, borers, and phloem and xylem feeders. Silicon may act directly on insect herbivores leading to a reduction in insect performance and plant damage. Various indirect effects may also be caused, for example, by delaying herbivore establishment and thus an increased chance of exposure to natural enemies, adverse weather events or control measures that target exposed insects. A further indirect effect of Si may be to increase tolerance of plants to abiotic stresses, notably water stress, which can in turn lead to a reduction in insect numbers and plant damage. There are two mechanisms by which Si is likely to increase resistance to herbivore feeding. Increased physical resistance (constitutive), based on solid amorphous silica, has long been considered the major mechanism of Si‐mediated defences of plants, although there is recent evidence for induced physical defence. Physical resistance involves reduced digestibility and/or increased hardness and abrasiveness of plant tissues because of silica deposition, mainly as opaline phytoliths, in various tissues, including epidermal silica cells. Further, there is now evidence that soluble Si is involved in induced chemical defences to insect herbivore attack through the enhanced production of defensive enzymes or possibly the enhanced release of plant volatiles. However, only two studies have tested for the effect of Si on an insect herbivore and third trophic level effects on the herbivore's predators and parasitoids. One study showed no effect of Si on natural enemies, but the methods used were not favourable for the detection of semiochemical‐mediated effects. Work recently commenced in Australia is methodologically and conceptually more advanced and an effect of Si on the plants' ability to generate an induced response by acting at the third trophic level was observed. This paper provides the first overview of Si in insect herbivore resistance studies, and highlights novel, recent hypotheses and findings in this area of research. Finally, we make suggestions for future research efforts in the use of Si to enhance plant resistance to insect herbivores.     

Characteristics of the common bean, Phaseolus vulgaris, associated with resistance to the leafhopper Empoasca kraemeri

Experiments were conducted using the common bean, Phaseolus vulgaris, and its most important pest in Latin America, Empoasca kraemeri, in order to assess the value of insect counts and various plant characteristics as selection criteria in a plant breeding programme. The combination of insect counts with measurements of damage symptoms should make it possible to distinguish tolerance from the resistance mechanisms of antibiosis and non-preference. By this means, and by a knowledge of the plant characteristics associated with resistance, different forms of resistance may be combined in the progeny of crosses. In a comparison of two contrasting genotypes the more severely damaged genotype was the more heavily infested at early stages of plant growth, but had the lower level of infestation at later stages. The association of high early counts with high subsequent damage was not confirmed in an experiment on six genotypes, but the association of high damage with low late counts was partially confirmed. These results indicate that the level of early infestation of E. kraemeri is not consistently reflected in the subsequent levels of damage which P. vulgaris genotypes display. This suggests that these two criteria represent distinct forms of resistance which can be combined in hybrid progeny. Resistance was also associated with late maturity, indeterminate growth habit, purple flowers and black or beige seeds. However, consumer preferences and the requirements of agricultural systems place constraints upon the use of these relationships in resistance breeding.     

昆虫几丁质酶及其在植物抗虫品种改良中的应用

几丁质是昆虫外壳和围食膜的重要组成成分 ,在适当的时期昆虫分泌适量的几丁质酶降解几丁质以保证昆虫的正常生长。植物几丁质酶能够抵御病原菌的入侵 ,但是对昆虫没有明显的效果 ,而昆虫几丁质酶基因在转基因植物中的组成型表达却对昆虫具有明显的抗性。本文综述了昆虫几丁质酶的特性 ,阐述了昆虫几丁质酶及其在植物抗虫方面应用的研究进展。     

An omics evolutionary perspective on phytophagous insect–host plant interactions in Anastrepha obliqua: a review

Phytophagous insects have a close relationship with their host plants. For this reason, their interactions can lead to important changes in insect population dynamics and evolutionary trajectories. Next generation sequencing (NGS) has provided an opportunity to analyze omics data on a large scale, facilitating the change from a classical genetics approach to a more holistic understanding of the underlying molecular mechanisms of host plant use by insects. Most studies have been carried out on model species in Holarctic and temperate zones. In tropical zones, however, the effects of use of various host plants on evolutionary insect history is less understood. In the current review, we describe how omics methodologies help us to understand phytophagous insect–host plant interactions from an evolutionary perspective, using as example the Neotropical phytophagous insect West Indian fruit fly, Anastrepha obliqua (Macquart) (Diptera: Tephritidae), an economically important fruit crop pest in the Americas. Anastrepha obliqua could adopt a generalist or a specialist lifestyle. We first review the adaptive molecular mechanisms of phytophagous insects to host plants, and then describe the main tools to study phytophagous insect–host plant interactions in the era of omics sciences. The omics approaches will advance the understanding of insect molecular mechanisms and their influence on diversification and evolution. Finally, we discuss the importance of a multidisciplinary approach that integrates the use of omics tools and other, more classical methodologies in evolutionary studies.     

