Abstract
Plant cell walls of Poaceae and eudicots differ substantially, both in the content and composition of their components. However, the genomic and genetic basis underlying these differences is ...not fully resolved. In this research, we analyzed multiple genomic properties of 150 cell wall gene families across 169 angiosperm genomes. The properties analyzed include gene presence/absence, copy number, synteny, occurrence of tandem gene clusters, and phylogenetic gene diversity. Results revealed a profound genomic differentiation of cell wall genes between Poaceae and eudicots, often associated with the cell wall diversity between these plant groups. For example, overall patterns of gene copy number variation and synteny were clearly divergent between Poaceae and eudicot species. Moreover, differential Poaceae–eudicot copy number and genomic contexts were observed for all the genes within the BEL1-like HOMEODOMAIN 6 regulatory pathway, which respectively induces and represses secondary cell wall synthesis in Poaceae and eudicots. Similarly, divergent synteny, copy number, and phylogenetic gene diversification were observed for the major biosynthetic genes of xyloglucans, mannans, and xylans, potentially contributing to the differences in content and types of hemicellulosic polysaccharides differences in Poaceae and eudicot cell walls. Additionally, the Poaceae-specific tandem clusters and/or higher copy number of PHENYLALANINE AMMONIA-LYASE, CAFFEIC ACID O-METHYLTRANSFERASE, or PEROXIDASE genes may underly the higher content and larger variety of phenylpropanoid compounds observed in Poaceae cell walls. All these patterns are discussed in detail in this study, along with their evolutionary and biological relevance for cell wall (genomic) diversification between Poaceae and eudicots.
Genomic analyses on 150 cell wall gene families revealed highly divergent patterns between Poaceae and eudicots that are associated with the distinct cell wall properties of these two plant clades.
Increased soil salinity is a significant agricultural problem that decreases yields for common agricultural crops. Its dynamics require cost and labour effective measurement techniques and widely ...acknowledged methods are not present yet. We investigated the potential of Unmanned Aerial Vehicle (UAV) remote sensing to measure salt stress in quinoa plants. Three different UAV sensors were used: a WIRIS thermal camera, a Rikola hyperspectral camera and a Riegl VUX-SYS Light Detection and Ranging (LiDAR) scanner. Several vegetation indices, canopy temperature and LiDAR measured plant height were derived from the remote sensing data and their relation with ground measured parameters like salt treatment, stomatal conductance and actual plant height is analysed. The results show that widely used multispectral vegetation indices are not efficient in discriminating between salt affected and control quinoa plants. The hyperspectral Physiological Reflectance Index (PRI) performed best and showed a clear distinction between salt affected and treated plants. This distinction is also visible for LiDAR measured plant height, where salt treated plants were on average 10 cm shorter than control plants. Canopy temperature was significantly affected, though detection of this required an additional step in analysis – Normalised Difference Vegetation Index (NDVI) clustering. This step assured temperature comparison for equally vegetated pixels. Data combination of all three sensors in a Multiple Linear Regression model increased the prediction power and for the whole dataset R2 reached 0.46, with some subgroups reaching an R2 of 0.64. We conclude that UAV borne remote sensing is useful for measuring salt stress in plants and a combination of multiple measurement techniques is advised to increase the accuracy.
•UAV mounted remote sensors are capable of salt stress detection in plants.•Canopy temperature is an important proxy parameter for salt stress assessment.•Multispectral indices like NDVI and OSAVI were less useful than hyperspectral PRI.•LiDAR data has an added value for salt stress detection.•Multiple measurement techniques and data integration are increasing accuracy.
This study deals with approaches for a social-ecological friendly European bioeconomy based on biomass from industrial crops cultivated on marginal agricultural land. The selected crops to be ...investigated are: Biomass sorghum, camelina, cardoon, castor, crambe, Ethiopian mustard, giant reed, hemp, lupin, miscanthus, pennycress, poplar, reed canary grass, safflower, Siberian elm, switchgrass, tall wheatgrass, wild sugarcane, and willow. The research question focused on the overall crop growth suitability under low-input management. The study assessed: (i) How the growth suitability of industrial crops can be defined under the given natural constraints of European marginal agricultural lands; and (ii) which agricultural practices are required for marginal agricultural land low-input systems (MALLIS). For the growth-suitability analysis, available thresholds and growth requirements of the selected industrial crops were defined. The marginal agricultural land was categorized according to the agro-ecological zone (AEZ) concept in combination with the marginality constraints, so-called ‘marginal agro-ecological zones’ (M-AEZ). It was found that both large marginal agricultural areas and numerous agricultural practices are available for industrial crop cultivation on European marginal agricultural lands. These results help to further describe the suitability of industrial crops for the development of social-ecologically friendly MALLIS in Europe.
