The genome of Chenopodium quinoa Jarvis, David E; Ho, Yung Shwen; Lightfoot, Damien J ...
Nature (London),
02/2017, Letnik:
542, Številka:
7641
Journal Article
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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.
Phosphorus (P) is often an important limiting factor for crop yields, but rock phosphate as fertilizer is a non-renewable resource and expected to become scarce in the future. High P input levels in ...agriculture have led to environmental problems. One of the ways to tackle these issues simultaneously is improving phosphorus use efficiency (PUE) of the crops through breeding. In this review, we describe plant architectural and physiological traits important for PUE. Subsequently, we discuss efficient methods of screening for PUE traits. We address targeted cultivation methods, including solid and hydroponic systems, as well as testing methods, such as image analysis systems, and biomass and photosynthesis measurements. Genetic variation for PUE traits has been assessed in many crops, and genetics of PUE has been studied by quantitative trait loci (QTL) analyses and genome-wide association study. A number of genes involved in the plant’s response to low P have been characterized. These genes include transcription factors, and genes involved in signal transduction, hormonal pathways, sugar signalling, P saving metabolic pathways, and in P scavenging, including transporters and metabolites and/or ATP-ases mobilizing P in the soil. In addition, the role of microorganisms promoting PUE of plants, particularly arbuscular mycorrhizal fungi is discussed. An overview is given of methods for selecting for optimal combinations of plant and fungal genotypes, and their genetics, incl. QTLs and genes involved. In conclusion, significant progress has been made in selecting for traits for PUE, developing systems for the difficult but highly relevant root phenotyping, and in identifying QTLs and genes involved.
Stress conditions in agricultural ecosystems can occur at variable intensities. Different resistance mechanisms against abiotic stress and pathogens are deployed by plants. Thus, it is important to ...examine plant responses to stress combinations under different scenarios. Here, we evaluated the effect of different levels of salt stress ranging from mild to severe (50, 100, and 150 mM NaCl) on powdery mildew resistance and overall performance of tomato introgression lines with contrasting levels of partial resistance, as well as near-isogenic lines (NILs) carrying the resistance gene Ol-1 (associated with a slow hypersensitivity response; HR), ol-2 (an mlo mutant associated with papilla formation), and Ol-4 (an R gene associated with a fast HR). Powdery mildew resistance was affected by salt stress in a genotype- and stress intensity-dependent manner. In susceptible and partial resistant lines, increased susceptibility was observed under mild salt stress (50 mM) which was accompanied by accelerated cell death-like senescence. In contrast, severe salt stress (150 mM) reduced disease symptoms. Na⁺ and Cl⁻ accumulation in the leaves was linearly related to the decreased pathogen symptoms under severe stress. In contrast, complete resistance mediated by ol-2 and Ol-4 was unaffected under all treatment combinations, and was associated with a decreased growth penalty. Increased susceptibility and senescence under combined stress in NIL-Ol-1 was associated with the induction of ethylene and jasmonic acid pathway genes and the cell wall invertase gene LIN6. These results highlight the significance of stress severity and resistance type on the plant’s performance under the combination of abiotic and biotic stress.
Plants have evolved to deal with different stresses during plant growth, relying on complex interactions or crosstalk between multiple signalling pathways in plant cells. In this sophisticated ...regulatory network, Ca2+ transients in the cytosol (Ca2+cyt) act as major physiological signals to initiate appropriate responses. The CALCINEURIN B‐LIKE PROTEIN (CBL)‐CBL‐INTERACTING PROTEIN KINASE (CIPK) network relays physiological signals characterised by Ca2+cyt transients during plant development and in response to environmental changes. Many studies are aimed at elucidating the role of the CBL‐CIPK network in plant growth and stress responses. This review discusses the involvement of the CBL‐CIPK pathways in two levels of crosstalk between plant development and stress adaptation: direct crosstalk through interaction with regulatory proteins, and indirect crosstalk through adaptation of correlated physiological processes that affect both plant development and stress responses. This review thus provides novel insights into the physiological roles of the CBL‐CIPK network in plant growth and stress adaptation.
