Using lipidomics to reveal details of lipid accumulation in developing seeds from oilseed rape (Brassica napus L.)

With dwindling available agricultural land, concurrent with increased demand for oil, there is much current interest in raising oil crop productivity. We have been addressing this issue by studying the regulation of oil accumulation in oilseed rape (Brassica napus L). As part of this research we have carried out a detailed lipidomic analysis of developing seeds.The molecular species distribution in individual lipid classes revealed quite distinct patterns and showed where metabolic connections were important. As the seeds developed, the molecular species distributions changed, especially in the period of early (20 days after flowering, DAF) to mid phase (27DAF) of oil accumulation. The patterns of molecular species of diacylglycerol, phosphatidylcholine and acyl-CoAs were used to predict the possible relative contributions of diacylglycerol acyltransferase (DGAT) and phospholipid:diacylglycerol acyltransferase to triacylglycerol production. Our calculations suggest that DGAT may hold a more important role in influencing the molecular composition of TAG. Enzyme selectivity had an important influence on the final molecular species patterns.Our data contribute significantly to our understanding of lipid accumulation in the world's third most important oil crop.     

Oil content,fatty acid composition and biodiesel properties among natural provenances of Siberian apricot (Prunus sibirica L.) from China

Siberian apricot (Prunus sibirica L.), an excellent woody oil plant unique to Asia, is well known for its ability to produce high‐oil seeds for use as a promising feedstock of biodiesel. Based on the investigation of natural Siberian apricot resources in China in the early stage, seeds of Siberian apricot from 74 geographic provenances which can fully reflect the overall information were collected. In this research, seeds oil content, fatty acid composition and biodiesel properties were evaluated, and the key environmental factors that caused the variation of these in different geographic provenance were analyzed. The oil content of Siberian apricot seeds is 45.48%–61.07%, and the average was 50.95% for all provenances. The characteristics of oil can identify and quantify eight fatty acids. The most abundant fatty acids were oleic acid (C18:1; 54.02%–76.54%), followed by linoleic acid (C18:2; 16.78%–38.49%) and erucic acid (C16:0; from 3.27% to 6.12%). Monounsaturated fatty acids are the most abundant in 54.75%–77.03% compared with saturated fatty acids and polyunsaturated fatty acids. The biodiesel properties of most provenance seeds meet the standards of the ASTM D6751 and GB/T 20828, and a few meet the standards of the EN14214. Through the clustering of oil content and fatty acid composition and the analysis of biodiesel properties indexes, it is concluded that KSK provenance is the most suitable for biodiesel production. The XBZ, HHE, AES, ZLQ and LD provenances may be preserved as potential biodiesel. RDA and VPA showed that the effects of environmental factors on the oil properties of Siberian apricot were ranked as terrain factor > climate factor > soil factor, among which longitude, latitude and altitude are the main terrain indicators. These evaluations can provide reference for the effective utilization and further development of Siberian apricot as a bioenergy feedstock.     

Influence of intraovular reserves on ovule fate in apricot (Prunus armeniaca L.)

 In many plant species with multiovulate ovaries, a considerable reduction in the number of ovules takes place. However, the underlying physiological causes are not clear. In Prunus spp., although flowers present two ovules, usually only one seed is produced. We have followed the development and degeneration of the two ovules in apricot (Prunus armeniaca L.) and examined the extent to which carbohydrates within the ovule might be involved in determining the fate of the ovule. While the primary ovule grows in the days following anthesis, growth of the secondary ovule is arrested. Starch distribution along the different ovular tissues exhibits several changes that are different in the two ovules. Primary ovule growth is inversely related to starch content and this growth takes place independently of pollination since it occurs in the same way in pollinated and unpollinated flowers. In the secondary ovule, starch disappears simultaneously from all ovular structures and callose is layered at the chalazal end of the nucellus. The size of the secondary ovule does not change significantly from anthesis to degeneration, and callose starts to accumulate 5 days after anthesis. Likewise, this process occurs independently of pollination. These results are discussed in terms of the implications of the starch content of ovules in fertilization success and ovule fate. Received: 26 August 1997 / Revision accepted: 17 December 1997     

Effect of iron chlorosis on mineral nutrition and lipid composition of thylakoid biomembrane in Prunus persica (L.) Bastch.

