Lipidomic and transcriptomic analysis reveals reallocation of carbon flux from cuticular wax into plastid membrane lipids in a glossy“Newhall”navel orange mutant

Both cuticle and membrane lipids play essential roles in quality maintenance and disease resistance in fresh fruits.Many reports have indicated the modification of alternative branch pathways in epicuticular wax mutants;however,the specific alterations concerning lipids have not been clarified thus far.Here,we conducted a comprehensive,timeresolved lipidomic,and transcriptomic analysis on the“Newhall”navel orange(WT)and its glossy mutant(MT)“Gannan No.1”.The results revealed severely suppressed wax formation accompanied by significantly elevated production of 36-carbon plastid lipids with increasing fruit maturation in MT.Transcriptomics analysis further identified a series of key functional enzymes and transcription factors putatively involved in the biosynthesis pathways of wax and membrane lipids.Moreover,the high accumulation of jasmonic acid(JA)in MT was possibly due to the need to maintain plastid lipid homeostasis,as the expression levels of two significantly upregulated lipases(CsDAD1 and CsDALL2)were positively correlated with plastid lipids and characterized to hydrolyze plastid lipids to increase the JA content.Our results will provide new insights into the molecular mechanisms underlying the natural variation of plant lipids to lay a foundation for the quality improvement of citrus fruit.

Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat

Despite recent advances in crop metabolomics,the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown.Here,we performed widely tar-geted metabolite profiling of kernels from three developmental stages(grain-filling kernels[FKs],mature kernels[MKs],and germinating kernels[GKs])using a population of 159 recombinant inbred lines.We de-tected 625 annotated metabolites and mapped 3173,3143,and 2644 metabolite quantitative trait loci(mQTLs)in FKs,MKs,and GKs,respectively.Only 52 mQTLs were mapped at all three stages,indicating the high stage specificity of the wheat kernel metabolome.Four candidate genes were functionally vali-dated by in vitro enzymatic reactions and/or transgenic approaches in wheat,three of which mediated the tricin metabolic pathway.Metaboliteflux efficiencies within the tricin pathway were evaluated,and su-perior candidate haplotypes were identified,comprehensively delineating the tricin metabolism pathway in wheat.Finally,additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study.Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.

Lipidomic insights into the response of Arabidopsis sepals to mild heat

Arabidopsis sepals coordinate flower opening in the morning as ambient temperature rises;however,the underlying molecular mechanisms are poorly understood. Mutation of one heat shock proteinencoding gene, HSP70-16, impaired sepal heat stress responses (HSR), disrupting lipid metabolism,especially sepal cuticular lipids, leading to abnormal flower opening. To further explore, to what extent,lipids play roles in this process, in this study, we compared lipidomic changes in sepals of hsp70-16 andvdac3 (mutant of a voltage-dependent anion channel, VDAC3, an HSP70-16 interactor) grown underboth normal (22 C) and mild heat stress (27 C, mild HS) temperatures. Under normal temperature,neither hsp70-16 nor vdac3 sepals showed significant changes in total lipids;however, vdac3 but nothsp70-16 sepals exhibited significant reductions in the ratios of all detected 11 lipid classes, except themonogalactosyldiacylglycerols (MGDGs). Under mild HS temperature, hsp70-16 but not vdac3 sepalsshowed dramatic reduction in total lipids. In addition, vdac3 sepals exhibited a significant accumulationof plastidic lipids, especially sulfoquinovosyldiacylglycerols (SQDGs) and phosphatidylglycerols (PGs),whereas hsp70-16 sepals had a significant accumulation of triacylglycerols (TAGs) and simultaneousdramatic reductions in SQDGs and phospholipids (PLs), such as phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), and phosphatidylserines (PSs). These findings revealed that the impact ofmild HS on sepal lipidome is influenced by genetic factors, and further, that HSP70-16 and VDAC3differently affect sepal lipidomic responses to mild HS. Our studies provide a lipidomic insight intofunctions of HSP and VDAC proteins in the plant’s HSR, in the context of floral development.

The LysM Receptor-Like Kinase LysM RLK1 Is Required to Activate Defense and Abiotic-Stress Responses Induced by Overexpression of Fungal Chitinases in Arabidopsis Plants

Application of crab shell chitin or pentamer chitin oligosaccharide to Arabidopsis seedlings increased toler- ance to salinity in wild-type but not in knockout mutants of the LysM Receptor-Like Kinasel （CERK1/LysM RLK1） gene, known to play a critical role in signaling defense responses induced by exogenous chitin. Arabidopsis plants overexpress- ing the endochitinase chit36 and hexoaminidase excyl genes from the fungus Trichoderma asperelleoides T203 showed increased tolerance to salinity, heavy-metal stresses, and Botrytis cinerea infection. Resistant lines, overexpressing fungal chitinases at different levels, were outcrossed to lysm rlkl mutants. Independent homozygous hybrids lost resistance to biotic and abiotic stresses, despite enhanced chitinase activity. Expression analysis of 270 stress-related genes, including those induced by reactive oxygen species （ROS） and chitin, revealed constant up-regulation （at least twofold） of 10 genes in the chitinase-overexpressing line and an additional 76 salt-induced genes whose expression was not elevated in the lysm rlkl knockout mutant or the hybrids harboring the mutation. These findings elucidate that chitin-induced signaling mediated by LysM RLK1 receptor is not limited to biotic stress response but also encompasses abiotic-stress signaling and can be conveyed by ectopic expression of chitinases in plants.