The biology of insecticidal activity and resistance

Identifying insecticide resistance mechanisms is paramount for pest insect control, as the understandings that underpin insect control strategies must provide ways of detecting and managing resistance. Insecticide resistance studies rely heavily on detailed biochemical and genetic analyses. Although there have been many successes, there are also many examples of resistance that still challenge us. As a precursor to rational pest insect control, the biology of the insect, within the contexts of insecticide modes of action and insecticide metabolism, must be well understood. It makes sense to initiate this research in the best model insect system, Drosophila melanogaster, and translate these findings and methodologies to other insects. Here we explore the usefulness of the D. melanogaster model in studying metabolic-based insecticide resistances, target-site mediated resistances and identifying novel insecticide targets, whilst highlighting the importance of having a more complete understanding of insect biology for insecticide studies.     

Effects of associational resistance and host density on woodland insect herbivores

1. Specialist herbivores often become less abundant per unit of host tissue as host density increases (resource dilution). They usually become less abundant when non-host species are mixed with their host plants (associational resistance). Most studies of these trends have involved herbaceous host plants and have not examined both trends for the same herbivores. 2. Three hypotheses were tested for the response of insect specialists to host plant density: resource concentration, plant apparency and resource dilution. Two hypotheses were tested for the response of herbivores to non-host plants: associational resistance and plant apparency. 3. From 1992 to 2007, I examined the responses of three monophagous insect herbivores to the densities of their host, Pinus edulis, and of two non-hosts, Pinus ponderosa and Juniperus spp. 4. Herbivore loads increased with host density, though the correlations were weak and often variable between generations. These results were consistent with the resource concentration and plant apparency hypotheses, but not with resource dilution. 5. Herbivore loads decreased as non-host density increased, consistent with the associational resistance hypothesis. This and other studies have shown that associational resistance is important in many types of plant communities. 6. The absence of resource dilution on woodland trees contrasted with studies of herbaceous host plants. Further comparisons of woody and herbaceous host plants are needed to elucidate the reasons for this difference.     

Use of cowpea trypsin inhibitor (CpTI) to protect plants against insect predation

Transgenic tobacco plants expressing a cowpea trypsin inhibitor gene have enhanced levels of insect resistance to a variety of insect pests. Furthermore, insect bioassay has shown the cowpea trypsin inhibitor to have anti-metabolic activity to insect pests of the orders Lepidoptera, Coleoptera and Orthoptera. The advantages and disadvantages of this approach to developing insect resistant crops is discussed in relationship to other methods, including conventional plant breeding and chemical control. Eventually it is hoped that African farmers will benefit from this industrially sponsored research.     

Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration

Traditional quantitative trait loci (QTL) mapping approaches are typically based on early or advanced generation analysis of bi-parental populations. A limitation associated with this methodology is the fact that mapping populations rarely give rise to new cultivars. Additionally, markers linked to the QTL of interest are often not immediately available for use in breeding and they may not be useful within diverse genetic backgrounds. Use of breeding populations for simultaneous QTL mapping, marker validation, marker assisted selection (MAS), and cultivar release has recently caught the attention of plant breeders to circumvent the weaknesses of conventional QTL mapping. The first objective of this study was to test the feasibility of using family-pedigree based QTL mapping techniques generally used with humans and animals within plant breeding populations (PBPs). The second objective was to evaluate two methods (linkage and association) to detect marker-QTL associations. The techniques described in this study were applied to map the well characterized QTL, Fhb1 for Fusarium head blight resistance in wheat (Triticum aestivum L.). The experimental populations consisted of 82 families and 793 individuals. The QTL was mapped using both linkage (variance component and pedigree-wide regression) and association (using quantitative transmission disequilibrium test, QTDT) approaches developed for extended family-pedigrees. Each approach successfully identified the known QTL location with a high probability value. Markers linked to the QTL explained 40–50% of the phenotypic variation. These results show the usefulness of a human genetics approach to detect QTL in PBPs and subsequent use in MAS.     