The effect of iron chlorosis on mineral, thylakoid lipids and fatty acids composition of field grown peach tree leaves was studied. Significant differences were found in iron extracted by using , -dipyridyl (active iron), total iron, P, K, Cu and the P/Fe and Fe/Mn ratios. The levels of total chlorophyll, total glycolipids and phospholipids were reduced under iron chlorosis. A slight iron deficiency does not modify the fatty acid composition of thylakoid membranes, while a strong deficiency changes the proportion of some fatty acids.Abbreviations Chl chlorophyll - DGDG digalactosyldiglycerol - MGDG mono-galactosyldiglycerol - PC phosphatidycholine - PE phophatidylethanolamine - PG phophatidylglycerol - TLC thin layer chromatography - 16:0 palmitic acid - 16:1 palmitoleic acid - 16:lt trans-hexadecenoic - 18:0 steric acid - 18:1 oleic acid - 18:2 linoleic acid - 18:3 linolenic acid     

The conversion of polyunsaturated fatty acids to prostaglandins by tissue homogenates of the turbot,Scophthalmus maximus (L.)

The conversion of [¹⁴C]20:4(n?6) and [¹⁴C]20:5(n?3) to prostaglandins was measured in homogenates of gills, liver and intestine of the turbot, Scophthalmus maximus (L.). Incorporation of radioactivity into prostaglandins was similar to or greater than into phospholipids, with gills being more active than liver or intestine. When measured at equimolar concentrations, 20:4(n?6) was a better precursor of prostaglandins than 20:5(n?3). Incorporation of 20:4(n?6) into prostaglandins was decreased in the presence of an equimolar concentration of 20:5(n?3), and vice versa. Incorporation of both precursors into prostaglandins was partially inhibited by aspirin and indomethacin. The results are discussed in relation to prostaglandin formation in fish and the abundance of (n?3) polyunsaturated fatty acids in marine lipids generally.     

Identification of bottlenecks in the accumulation of cyclic fatty acids in camelina seed oil

Modified fatty acids (mFA) have diverse uses; for example, cyclopropane fatty acids (CPA) are feedstocks for producing coatings, lubricants, plastics and cosmetics. The expression of mFA‐producing enzymes in crop and model plants generally results in lower levels of mFA accumulation than in their natural‐occurring source plants. Thus, to further our understanding of metabolic bottlenecks that limit mFA accumulation, we generated transgenic Camelina sativa lines co‐expressing Escherichia coli cyclopropane synthase (EcCPS) and Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT). In contrast to transgenic CPA‐accumulating Arabidopsis, CPA accumulation in camelina caused only minor changes in seed weight, germination rate, oil accumulation and seedling development. CPA accumulated to much higher levels in membrane than storage lipids, comprising more than 60% of total fatty acid in both phosphatidylcholine (PC) and phosphatidylethanolamine (PE) versus 26% in diacylglycerol (DAG) and 12% in triacylglycerol (TAG) indicating bottlenecks in the transfer of CPA from PC to DAG and from DAG to TAG. Upon co‐expression of SfLPAT with EcCPS, di‐CPA‐PC increased by ~50% relative to lines expressing EcCPS alone with the di‐CPA‐PC primarily observed in the embryonic axis and mono‐CPA‐PC primarily in cotyledon tissue. EcCPS‐SfLPAT lines revealed a redistribution of CPA from the sn‐1 to sn‐2 positions within PC and PE that was associated with a doubling of CPA accumulation in both DAG and TAG. The identification of metabolic bottlenecks in acyl transfer between site of synthesis (phospholipids) and deposition in storage oils (TAGs) lays the foundation for the optimizing CPA accumulation through directed engineering of oil synthesis in target crops.     

