A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways

Much remains unknown of molecular events controlling the plant hypersensitive defense response (HR), a rapid localized cell death that limits pathogen spread and is mediated by resistance (R-) genes. Genetic control of the HR is hard to quantify due to its microscopic and rapid nature. Natural modifiers of the ectopic HR phenotype induced by an aberrant auto-active R-gene (Rp1-D21), were mapped in a population of 3,381 recombinant inbred lines from the maize nested association mapping population. Joint linkage analysis was conducted to identify 32 additive but no epistatic quantitative trait loci (QTL) using a linkage map based on more than 7000 single nucleotide polymorphisms (SNPs). Genome-wide association (GWA) analysis of 26.5 million SNPs was conducted after adjusting for background QTL. GWA identified associated SNPs that colocalized with 44 candidate genes. Thirty-six of these genes colocalized within 23 of the 32 QTL identified by joint linkage analysis. The candidate genes included genes predicted to be in involved programmed cell death, defense response, ubiquitination, redox homeostasis, autophagy, calcium signalling, lignin biosynthesis and cell wall modification. Twelve of the candidate genes showed significant differential expression between isogenic lines differing for the presence of Rp1-D21. Low but significant correlations between HR-related traits and several previously-measured disease resistance traits suggested that the genetic control of these traits was substantially, though not entirely, independent. This study provides the first system-wide analysis of natural variation that modulates the HR response in plants.     

Quantitative resistance against Bemisia tabaci in Solanum pennellii: Genetics and metabolomics

The whitefly Bemisia tabaci is a serious threat in tomato cultivation worldwide as all varieties grown today are highly susceptible to this devastating herbivorous insect.Many accessions of the tomato wild relative Solanum pennellii show a high resistance towards B. tabaci. A mapping approach was used to elucidate the genetic background of whiteflyresistance related traits and associated biochemical traits in this species. Minor quantitative trait loci(QTLs) for whitefly adult survival(AS) and oviposition rate(OR) were identified and some were confirmed in an F2BC1 population, where they showed increased percentages of explained variance(more than 30%). Bulked segregant analyses on pools of whiteflyresistant and-susceptible F2 plants enabled the identification of metabolites that correlate either with resistance or susceptibility. Genetic mapping of these metabolites showed that a large number of them co-localize with whiteflyresistance QTLs. Some of these whitefly-resistance QTLs are hotspots for metabolite QTLs. Although a large number of metabolite QTLs correlated to whitefly resistance or susceptibility, most of them are yet unknown compounds and further studies are needed to identify the metabolic pathways and genes involved. The results indicate a direct genetic correlation between biochemical-based resistance characteristics and reduced whitefly incidence in S. pennellii.     

Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought

Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short‐day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome‐wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (G×E) for all traits in response to different watering regimes. For the RIL population, the observed G×E was reflected in 17 QTL by environment interactions (Q×E), while 17 additional QTLs were mapped not showing Q×E. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying Q×E and an additional 16 SNPs associated with loci not showing Q×E. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co‐located with a QTL mapped in the RIL population.     

Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton

Key message

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton.

Abstract

A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.

     

Association Mapping for Fruit,Plant and Leaf Morphology Traits in Eggplant

An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders’ traits.     

Genetic basis of natural variation in body pigmentation in Drosophila melanogaster

Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at bab1, t and e affect variation in abdominal pigmentation in several populations of Drosophila melanogaster. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in bab1, t and e; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including bab1, t and e and 7 genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of Drosophila pigmentation is complex, with a few major genes and many other loci with smaller effects.     