QTL analysis of trichome-mediated insect resistance in potato

Genetic mapping of several components of a complex type of insect resistance has been undertaken as a means toward more efficient use of the valuable characteristics of a wild relative of potato. RFLP maps constructed on interspecific diploid progenies of Solanum tuberosum × S. berthaultii were used in conjunction with morphological, biochemical and biological phenotyping to identify quantitative trait loci (QTLs) contributing to trichome-mediated insect resistance. By superimposing QTL data for a wide range of phenotypes including biochemical assays, correlative and direct screens for insect resistance, and adaptation to the target environment on the genetic maps, we have addressed the organization, action and interaction of genes controlling the resistance mechanism. The outcome contributes to an understanding of the association between component traits and between desirable and undesirable features of the donor species generated in an applied breeding program. Research is proceeding toward the development of selectable markers for the introgression and transfer of this resistance among potato gene pools.     

Plant cover associated with aboveground net primary productivity (ANPP) mediates insect community composition in steppes of Northwest China

Temperate steppe is one of the most important natural habitats for the conservation of arthropod and bird biodiversity across the Eurasian Tectonic Plate. Since 1950, fragmentation of the steppe habitat has caused a loss of biodiversity and degradation of the species communities found in natural steppe. Therefore, in this study, both plants and insects were sampled at 56 sites in the steppe biome of northwestern China to explore the effects of plant community on insect community composition and diversity. The insect community structure varied in the four different steppe types (meadow steppe, typical steppe, desert steppe, and steppe desert). Plant cover (diversity) was an important driving force, which could enhance number of families and abundance of an insect community. Aboveground net primary productivity and water content of plants had no significant effects on insect community, although the plant community as a whole did mediate insect composition and community structure. Future research should explore the ecological role of particular functional groups in plant and insect communities. Supplemental sowing to improve plant diversity in steppe habitat may be another strategy to enhance biodiversity and achieve sustainable management.     

Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

Environmental sequencing shows that plants harbor complex communities of microbes that vary across environments. However, many approaches for mapping plant genetic variation to microbe‐related traits were developed in the relatively simple context of binary host–microbe interactions under controlled conditions. Recent advances in sequencing and statistics make genome‐wide association studies (GWAS) an increasingly promising approach for identifying the plant genetic variation associated with microbes in a community context. This review discusses early efforts on GWAS of the plant phyllosphere microbiome and the outlook for future studies based on human microbiome GWAS. A workflow for GWAS of the phyllosphere microbiome is then presented, with particular attention to how perspectives on the mechanisms, evolution and environmental dependence of plant–microbe interactions will influence the choice of traits to be mapped.     

Endophytic fungus-vascular plant-insect interactions

Insect association with fungi has a long history. Theories dealing with the evolution of insect herbivory indicate that insects used microbes including fungi as their principal food materials before flowering plants evolved. Subtlety and the level of intricacy in the interactions between insects and fungi indicate symbiosis as the predominant ecological pattern. The nature of the symbiotic interaction that occurs between two organisms (the insect and the fungus), may be either mutualistic or parasitic, or between these two extremes. However, the triangular relationship involving three organisms, viz., an insect, a fungus, and a vascular plant is a relationship that is more complicated than what can be described as either mutualism or parasitism, and may represent facets of both. Recent research has revealed such a complex relationship in the vertically transmitted type-I endophytes living within agriculturally important grasses and the pestiferous insects that attack them. The intricacy of the association depends on the endophytic fungus-grass association and the insect present. Secondary compounds produced in the endophytic fungus-grass association can provide grasses with resistance to herbivores resulting in mutualistic relationship between the fungus and the plant that has negative consequences for herbivorous insects. The horizontally transmitted nongrass type-II endophytes are far less well studied and as such their ecological roles are not fully understood. This forum article explores the intricacy of dependence in such complex triangular relationships drawing from well-established examples from the fungi that live as endophytes in vascular plants and how they impact on the biology and evolution of free-living as well as concealed (e.g., gall-inducing, gall-inhabiting) insects. Recent developments with the inoculation of strains of type-I fungal endophytes into grasses and their commercialization are discussed, along with the possible roles the endophytic fungi play in the galls induced by the Cecidomyiidae (Diptera).