Mapping QTLs controlling fruit quality in peach (Prunus persica (L.) Batsch)

 The organoleptic quality of fleshy fruits is in a large part defined by their composition of soluble sugars and organic acids. An F₂ population issuing from a cross between two peach varieties, ‘Ferjalou Jalousia’, a non-acid peach, and ‘Fantasia’, an acid nectarine, was analysed over 2 successive years for agronomic characters and for molecular-marker (isoenzymes, RFLPs, RAPDs, IMAs and AFLPs) segregations. Blooming and maturity dates, as well as productivity, were noted for each tree. Four fruits per tree were analysed at maturity for fresh weight, colour, pH, titratable acidity, soluble-solids content (SSC), acid (malic, citric and quinic acids) and sugar (sucrose, glucose, fructose, sorbitol) contents. QTLs were detected for all fruit components analysed, except for fruit colour. The QTLs for nearly all components were present on two linkage groups. For productivity, fresh weight, pH, quinic acid, sucrose and sorbitol content, all the detected QTLs displayed the same effect as the parental phenotypes. By contrast, for maturity date, titratable acidity, malic and citric acids and fructose, some QTLs displayed the same effect as the parental phenotypes while others displayed the opposite effect. The fraction of the total variation in each trait throughout the population explained by the QTLs was very high and reached more than 90% for some characters. For most of the characters analysed, epistasis was observed between QTLs. Received: 10 October 1997 / Accepted: 18 August 1998     

A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety “Big Star*” and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.     

Modelling the potential distribution of endangered Prunus africana (Hook.f.) Kalkm. in East Africa

Continued harvesting and climate change are affecting the distributions of many plant species and may lead to numerous extinctions over the next century. Endangered species are likely to be a special concern, but the extent to which they are sensitive to climate is currently unclear. Species distribution modelling, if carefully implemented, can be used to assess climate sensitivity and potential climate change impacts, of tree species. We used MaxEnt algorithm for species distribution modelling to assess the potential distribution and climate change risks for a threatened Prunus africana, in East Africa. Data from different herbaria on its distribution were linked to data on climate to test hypotheses on the factors determining its distribution. Predictive models were developed and projected onto a climate scenario for 2050 to assess climate change risks. Precipitation of driest quarter and annual precipitation appeared to be the main factors influencing its distribution. Climate change was predicted to result in reductions of the species' habitats (e.g. Erasmus et al., Glob. Change Biol. 2002; 8 : 679). Prunus africana distribution is thus highly vulnerable to a warming climate and highlights the fact that both in‐situ and ex‐situ conservation will be a solution to global warming.     

Development of SSR markers located in the G1 linkage group of apricot (Prunus armeniaca L.) using a bacterial artificial chromosome library

Sixteen simple sequence repeats (SSRs) of apricot (Prunus armeniaca L.) were isolated from a bacterial artificial chromosome (BAC) library. Twelve restriction fragment length polymorphism (RFLP) probes mapped on LG1 of the Prunus general map were hybridized to the BAC library in order to select clones belonging to G1 linkage group of apricot. Selected BACs were digested, subcloned and hybridized with probes containing repeat motifs (GA)₁₀ and (TA)₁₀. Sequencing of the positive subclones revealed 18 unique SSR sequences of which 16 allowed the design of primers flanking the SSR. From the 16 primer pairs, 10 amplified polymorphic markers with an average of observed and expected heterozygosities of 0.44 and 0.68, respectively. The procedure described here proves to be a useful technique for obtaining markers in target areas of a genome.     

Characterization of microsatellite markers in peach [Prunus persica (L.) Batsch]