•Camelina proved to be a broadly adapted species.•The highest yielding camelina lines performed well in all test environments.•Camelina grew better in environments with milder temperature during seed ...ripening, resulting in higher seed yields and seed oil contents.•Camelina genotypes with improved oil composition (increased oleic acid and lower linoleic acid contents) were identified across Europe and Canada.
Camelina (Camelina sativa L. Crantz) is considered a relatively new oilseed Brassicacea in both Europe and North America, even though its history as a crop dates back to the Bronze Age. Camelina has recently received renewed interest from both the scientific community and bio-based industries around the world. The main attractive features of this species are: drought and frost tolerance, disease and pest resistance, a unique seed oil composition with high levels of n-3 fatty acids, a considerably high seed oil content, and satisfactory seed yields, in particular under low-input management and in limiting environments. Aiming at evaluating the feasible introduction of recently released camelina breeding lines under different environmental conditions and their productive potential a multi-location trial was set up. The agronomic performance of nine improved genotypes of camelina was evaluated in a wide range of environments in Europe (Greece, Italy, Poland) and in five locations across Canada, in two consecutive growing seasons (2015 and 2016). Sowing time was optimized for each location according to the different climatic conditions. Camelina proved to be a highly adaptable species, reaching seed yields of about 1MgDMha−1 under the most limiting conditions (i.e., low precipitation, poor soil quality, extremely high temperature at flowering). Growing environments characterized by mild temperatures and adequate rainfall (>170mm, during the growing season) resulted in higher average seed yields. The length of the growing cycle varied greatly between different locations (80–110d), but the cumulative thermal time was quite stable (∼1200 GDD, growing degree days). The advanced breeding line 787–08, which possesses up to 30% larger seed compared to the mean seed size of all other test entries, proved to be the most promising genotype across all locations in Europe and Canada, combining high seed yields (1.1–2.7MgDMha−1) with improved yield stability. To the best of our knowledge, for the first time, camelina lines with improved oil composition (i.e., increased oleic and α-linolenic and lower linoleic acid contents) for feed, food and industrial applications were identified (789–02 and 887).
Feedstocks for industrial applications ranging from polymers to lubricants are largely derived from petroleum, a non-renewable resource. Vegetable oils with fatty acid structures and storage forms ...tailored for specific industrial uses offer renewable and potentially sustainable sources of petrochemical-type functionalities. A wide array of industrial vegetable oils can be generated through biotechnology, but will likely require non-commodity oilseed platforms dedicated to specialty oil production for commercial acceptance. Here we show the feasibility of three Brassicaceae oilseeds crambe, camelina, and carinata, none of which are widely cultivated for food use, as hosts for complex metabolic engineering of wax esters for lubricant applications. Lines producing wax esters >20% of total seed oil were generated for each crop and further improved for high temperature oxidative stability by down-regulation of fatty acid polyunsaturation. Field cultivation of optimized wax ester-producing crambe demonstrated commercial utility of these engineered crops and a path for sustainable production of other industrial oils in dedicated specialty oilseeds.
The
superfamily synthesizes cellulose and different hemicellulosic polysaccharides in plant cell walls. While much has been discovered about the evolution and function of these genes, their genomic ...architecture and relationship with gene (sub-)functionalization and evolution remains unclear. By using 242 genomes covering plant evolution from green algae to eudicots, we performed a large-scale analysis of synteny, phylogenetic, and functional data of the
superfamily. Results revealed considerable gene copy number variation across species and gene families, and also two patterns - singletons vs. tandem arrays - in chromosomic gene arrangement. Synteny analysis revealed exceptional conservation of gene architecture across species, but also lineage-specific patterns across gene (sub-)families. Synteny patterns correlated with gene sub-functionalization into primary and secondary
and distinct CslD functional isoforms. Furthermore, a genomic context shift of a group of cotton secondary
was associated with peculiar properties of cotton fiber synthesis. Finally, phylogenetics suggested that primary
sequences appeared before the secondary
, while phylogenomic analyses unveiled the genomic trace of the
duplication that initiated the
family. Our results describe in detail the genomic architecture of the
superfamily in plants, highlighting its crucial relevance for gene diversification and sub-functionalization, and for understanding their evolution.