Mapping theArabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions

Metabolic genome-wide association studies （mGWAS）, whereupon metabolite levels are regarded as traits, can help unravel the genetic basis of metabolic networks. A total of 309Arabidopsis accessions were grown under two independent environmental conditions （control and stress） and subjected to untargeted LC-MS- based metabolomic profiling; levels of the obtained hydrophilic metabolites were used in GWAS. Our two- condition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci （p ≤ 1.0E-08）, 24.39% of which were environment-specific. Interestingly, differently from natural variation in Arabidopsis primary metabolites, which tends to be controlled by a large number of small-effect loci, we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites. The two-condition-based GWAS was fol- lowed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment. Through this integrative approach, we selected 70 key candidate associations between struc- tural genes and metabolites, and experimentally validated eight novel associations, two of them showing differential genetic regulation in the two environments studied. We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different ablotic environments for identifying metabollte-gene associations, providing novel global insights into the metabolic landscape of Arabidopsis.

Quantitative Trait Loci Analysis Identifies a Prominent Gene Involved in the Production of Fatty Acid-Derived Flavor Volatiles in Tomato

To gain insight into the genetic regulation of lipid metabolism in tomato, we conducted metabolic trait loci （mQTL） analysis following the lipidomic profiling of fruit pericarp and leaf tissue of the Solanum pennellii introgression lines （IL）. To enhance mapping resolution for selected fruit-specific mQTL, we profiled the lipids in a subset of independently derived S. pennellii backcross inbred lines, as well as in a nearsogenic sub-iL population. We identified a putative lecithin：cholesterol acyltransferase that controls the levels of several lipids, and two members of the class III lipase family, LIP1 and LIP2, that were associated with decreased levels of diacylglycerols （DAGs） and triacylglycerols （TAGs）. Lipases of this class cleave fatty acids from the glycerol backbone of acylglycerols. The released fatty acids serve as precursors of flavor volatiles. We show that LIP1 expression correlates with fatty acid-derived volatile levels. We further confirm the function of LIP1 in TAG and DAG breakdown and volatile synthesis using transgenic plants. Taken together, our study extensively characterized the genetic architecture of Upophilic compounds in tomato and demonstrated at molecular level that release of free fatty acids from the glycerol backbone can have a major impact on downstream volatile synthesis.

The utility of metabolomics as a tool to inform maize biology

With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol,maize metabolism has been extensively explored.Modern maize is still rich in genetic and phenotypic variation,yielding a wide range of structurally and functionally diversemetabolites.The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization.In this review,we examine a broad range of studies that cover recent developments in maize metabolism.Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions.We also touch upon the use of metabolomics to understand maize natural variation and evolution,with a special focus on research that has used metabolite-based genome-wide association studies(mGWASs).

Dual Resistance of Melon to Fusarium oxysporum Races 0 and 2 and to Papaya ring-spot virus is Controlled by a Pair of Head-to-Head-Oriented NB-LRR Genes of Unusual Architecture

Dear Editor, Potyviruses such as Papaya ring-spot virus （PRSV） cause important yield losses in cucurbits. Two distinct resistant alleles were identified in the Cucumis melo germplasm. Accession PI 414723 （Supplemental Table 1） possesses mono- genic resistance, controlled by the Prv2 allele, and reacts to PRSV by systemic necrotic lesions; plants with the PryI allele, described in cultivar WMR-29, remain symptomless （Pitrat and Lecoq, 1983）. Fusarium oxysporum f. sp. melonis （FUS） exclusively attacks melon, causing severe wilt. Monogenic dominant resistance was described against races O, 1, and 2. The Fore-2 gene, controlling resistance to races 0 and 1, was cloned by Joobeur et al. （2004）, and encodes a nucleotide bindina domain （NB）-Ieucine rich repeat （LRR） protein.

Involvement of the Hexose Transporter Gene LeHT1 and of Sugars in Resistance of Tomato to Tomato Yellow Leaf Curl Virus

Dear Editor, Tomato yellow leaf curl virus （TYLCV） is a whitefly-trans- mitted geminivirus infecting tomato crops （Czosnek, 2007）. TYLCV-resistant （R） and susceptible （S） lines with the same genetic background have been bred using Solanum habro- chaites as the resistance source. The gene（s） conferring resist- ance are unknown. Previously, we demonstrated that the hexose transporter gene LeHT1 is up-regulated upon infec- tion in R plants and its silencing in R plants （RH） leads to the collapse of resistance （Eybishtz et al., 2010）. To uncover the role of LeHT1 in resistance, we （1） analyzed the transcriptome reprogramming in leaves of S, R, and RH plants using a home- designed microarray, before and 7 d after TYLCV inoculation （0, 7 dpi）, and （2） measured the concentration of sugars and their derivatives in S, R, and RH leaves at 1 and 7 dpi because LeHT1 is transporting both glucose and fructose （McCurdy et al., 2010）.