Microsatellites have emerged as an important system of molecular markers. We evaluated the potential of microsatellites for use in genetic studies of peach [Prunus persica (L.) Batsch]. Microsatellite loci in peach were identified by screening a pUC8 genomic library, a λZAPII leaf cDNA library, as well as through database searches. Primer sequences for the microsatellite loci were tested from the related Rosaceae species apple (Malus×domestica) and sour cherry (Prunus cerasus L.). The genomic library was screened for CT, CA and AGG repeats, while the cDNA library was screened for (CT)_n- and (CA)_n-containing clones. Estimates of microsatellite frequencies were determined from the genomic library screening, and indicate that CT repeats occur every 100 kb, CA repeats every 420 kb, and AGG repeats every 700 kb in the peach genome. Microsatellite- containing clones were sequenced, and specific PCR primers were designed to amplify the microsatellite- containing regions from genomic DNA. The level of microsatellite polymorphism was evaluated among 28 scion peach cultivars which displayed one to four alleles per primer pair. Five microsatellites were found to segregate in intraspecific peach-mapping crosses. In addition, these microsatellite markers were tested for their utility in cross-species amplification for use in comparative mapping both within the Rosaceae, and with the un- related species Arabidopsis thaliana L. Received: 18 June 1999 / Accepted: 6 December 1999     

Inheritance of resistance to Plum pox virus in apricot (Prunus armeniaca L.)

The inheritance of resistance to Plum pox virus (PPV) has been studied in 1,178 apricot hybrids. Seven hundred and eighteen F1 hybrids, obtained from controlled crosses between the susceptible Greek cultivar “Bebecou” and the resistant PPV cultivars of American origin (“Stark Early Orange,” ‘NJA2,” ‘Veecot,” “Sunglo,” “Harlayne,” and “Orangered”) were evaluated for resistance to the PPV-M (Marcus) strain, 8 years after artificial inoculation. The inheritance of resistance to PPV has been additionally studied for the first time in a BC₁ population of 95 apricot hybrids for four vegetative periods. Reaction of each hybrid to PPV-M was scored through visual symptoms, indexing onto GF-305 and double-antibody sandwich enzyme-linked immunosorbent assay tests. Segregation within the hybrids, determined by Chi-squared analysis, fits a 1:1 ratio (P ≤ 0.05) of the resistant vs susceptible, indicating that resistance to PPV is controlled by a single dominant gene locus and that the above six resistant cultivars are heterozygous for the trait. Plants carrying this gene may initially develop disease symptoms on leaves but eventually recover and no virus can be detected in leaves. Susceptible plants show similar symptoms initially but remain symptomatic. Inheritance of resistance to PPV also has been studied in 365 F1 hybrids by crossing the resistant cultivar “Stella” with the susceptible “Bebecou” and the resistant cultivars “Sunglo” and “NJA2,” for 8 years after inoculation. The segregation ratio was 1:0 (resistant/susceptible) suggesting that “Stella” is homozygous for the resistance trait. The purpose of this work was the enhancement of the knowledge of inheritance of resistance to PPV for the selection of new cultivars.     

Genetic enhancement of palmitic acid accumulation in cotton seed oil through RNAi down‐regulation of ghKAS2 encoding β‐ketoacyl‐ACP synthase II (KASII)

Palmitic acid (C16:0) already makes up approximately 25% of the total fatty acids in the conventional cotton seed oil. However, further enhancements in palmitic acid content at the expense of the predominant unsaturated fatty acids would provide increased oxidative stability of cotton seed oil and also impart the high melting point required for making margarine, shortening and confectionary products free of trans fatty acids. Seed‐specific RNAi‐mediated down‐regulation of β‐ketoacyl‐ACP synthase II (KASII) catalysing the elongation of palmitoyl‐ACP to stearoyl‐ACP has succeeded in dramatically increasing the C16 fatty acid content of cotton seed oil to well beyond its natural limits, reaching up to 65% of total fatty acids. The elevated C16 levels were comprised of predominantly palmitic acid (C16:0, 51%) and to a lesser extent palmitoleic acid (C16:1, 11%) and hexadecadienoic acid (C16:2, 3%), and were stably inherited. Despite of the dramatic alteration of fatty acid composition and a slight yet significant reduction in oil content in these high‐palmitic (HP) lines, seed germination remained unaffected. Regiochemical analysis of triacylglycerols (TAG) showed that the increased levels of palmitic acid mainly occurred at the outer positions, while C16:1 and C16:2 were predominantly found in the sn‐2 position in both TAG and phosphatidylcholine. Crossing the HP line with previously created high‐oleic (HO) and high‐stearic (HS) genotypes demonstrated that HP and HO traits could be achieved simultaneously; however, elevation of stearic acid was hindered in the presence of high level of palmitic acid.     

