Translational genomics can enable a quicker improvement of orphan crops toward novel agricultural applications, including the advancement of orphan biomass species for cultivation on marginal lands. ...In this sense, cell wall quality is a preeminent breeding target. However, tools to efficiently project genetic data on target traits across large sets of species are currently missing. This study aimed at closing this gap by developing a strategy to project a set of cell wall QTLs across a large group of plants by using genome synteny. This strategy is suited for large-scale analyses and detected 362 syntenic cell wall QTLs (SQTLs) across 74 angiosperms, including several (orphan) biomass species. SQTLs analyses revealed that they span large portions of the initial cell wall QTLs and are extensively conserved across diverse species. Moreover, numerous QTLs cell wall genes were conserved through SQTLs, including genes displaying allelic variation associated with cell wall composition. Functional analyses showed that highly conserved genes of SQTLs include important cell wall transcription factors and genes involved in the remodeling of cell wall polymers. For some of these gene families, SQTLs indicated the presence of differentially conserved genomic contexts for different gene members, highlighting their utility as a tool to pinpoint gene targets that maximize the likelihood of functional gene conservation. Overall, the results of this study can facilitate "universal" approaches for breeding (orphan) biomass crops, while the strategy for QTLs translation can be applied to other sets of traits and species, helping to unlock the potential of orphan species.
The establishment of mutant populations together with the strategies for targeted mutation detection has been applied successfully to a large number of organisms including many species in the plant ...kingdom. Considerable efforts have been invested into research on tomato as a model for berry-fruit plants. With the progress of the tomato sequencing project, reverse genetics becomes an obvious and achievable goal.
Here we describe the treatment of Solanum lycopersicum seeds with 1% EMS and the development of a new mutated tomato population. To increase targeted mutant detection throughput an automated seed DNA extraction has been combined with novel mutation detection platforms for TILLING in plants. We have adapted two techniques used in human genetic diagnostics: Conformation Sensitive Capillary Electrophoresis (CSCE) and High Resolution DNA Melting Analysis (HRM) to mutation screening in DNA pools. Classical TILLING involves critical and time consuming steps such as endonuclease digestion reactions and gel electrophoresis runs. Using CSCE or HRM, the only step required is a simple PCR before either capillary electrophoresis or DNA melting curve analysis. Here we describe the development of a mutant tomato population, the setting up of two polymorphism detection platforms for plants and the results of the first screens as mutation density in the populations and estimation of the false-positives rate when using HRM to screen DNA pools.
These results demonstrate that CSCE and HRM are fast, affordable and sensitive techniques for mutation detection in DNA pools and therefore allow the rapid identification of new allelic variants in a mutant population. Results from the first screens indicate that the mutagen treatment has been effective with an average mutation detection rate per diploid genome of 1.36 mutation/kb/1000 lines.
Hemp (
L.) is a bast-fiber crop with a great potential in the emerging bio-based economy. Yet, hemp breeding for fiber quality is restricted and that is mainly due to the limited knowledge of the ...genetic architecture of its fiber quality. A panel of 123 hemp accessions, with large phenotypic variability, was used to study the genetic basis of seven cell wall and bast fiber traits relevant to fiber quality. These traits showed large genetic variance components and high values of broad sense heritability in this hemp panel, as concluded from the phenotypic evaluation across three test locations with contrasting environments. The hemp panel was genotyped using restriction site associated DNA sequencing (RAD-seq). Subsequently, a large set (> 600,000) of selected genome-wide single nucleotide polymorphism (SNP) markers was used for a genome-wide association study (GWAS) approach to get insights into quantitative trait loci (QTLs) controlling fiber quality traits. In absence of a complete hemp genome sequence, identification of QTLs was based on the following characteristics: (i) association level to traits, (ii) fraction of explained trait variance, (iii) collinearity between QTLs, and (iv) detection across different environments. Using this approach, 16 QTLs were identified across locations for different fiber quality traits, including contents of glucose, glucuronic acid, mannose, xylose, lignin, and bast fiber content. Among them, six were found across the three environments. The genetic markers composing the QTLs that are common across locations are valuable tools to develop novel genotypes of hemp with improved fiber quality. Underneath the QTLs, 12 candidate genes were identified which are likely to be involved in the biosynthesis and modification of monosaccharides, polysaccharides, and lignin. These candidate genes were suggested to play an important role in determining fiber quality in hemp. This study provides new insights into the genetic architecture of fiber traits, identifies QTLs and candidate genes that form the basis for molecular breeding for high fiber quality hemp cultivars.