Summary
Crop plants are subjected to a variety of stresses during their lifecycle, including abiotic stress factors such as salinity and biotic stress factors such as pathogens. Plants have developed ...a multitude of defense and adaptation responses to these stress factors. In the field, different stress factors mostly occur concurrently resulting in a new state of stress, the combined stress. There is evidence that plant resistance to pathogens can be attenuated or enhanced by abiotic stress factors. With stress tolerance research being mostly focused on plant responses to individual stresses, the understanding of a plant's ability to adapt to combined stresses is limited. In the last few years, we studied powdery mildew resistance under salt stress conditions in the model crop plant tomato with the aim to understand the requirements to achieve plant resilience to a wider array of combined abiotic and biotic stress combinations. We uncovered specific responses of tomato plants to combined salinity‐pathogen stress, which varied with salinity intensity and plant resistance genes. Moreover, hormones, with their complex regulation and cross‐talk, were shown to play a key role in the adaptation of tomato plants to the combined stress. In this review, we attempt to understand the complexity of plant responses to abiotic and biotic stress combinations, with a focus on tomato responses (genetic control and cross‐talk of signaling pathways) to combined salinity and pathogen stresses. Further, we provide recommendations on how to design novel strategies for breeding crops with a sustained performance under diverse environmental conditions.
Significance Statement
This manuscript addresses the particularly interesting and important topic of plant responses to combined stresses, an area of research that is still poorly understood. Combined stresses occur in field conditions and have been described to affect crop development and ultimately yield. After reviewing the complexity of plant responses to combined abiotic and biotic stresses, we propose requirements and strategies for consideration in plant breeding programs in order to maintain high crop performances.
This paper describes the complete findings of the EU-funded research project OPTIMISC, which investigated methods to optimize the production and use of miscanthus biomass. Miscanthus bioenergy and ...bioproduct chains were investigated by trialing 15 diverse germplasm types in a range of climatic and soil environments across central Europe, Ukraine, Russia, and China. The abiotic stress tolerances of a wider panel of 100 germplasm types to drought, salinity, and low temperatures were measured in the laboratory and a field trial in Belgium. A small selection of germplasm types was evaluated for performance in grasslands on marginal sites in Germany and the UK. The growth traits underlying biomass yield and quality were measured to improve regional estimates of feedstock availability. Several potential high-value bioproducts were identified. The combined results provide recommendations to policymakers, growers and industry. The major technical advances in miscanthus production achieved by OPTIMISC include: (1) demonstration that novel hybrids can out-yield the standard commercially grown genotype
(2) characterization of the interactions of physiological growth responses with environmental variation within and between sites; (3) quantification of biomass-quality-relevant traits; (4) abiotic stress tolerances of miscanthus genotypes; (5) selections suitable for production on marginal land; (6) field establishment methods for seeds using plugs; (7) evaluation of harvesting methods; and (8) quantification of energy used in densification (pellet) technologies with a range of hybrids with differences in stem wall properties. End-user needs were addressed by demonstrating the potential of optimizing miscanthus biomass composition for the production of ethanol and biogas as well as for combustion. The costs and life-cycle assessment of seven miscanthus-based value chains, including small- and large-scale heat and power, ethanol, biogas, and insulation material production, revealed GHG-emission- and fossil-energy-saving potentials of up to 30.6 t CO
C ha
y
and 429 GJ ha
y
, respectively. Transport distance was identified as an important cost factor. Negative carbon mitigation costs of -78€ t
CO
C were recorded for local biomass use. The OPTIMISC results demonstrate the potential of miscanthus as a crop for marginal sites and provide information and technologies for the commercial implementation of miscanthus-based value chains.
Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, ...and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops.
•Novel stress conditions such as high CO2 and stress combinations.•Manipulation of stress tolerance traits with significant yield scalability.•Introducing de novo variation for photosynthesis, ...abiotic/biotic stress tolerance.•Adoption/improvement of extremophiles as crops.•Integration of genomics with precise phenotyping and environmental monitoring.