Summary
Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most ...provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring ‘nontoxic’ provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F2 mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F2 plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker‐assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties.
Establishing
as a protein and oil crop requires improved varieties adapted to EU climates. The genetic regulation of strategic breeding traits, including plant architecture, growing cycle length and ...yield, is unknown. This study aimed to identify associations between 16 669 single nucleotide polymorphisms (SNPs) and 9 agronomic traits on a panel of 223
accessions, grown in four environments, by applying a genome wide association study (GWAS). Seven environment-specific QTLs linked to vegetative yield, plant height, pods number and flowering time, were identified as major effect QTLs, being able to capture 6 to 20% of the phenotypic variation observed in these traits. Furthermore, two QTLs across environments were identified for flowering time on chromosome 8. The genes
,
and
, regulating major pathways involved in flowering and growth habit, as well as
,
,
,
,
, interacting with these pathways in response to hormonal and environmental cues, were prosed as candidate genes. These results are pivotal to accelerate the development of
varieties adapted to European cropping conditions by using marker-assisted selection (MAS), as well as to provide a framework for further functional studies on plant development and phenology in this species.
The Plantarray 3.0 phenotyping platform
®
was used to monitor the growth and water use of the quinoa varieties Pasto and selRiobamba under salinity (0–300 mM NaCl). Salinity reduced the cumulative ...transpiration of both varieties by 60% at 200 mM NaCl and by 75 and 82% at 300 mM NaCl for selRiobamba and Pasto, respectively. Stomatal conductance was reduced by salinity, but at 200 mM NaCl Pasto showed a lower reduction (15%) than selRiobamba (35%), along with decreased specific leaf area. Diurnal changes in water use parameters indicate that under salt stress, daily transpiration in quinoa is less responsive to changes in light irradiance, and stomatal conductance is modulated to maximize CO
2
uptake and minimize water loss following the changes in VPD (vapor pressure deficit). These changes might contribute to the enhanced water use efficiency of both varieties under salt stress. The mechanistic crop model LINTUL was used to integrate physiological responses into the radiation use efficiency of the plants (RUE), which was more reduced in Pasto than selRiobamba under salinity. By the end of the experiment (eleven weeks after sowing, six weeks after stress), the growth of Pasto was significantly lower than selRiobamba, fresh biomass was 50 and 35% reduced at 200 mM and 70 and 50% reduced at 300 mM NaCl for Pasto and selRiobamba, respectively. We argue that contrasting water management strategies can at least partly explain the differences in salt tolerance between Pasto and selRiobamba. Pasto adopted a “conservative-growth” strategy, saving water at the expense of growth, while selRiobamba used an “acquisitive-growth” strategy, maximizing growth in spite of the stress. The implementation of high-resolution phenotyping could help to dissect these complex growth traits that might be novel breeding targets for abiotic stress tolerance.
Summary
Erucic acid (22 : 1) is a major feedstock for the oleochemical industry. In this study, a gene stacking strategy was employed to develop transgenic Crambe abyssinica lines with increased 22 : ...1 levels. Through integration of the LdLPAAT, BnFAE1 and CaFAD2‐RNAi genes into the crambe genome, confirmed by Southern blot and qRT‐PCR, the average levels of 18 : 1, 18 : 2 and 18 : 3 were markedly decreased and that of 22 : 1 was increased from 60% in the wild type to 73% in the best transgenic line of T4 generation. In single seeds of the same line, the 22 : 1 level could reach 76.9%, an increase of 28.0% over the wild type. The trierucin amount was positively correlated to 22 : 1 in the transgenic lines. Unlike high erucic rapeseed, the wild‐type crambe contains 22 : 1 in the seed phosphatidylcholine and in the sn‐2 position of triacylglycerols (5% and 8%, respectively). The transgenic line with high 22 : 1 had decreased 22 : 1 level in phosphatidylcholine, and this was negatively correlated with the 22 : 1 level at the sn‐2 position of TAG. The significances of this study include (i) achieving an unprecedented level of 22 : 1 in an oil crop; (ii) disclosing mechanisms in the channelling of a triacylglycerol‐specific unusual fatty acid in oil seeds; (iii) indicating potential limiting factors involved in the erucic acid biosynthesis and paving the way for further increase of this acid and (iv) development of an added value genetically modified oil crop having no risk of gene flow into feed and food crops.
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