韧皮部取食昆虫诱导的植物防御反应

刺吸式昆虫与寄主植物之间具有特殊的生物互作关系。本文对刺吸式昆虫取食韧皮部诱导的植物防御反应类型、 防御物质变化、 信号途径以及植物反应转录组学研究等方面进行综述。韧皮部取食昆虫取食诱导的植物防御反应机制主要包括： (1)改变自身的营养状况; (2)产生有毒的次生化合物; (3)产生防御蛋白。防御反应与植物水杨酸、 茉莉酸、 乙烯等信号分子密切相关。研究表明, 刺吸式昆虫取食诱导的植物防御反应主要引发以水杨酸为主的信号途径, 但相关分子互作机制还有待明确。日益丰富的基因组资源和不断发展的分子生物学技术为揭示植物防御反应中信号分子的作用机制、 找出植物内生抗性的特异因子以及阐明诱导防御机制奠定了基础。了解刺吸式昆虫取食诱导的植物防御反应, 为深入理解植物-昆虫间协同进化关系提供了依据, 为害虫治理和抗虫植物的培育提供了新的思路。     

Identification of genes differentially expressed in husk tomato (<Emphasis Type="Italic">Physalis philadelphica</Emphasis>) in response to whitefly (<Emphasis Type="Italic">Trialeurodes vaporariorum</Emphasis>) infestation

Plants respond to phloem-feeding whiteflies by extensive changes in gene expression. To identify differentially expressed genes in husk tomato plants (Physalis philadelphica) infested with Trialeurodes vaporariorum, young plants were challenged with adult whiteflies, and forward and reverse subtractive libraries were constructed from infested leaves at 5 and 15 days after infestation. Several genes were identified as up-regulated; these included a diversity of genes involved in plant defense responses, protein synthesis or degradation, and cell wall fortification or modification. Genes required for amino acid biosynthesis, lipid metabolism and synthesis, including cell surface components such as suberin, responses to stress, photosynthesis and other functions, were similarly induced. Down-regulated genes were also identified, most prominently kinases and aquaporin genes. Similarities in defense responses between tomato and P. philadelphica were noted regarding the expression of certain genes in response to nematode, aphid, or whitefly. A role for abscisic acid, brassinosteroids, and cytokinins in the regulated response to whitefly infestation in P. philadelphica was also implied by the expression pattern of phytohormone-associated genes, including genes coding for proteins containing F-box motifs. Differential expression of selected genes was validated by quantitative real-time PCR. The possible role played by some of these genes during whitefly infestation is discussed.     

Effector-Triggered Immune Response in Arabidopsis thaliana Is a Quantitative Trait

We identified loci responsible for natural variation in Arabidopsis thaliana (Arabidopsis) responses to a bacterial pathogen virulence factor, HopAM1. HopAM1 is a type III effector protein secreted by the virulent Pseudomonas syringae strain Pto DC3000. Delivery of HopAM1 from disarmed Pseudomonas strains leads to local cell death, meristem chlorosis, or both, with varying intensities in different Arabidopsis accessions. These phenotypes are not associated with differences in bacterial growth restriction. We treated the two phenotypes as quantitative traits to identify host loci controlling responses to HopAM1. Genome-wide association (GWA) of 64 Arabidopsis accessions identified independent variants highly correlated with response to each phenotype. Quantitative trait locus (QTL) mapping in a recombinant inbred population between Bur-0 and Col-0 accessions revealed genetic linkage to regions distinct from the top GWA hits. Two major QTL associated with HopAM1-induced cell death were also associated with HopAM1-induced chlorosis. HopAM1-induced changes in Arabidopsis gene expression showed that rapid HopAM1-dependent cell death in Bur-0 is correlated with effector-triggered immune responses. Studies of the effect of mutations in known plant immune system genes showed, surprisingly, that both cell death and chlorosis phenotypes are enhanced by loss of EDS1, a regulatory hub in the plant immune-signaling network. Our results reveal complex genetic architecture for response to this particular type III virulence effector, in contrast to the typical monogenic control of cell death and disease resistance triggered by most type III effectors.     