Breeding for stress-resilient crops strongly depends on technological and biological advancements that have provided a wealth of information on genetic variants and their contribution to stress tolerance. In the context of the upcoming challenges for agriculture due to climate change, such as prolonged and/or increased stress intensities, CO2 increase and stress combinations, hierarchizing this information is key to accelerating crop improvement towards sustained or even increased productivity. We propose traits with high scalability to yield and crop performance that can be targeted for improvement and provide examples of recent discoveries with potential applicability in breeding. Critical to success is the integrated analysis of the phenotypes of genetic variants across different environmental variables using modelling approaches and high-throughput phenotyping.
•Delayed exponential and maximum canopy growths enhance drought tolerance.•Late foliage maturity is advantageous for drought tolerance.•Drought stress impacts tuber bulking of potatoes more severely ...than tuber formation.•Canopy growth parameters affect tuber weight more than their effect on tuber number.
Potato is an important food crop with high yields. However when exposed to drought it suffers major yield losses. Considering its global importance and the increasing incidence of drought due to climate change, research toward drought tolerance in potato remains imperative. We have studied a set of 103 commercial cultivars representing the genetic diversity in the European potato market. The cultivars were grown in different field locations in three subsequent years (2013–2015). Our aim was to understand how different field drought regimes affect canopy growth in potato, and how these effects translate to tuber yield. The field environmental conditions were monitored, and pictures of canopy ground cover during the growing season were taken. Canopy growth parameters were extracted by an iterative method using the beta sigmoid growth function to model canopy growth. At harvest, tuber yield was scored and tuber size was graded. The GGE (Genotype and Genotype-by-Environment) bi-plot and Finlay Wilkinson’s Regression were used to investigate Genotype x Environment interactions. We observed that the timing of the drought occurrence differentially affected canopy growth and tuber yield. Under drought stress, fast attainment of exponential growth and maximum canopy cover had negative effects on tuber formation and tuber bulking. Growth rate, maximum canopy cover, and area under the canopy curve (photosynthetic capacity over the growth season) were more important for tuber bulking than they were for tuber formation under drought stress. Cultivars with high yield were identified as potential material for improvement to drought tolerance. These findings will contribute to the breeding for drought-tolerant potato amidst the threats of climate change.
In plants, tolerance to drought stress is a result of numerous minor effect loci in which transcriptional regulation contributes significantly to the observed phenotypes. Under severe drought ...conditions, a major expression quantitative trait loci hotspot was identified on chromosome five in potato. A putative Nuclear factor y subunit C4 was identified as key candidate in the regulatory cascade in response to drought. Further investigation of the eQTL hotspots suggests a role for a putative Homeobox leucine zipper protein 12 in relation to drought in potato. Genes strongly co‐expressed with Homeobox leucine zipper protein 12 were plant growth regulators responsive to water deficit stress in Arabidopsis thaliana, implying a possible conserved mechanism. Integrative analysis of genetic, genomic, phenotypic and transcriptomic data provided insights in the downstream functional components of the drought response. The abscisic acid‐ and environmental stress‐inducible protein TAS14 was highly induced by severe drought in potato and acts as a reliable biomarker for the level of stress perceived by the plant. The systems genetics approach supported a role for multiple genes responsive to severe drought stress of Solanum tuberosum. The combination of gene regulatory networks, expression quantitative trait loci mapping and phenotypic analysis proved useful for candidate gene selection.
Solanum tuberosum is a water efficient staple crop yet highly sensitive to drought. A systems genetics approach was used to identify genes and loci involved in drought response. Systems genetics analysis pinpoints to a putative Nuclear factor y subunit C4 gene as key candidate underlying a major trans eQTL hotspot specific to an early response to drought. Further investigation of other eQTL hotspots suggests a role for a putative Homeobox leucine zipper protein 12 in relation to drought in potato.
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