Comparative lipidomic studies of Scenedesmus sp. (Chlorophyceae) and Cylindrotheca closterium (Bacillariophyceae) reveal their differences in lipid production under nitrogen starvation

Microalgae are a promising resource for the highly sustainable production of various biomaterials (food and feed), high‐value biochemicals, or biofuels. However, factors influencing the valued lipid production from oleaginous algae require a more detailed investigation. This study elucidates the variations in lipid metabolites between a marine diatom (Cylindrotheca closterium) and a freshwater green alga (Scenedesmus sp.) under nitrogen starvation at the molecular species level, with emphasis on triacylglycerols using liquid chromatography–electrospray ionization mass spectrometry techniques. A comprehensive analysis was carried out by comparing the changes in total lipids, growth kinetics, fatty acid compositions, and glycerolipid profiles at the molecular species level at different time points of nitrogen starvation. A total of 60 and 72 triacylglycerol molecular species, along with numerous other polar lipids, were identified in Scenedesmus sp. and C. closterium, respectively, providing the most abundant triacylglycerol profiles for these two species. During nitrogen starvation, more triacylglycerol of Scenedesmus sp. was synthesized via the “eukaryotic pathway” in the endoplasmic reticulum, whereas the increase in triacylglycerol in C. closterium was mainly a result of the “prokaryotic pathway” in the chloroplasts after 96 h of nitrogen starvation. The distinct responses of lipid synthesis to nitrogen starvation exhibited by the two species indicate different strategies of lipid accumulation, notably triacylglycerols, in green algae and diatoms. Scenedesmus sp. and Cylindrotheca closterium could serve as excellent candidates for the mass production of biofuels or polyunsaturated fatty acids for nutraceutical purposes.     

Detection of induced mutations in CaFAD2 genes by next‐generation sequencing leading to the production of improved oil composition in Crambe abyssinica

Crambe abyssinica is a hexaploid oil crop for industrial applications. An increase of erucic acid (C22:1) and reduction of polyunsaturated fatty acid (PUFA) contents in crambe oil is a valuable improvement. An increase in oleic acid (C18:1), a reduction in PUFA and possibly an increase in C22:1 can be obtained by down‐regulating the expression of fatty acid desaturase2 genes (CaFAD2), which code for the enzyme that converts C18:1 into C18:2. We conducted EMS‐mutagenesis in crambe, followed by Illumina sequencing, to screen mutations in three expressed CaFAD2 genes. Two novel analysis strategies were used to detect mutation sites. In the first strategy, mutation detection targeted specific sequence motifs. In the second strategy, every nucleotide position in a CaFAD2 fragment was tested for the presence of mutations. Seventeen novel mutations were detected in 1100 one‐dimensional pools (11 000 individuals) in three expressed CaFAD2 genes, including non‐sense mutations and mis‐sense mutations in CaFAD2‐C1, ‐C2 and ‐C3. The homozygous non‐sense mutants for CaFAD2‐C3 resulted in a 25% higher content of C18:1 and 25% lower content of PUFA compared to the wild type. The mis‐sense mutations only led to small changes in oil composition. Concluding, targeted mutation detection using NGS in a polyploid was successfully applied and it was found that a non‐sense mutation in even a single CaFAD2 gene can lead to changes in crambe oil composition. Stacking the mutations in different CaFAD2 may gain additional changes in C18:1 and PUFA contents.     

TaDA1, a conserved negative regulator of kernel size,has an additive effect with TaGW2 in common wheat (Triticum aestivum L.)