Flower nectar of an autogamous perennialRorippa indica as an indirect defense mechanism against herbivorous insects

This report shows that one of the most important roles of the flower nectar of an autogamous perennialRorippa indica (L.) Hieron is as an attractant for employing some ant species as a defense against herbivorous insects. The plant has flowers from spring to early winter. Its flower nectar is frequently stolen by some ant species (hereafter cited as ants) which also feed on small herbivorous insects on the plant. Internations among the tritrophic levels (R. indica, herbivores, ants) were experimentally examined and the followings became clear. (1) Ants were attracted toR. indica in search of its flower nectar. (2) The gradual secretion of flower nectar seemed to detain ants on the plant. (3)Pieris butterfly lavae were the major herbivores onR. indica and were potentially harmful to the plant. (4) The presence of ants reduced the survival rate ofP. rapae larvae onR. indica. (5) The presence of ants reduced the feeding damage toR. indica. (6) The disadvantage of nectar use by ants seemed to be minimal for the plant since the ants did not disturb the other flower visitors. These facts suggest a mutualistic relationship betweenR. indica and ants. That is, the flower nectar serves as an indirect defense against herbivorous insects.     

Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana

Background

Genome-wide association (GWA) is gaining popularity as a means to study the architecture of complex quantitative traits, partially due to the improvement of high-throughput low-cost genotyping and phenotyping technologies. Glucosinolate (GSL) secondary metabolites within Arabidopsis spp. can serve as a model system to understand the genomic architecture of adaptive quantitative traits. GSL are key anti-herbivory defenses that impart adaptive advantages within field trials. While little is known about how variation in the external or internal environment of an organism may influence the efficiency of GWA, GSL variation is known to be highly dependent upon the external stresses and developmental processes of the plant lending it to be an excellent model for studying conditional GWA.

Methodology/Principal Findings

To understand how development and environment can influence GWA, we conducted a study using 96 Arabidopsis thaliana accessions, >40 GSL phenotypes across three conditions (one developmental comparison and one environmental comparison) and ∼230,000 SNPs. Developmental stage had dramatic effects on the outcome of GWA, with each stage identifying different loci associated with GSL traits. Further, while the molecular bases of numerous quantitative trait loci (QTL) controlling GSL traits have been identified, there is currently no estimate of how many additional genes may control natural variation in these traits. We developed a novel co-expression network approach to prioritize the thousands of GWA candidates and successfully validated a large number of these genes as influencing GSL accumulation within A. thaliana using single gene isogenic lines.

Conclusions/Significance

Together, these results suggest that complex traits imparting environmentally contingent adaptive advantages are likely influenced by up to thousands of loci that are sensitive to fluctuations in the environment or developmental state of the organism. Additionally, while GWA is highly conditional upon genetics, the use of additional genomic information can rapidly identify causal loci en masse.     

Towards an understanding of the molecular basis of effective RNAi against a global insect pest,the whitefly Bemisia tabaci

In planta RNAi against essential insect genes offers a promising route to control insect crop pests, but is constrained for many insect groups, notably phloem sap-feeding hemipterans, by poor RNAi efficacy. This study conducted on the phloem-feeding whitefly Bemisia tabaci reared on tomato plants investigated the causes of low RNAi efficacy and routes to ameliorate the problem. Experiments using tomato transgenic lines containing ds-GFP (green fluorescent protein) revealed that full-length dsRNA is phloem-mobile, ingested by the insects, and degraded in the insect. We identified B. tabaci homologs of nuclease genes (dsRNases) in other insects that degrade dsRNA, and demonstrated that degradation of ds-GFP in B. tabaci is suppressed by administration of dsRNA against these genes. dsRNA against the nuclease genes was co-administered with dsRNA against two insect genes, an aquaporin AQP1 and sucrase SUC1, that are predicted to protect B. tabaci against osmotic collapse. When dsRNA constructs for AQP1, SUC1, dsRNase1 and dsRNase2 were stacked, insect mortality was significantly elevated to 50% over 6 days on artificial diets. This effect was accompanied by significant reduction in gene expression of the target genes in surviving diet-fed insects. This study offers proof-of-principle that the efficacy of RNAi against insect pests can be enhanced by using dsRNA to suppress the activity of RNAi-suppressing nuclease genes, especially where multiple genes with related physiological function but different molecular function are targeted.     