The genome of Chenopodium quinoa Jarvis, David E; Ho, Yung Shwen; Lightfoot, Damien J ...
Nature (London),
02/2017, Letnik:
542, Številka:
7641
Journal Article
Recenzirano
Odprti dostop
Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic ...improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.
Summary
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.
Syntenic cell wall QTLs (SQTLs) can identify genetic determinants of biomass traits in understudied species based on results from model crops. However, their effective use in plant breeding requires ...SQTLs to display intraspecific allelic variability and to predict causative loci in other populations/species than the ones used for SQTLs identification. In this study, genome assemblies from different accessions of Arabidopsis, rapeseed, tomato, rice, Brachypodium and maize were used to evaluate the intraspecific variability of SQTLs. In parallel, a genome-wide association study (GWAS) on cell wall quality traits was performed in miscanthus to verify the colocalization between GWAS loci and miscanthus SQTLs. Finally, an analogous approach was applied on a set of switchgrass cell wall QTLs retrieved from the literature. These analyses revealed large SQTLs intraspecific genetic variability, ranging from presence-absence gene variation to SNPs/INDELs and changes in coded proteins. Cell wall genes displaying gene dosage regulation, such as PAL and CAD, displayed presence-absence variation in Brachypodium and rapeseed, while protein INDELs were detected for the Brachypodium homologs of the rice brittle culm-like 8 locus, which may likely impact cell wall quality. Furthermore, SQTLs significantly colocalized with the miscanthus and switchgrass QTLs, with relevant cell wall genes being retained in colocalizing regions. Overall, SQTLs are useful tools to screen germplasm for relevant genes and alleles to improve biomass quality and can increase the efficiency of plant breeding in understudied biomass crops.
Economical cultivation of the oilseed crop Jatropha curcas is currently hampered in part due to the non-availability of purpose-bred cultivars. Although genetic maps and genome sequence data exist ...for this crop, marker-assisted breeding has not yet been implemented due to a lack of available marker-trait association studies. To identify the location of beneficial alleles for use in plant breeding, we performed quantitative trait loci (QTL) analysis for a number of agronomic traits in two biparental mapping populations.
The mapping populations segregated for a range of traits contributing to oil yield, including plant height, stem diameter, number of branches, total seeds per plant, 100-seed weight, seed oil content and fatty acid composition. QTL were detected for each of these traits and often over multiple years, with some variation in the phenotypic variance explained between different years. In one of the mapping populations where we recorded vegetative traits, we also observed co-localization of QTL for stem diameter and plant height, which were both overdominant, suggesting a possible locus conferring a pleotropic heterosis effect. By using a candidate gene approach and integrating physical mapping data from a recent high-quality release of the Jatropha genome, we were also able to position a large number of genes involved in the biosynthesis of storage lipids onto the genetic map. By comparing the position of these genes with QTL, we were able to detect a number of genes potentially underlying seed traits, including phosphatidate phosphatase genes.
The QTL we have identified will serve as a useful starting point in the creation of new varieties of J. curcas with improved agronomic performance for seed and oil productivity. Our ability to physically map a significant proportion of the Jatropha genome sequence onto our genetic map could also prove useful in identifying the genes underlying particular traits, allowing more controlled and precise introgression of desirable alleles and permitting the pyramiding or stacking of multiple QTL.
► ASE was selected as reference method owing to lower experimental error. ► Acetone and hexane were used for quantifying resin and rubber in guayule. ► Developed NIRS predictive models are efficient ...and accurate. ► The method allow high-throughput solvent-free analysis of powdered biomass.
Guayule (Parthenium argentatum), a plant native of semi-arid regions of northern Mexico and southern Texas, United States, is an under-used source of hypoallergenic latex, a solution to the serious latex allergy IgE problem worldwide. This study aimed to develop near infrared spectroscopy (NIRS) calibrations to assess resin and rubber contents in guayule plants. For achieving this goal a reference method (ASE; accelerated solvent extraction) was selected and optimized among three alternatives also including Soxhlet and Polytron. First resin (lipids, terpenes) was extracted with acetone from ground biomass at 40°C, and then rubber was extracted with hexane from left solid at 120°C. A set of 215 samples of guayule biomass (stems and branches) was collected from plants in two experimental fields located in France and in Spain and was analyzed for moisture, rubber and resin contents using the two solvent selected ASE methods. Near infrared spectra were recorded for all samples. Two thirds of the samples were randomly selected for calibration, the remaining being used for validation. For each constituent, calibration equations were developed using modified partial least squares regression. The equation performances were evaluated using the performance to deviation ratio (RPDp) and Rp2 parameters, obtained by comparison of the validation set NIR predictions and corresponding laboratory values. Moisture content (RPDp=6.91; Rp2=0.98) calibration enabled accurate determination of these traits. NIR models for hexane extract (rubber content) (RPDp=4.59; Rp2=0.96) and acetone extract (resin content) (RPDp=4.87; Rp2=0.96) were highly efficient and enabled accurate characterization of guayule biomass. On the other hand, this analysis showed that both laboratory tools, coupled with multivariate analytical techniques, could be used to differentiate the samples and accurately predict the chemical composition of this disparate set of agricultural biomass samples. This study demonstrated the ability of NIRS analysis for high throughput determination of resin and rubber contents in guayule biomass.