Kernel size is an important trait determining cereal yields. In this study, we cloned and characterized TaDA1, a conserved negative regulator of kernel size in wheat (Triticum aestivum). The overexpression of TaDA1 decreased the size and weight of wheat kernels, while its down‐regulation using RNA interference (RNAi) had the opposite effect. Three TaDA1‐A haplotypes were identified in Chinese wheat core collections, and a haplotype association analysis showed that TaDA1‐A‐HapI was significantly correlated with the production of larger kernels and higher kernel weights in modern Chinese cultivars. The haplotype effect resulted from a difference in TaDA1‐A expression levels between genotypes, with TaDA1‐A‐HapI resulting in lower TaDA1‐A expression levels. This favourable haplotype was found having been positively selected during wheat breeding over the last century. Furthermore, we demonstrated that TaDA1‐A physically interacts with TaGW2‐B. The additive effects of TaDA1‐A and TaGW2‐B on kernel weight were confirmed not only by the phenotypic enhancement arising from the simultaneous down‐regulation of TaDA1 and TaGW2 expression, but also by the combinational haplotype effects estimated from multi‐environment field data from 348 wheat cultivars. A comparative proteome analysis of developing transgenic and wild‐type grains indicated that TaDA1 and TaGW2 are involved in partially overlapping but relatively independent protein regulatory networks. Thus, we have identified an important gene controlling kernel size in wheat and determined its interaction with other genes regulating kernel weight, which could have beneficial applications in wheat breeding.     

Successful high‐level accumulation of fish oil omega‐3 long‐chain polyunsaturated fatty acids in a transgenic oilseed crop

Omega‐3 (also called n‐3) long‐chain polyunsaturated fatty acids (≥C20; LC‐PUFAs) are of considerable interest, based on clear evidence of dietary health benefits and the concurrent decline of global sources (fish oils). Generating alternative transgenic plant sources of omega‐3 LC‐PUFAs, i.e. eicosapentaenoic acid (20:5 n‐3, EPA) and docosahexaenoic acid (22:6 n‐3, DHA) has previously proved problematic. Here we describe a set of heterologous genes capable of efficiently directing synthesis of these fatty acids in the seed oil of the crop Camelina sativa, while simultaneously avoiding accumulation of undesirable intermediate fatty acids. We describe two iterations: RRes_EPA in which seeds contain EPA levels of up to 31% (mean 24%), and RRes_DHA, in which seeds accumulate up to 12% EPA and 14% DHA (mean 11% EPA and 8% DHA). These omega‐3 LC‐PUFA levels are equivalent to those in fish oils, and represent a sustainable, terrestrial source of these fatty acids. We also describe the distribution of these non‐native fatty acids within C. sativa seed lipids, and consider these data in the context of our current understanding of acyl exchange during seed oil synthesis.     

Lipid composition and utilization in developing eggs of two tropical marine caridean shrimps (Decapoda: Caridea: Alpheidae, Palaemonidae)

Changes in biomass and lipid biochemistry during egg development were studied in the tropical shrimps, Alpheus saxidomus and Palaemonetes schmitti, from Pacific Costa Rica. Freshly-laid eggs of P. schmitti were substantially smaller than those of A. saxidomus; dry mass decreased during embryogenesis in the former species but remained almost constant in the latter one. Water content of eggs close to hatching were similar among both species (roughly 75%). Newly-produced eggs of the two species contained ≈20% fatty acids per egg dry mass; a comparison with data concerning decapods inhabiting tropical and temperate waters revealed that eggs produced by shrimps inhabiting tropical waters tend to have a higher lipid egg content per dry mass than those from temperate regions. Major lipid classes in the eggs of both species were phospholipids and triacylglycerols which increased and decreased during the incubation period, respectively. The predominant fatty acids of P. schmitti eggs were 16:0, 20:5(n-3) and 22:6(n-3) whereas eggs of A. saxidomus showed high amounts of 16:0, 20:5(n-3) and 16:1(n-7), and remarkably low values of 22:6(n-3) fatty acid. Lipid utilization was more pronounced in P. schmitti; in A. saxidomus, eggs close to hatching still contained 70% of the initially deposited fatty acid content which may indicate an enhanced independence of the newly-hatched larvae on external energy resources. The observed differences may partially be related to different habitat preferences, however, the role of adaptation and phylogeny as determinants of egg lipid biochemistry in caridean shrimps remains to be clarified.