Tiadinil, a plant activator of systemic acquired resistance, boosts the production of herbivore-induced plant volatiles that attract the predatory mite Neoseiulus womersleyi in the tea plant Camellia sinensis

Plants respond with various defense mechanisms to pathogenic or herbivorous attack. Some chemicals called plant activators that induce the plant defense response against pathogens have been commercially used to protect plants. Here we studied the effects of tiadinil (TDL) on defense mechanisms against herbivores. TDL suppresses pathogenic fungi on tea leaves by inducing defense mechanisms. We used one of the major trophic systems in tea consisting of the herbivorous mite, Tetranychus kanzawai, and the predatory mite, Neoseiulus womersleyi. TDL enhanced the production of herbivore-induced plant volatiles that attract predatory mites. The predatory mites preferred the T. kanzawai-induced volatiles from TDL-treated plants to those produced by untreated plants. These results suggest that TDL activates the plant defense response via an indirect process mediated by plant volatiles that attract natural enemies of the herbivores. In contrast, the oviposition rate, adult maturation rate, and sex ratio of T. kanzawai were not affected by TDL treatment. These results suggest that TDL did not activate any direct defense against the herbivorous mite.     

Molecular strategies of plant defense and insect counter-defense

The prediction of human population growth worldwide indicates there will be a need to substantially increase food production in order to meet the demand on food supply.This can be achieved in part by the effective management of insect pests. Since plants have co-evolved with herbivorous insects for millions of years, they have developed an array of defense genes to protect themselves against a wide variety of chewing and sucking insects.Using these naturally-occurring genes via genetic engineering represents an environmentally friendly insect pest-control measure. Insects, however, have been actively evolving adaptive mechanisms to evade natural plant defenses. Such evolved adaptability undoubtedly has helped insects during the last century to rapidly overcome a great many humanimposed management practices and agents, including chemical insecticides and genetically engineered plants. Thus, better understanding of the molecular and genetic basis of plant defense and insect counter-defense mechanisms is imperative, not only from a basic science perspective, but also for biotechnology-based pest control practice. In this review, we emphasize the recent advance and understanding of molecular strategies of attack-counterattack and defense-counter-defense between plants and their herbivores.     

Root and shoot jasmonic acid induced plants differently affect the performance of Bemisia tabaci and its parasitoid Encarsia formosa

Plants employ both direct and indirect defenses to protect themselves from attacks by herbivores and pathogens. To date most aboveground and belowground interaction studies have focused on interactions between plants and leaf-chewing herbivores, while the plant defence on the performance of phloem-feeding insects, induced by above- and belowground interaction, has been less explored. Here, jasmonic acid (JA) was used to mimic herbivore-induced responses in Chinese broccoli (Brassica oleracea var. alboglabra) roots (RJA) and shoots (SJA). The effects of JA-induced plant defenses on the performance of the phloem-feeding whitefly, Bemisia tabaci, and its aphelinid parasitoid Encarsia formosa were investigated. The results indicated that SJA induction has a much larger negative effect on B. tabaci than RJA: nymphs develop slower and have a lower survivorship. Also, females live shorter and have a lower fecundity on SJA plants compared to those on RJA and untreated control (CON) plants. The intrinsic rate of increase (r_m) of B. tabaci on SJA plants was 0.089, which was significantly lower than those on CON and RJA plants (0.115 and 0.104, respectively). The parasitoid E. formosa, on the other hand, shows a significantly faster development when parasitizing whitefly hosts feeding on SJA plants, whereas parasitism rate, longevity and fecundity were similar to those on RJA and CON plants. The current study reveals that plants induced with exogenous JA vary in both their resistance to whitefly and suitability for parasitoids, depending on the organ to which the JA was applied. Root and shoot JA applications also have contrasting effects on the phloem-feeding insect B. tabaci and its parasitoid, that is, SJA induction leads to more negative effects on whitefly performance than RJA induction, but its parasitoid performs better on hosts reared on SJA plants. These results show that top-down and bottom-up processes governing herbivore populations on Chinese broccoli are working in concert to increase plant resistance when plants are induced by SJA application.