Crambe abyssinica (crambe) is a non-food oil seed crop. Its seed oil is widely used in the chemical industry because of the high erucic acid content. Furthermore, it is a potential platform for ...various feedstock oils for industrial uses based on genetic modification. Here, we describe the development of a series of protocols for all steps required in the process of generating genetically modified crambe.
Different explant types from crambe seedlings were tested for shoot regeneration using different hormone-combinations. Cotyledonary nodes on basic medium with 0.5 μM NAA and 2.2 μM BAP gave the highest regeneration percentages. For propagation by tissue culture, explants of stems, petioles, leaves and axillary buds of in vitro plantlets were tested using the optimized medium. Axillary buds showed the highest shoot proliferation efficiency. Cotyledonary nodes were used to test the proper concentration of kanamycin for selection of transformation events, and 10 to 25 mg · L(-1) were identified as effective. The cotyledonary nodes and cotyledons from 7-day-old seedlings were used in Agrobacterium-mediated transformations with two kinds of selection strategies, shifting or consistent. Using the shifting selection method (10 mg · L(-1) kanamycin, 25 mg · L(-1), then back to 10 mg · L(-1)) cotyledonary nodes gave 10% transformation frequency, and cotyledons 4%, while with the consistent method (25 mg · L(-1)) lower frequencies were found, 1% for cotyledonary nodes and 0% for cotyledons). Later, in vitro plant axillary buds were tried as explants for transformation, however, transformation frequency was low ranging from 0.5 to 2%. Overall, testing six different vectors and two kinds of Agrobacterium strains, the average transformation frequency using the shifting method was 4.4%. Determining T-DNA insertion numbers by Southern blotting showed that approximately 50% of the transgenic lines had a single-copy insertion.
Present research revealed the potential of using crambe meristematic tissue for genetic transformation and in vitro propagation. The most efficient method of transformation used cotyledonary node explants from 7-days-old seedlings with a shifting kanamycin selection. Meristematic tissues (cotyledonary node or axillary bud) had the highest ability for shoot proliferation. Single-copy T-DNA insert lines could be efficiently and reproducibly generated.
Crambe abyssinica produces high erucic acid (C22:1, 55-60%) in the seed oil, which can be further increased by reduction of polyunsaturated fatty acid (PUFA) levels. The omega-6 fatty acid desaturase ...enzyme (FAD2) is known to be involved in PUFA biosynthesis. In crambe, three CaFAD2 genes, CaFAD2-C1, CaFAD2-C2 and CaFAD2-C3 are expressed.
The individual effect of each CaFAD2 gene on oil composition was investigated through studying transgenic lines (CaFAD2-RNAi) for differential expression levels in relation to the composition of seed-oil. Six first generation transgenic plants (T1) showed C18:1 increase (by 6% to 10.5%) and PUFA reduction (by 8.6% to 10.2%). The silencing effect in these T1-plants ranged from the moderate silencing (40% to 50% reduction) of all three CaFAD2 genes to strong silencing (95% reduction) of CaFAD2-C3 alone. The progeny of two T1-plants (WG4-4 and WG19-6) was further analysed. Four or five transgene insertions are characterized in the progeny (T2) of WG19-6 in contrast to a single insertion in the T2 progeny of WG4-4. For the individual T2-plants of both families (WG19-6 and WG4-4), seed-specific silencing of CaFAD2-C1 and CaFAD2-C2 was observed in several individual T2-plants but, on average in both families, the level of silencing of these genes was not significant. A significant reduction in expression level (P < 0.01) in both families was only observed for CaFAD2-C3 together with significantly different C18:1 and PUFA levels in oil.
CaFAD2-C3 expression is highly correlated to levels of C18:1 (r = -0.78) and PUFA (r = 0.75), which suggests that CaFAD2-C3 is the most important one for changing the oil composition of crambe.
PDF
