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Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security. Deep characterization of quinoa diversity is needed to support the agronomic improvement and adaptation of quinoa as its worldwide cultivation expands. In this study, we report the construction of chromosome-scale genome assemblies of eight quinoa accessions covering the range of phenotypic and genetic diversity of both lowland and highland quinoas. The assemblies were produced from a combination of PacBio HiFi reads and Bionano Saphyr optical maps, with total assembly sizes averaging 1.28 Gb with a mean N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for the eight new quinoa genomes, and on average, 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies allowed the identification of structural rearrangements including inversions, translocations, and duplications. These eight novel quinoa genome assemblies provide a resource for association genetics, comparative genomics, and pan-genome analyses for the discovery of genetic components and variations underlying agriculturally important traits.
- MeSH
- Chenopodium quinoa * genetika MeSH
- genetická variace MeSH
- genom rostlinný * MeSH
- Publikační typ
- časopisecké články MeSH
- dataset MeSH
Quinoa (Chenopodium quinoa), an Andean pseudocereal, attained global popularity beginning in the early 2000s due to its protein quality, glycemic index, and high fiber, vitamin, and mineral contents. Pitseed goosefoot (Chenopodium berlandieri), quinoa's North American free-living sister species, grows on disturbed and sandy substrates across the North America, including saline coastal sands, southwestern deserts, subtropical highlands, the Great Plains, and boreal forests. Together with South American avian goosefoot (Chenopodium hircinum) they comprise the American tetraploid goosefoot complex (ATGC). Superimposed on pitseed goosefoot's North American range are approximately 35 AA diploids, most of which are adapted to a diversity of niche environments. We chose to assemble a reference genome for Sonoran A-genome Chenopodium watsonii due to fruit morphological and high (>99.3%) preliminary sequence-match similarities with quinoa, along with its well-established taxonomic status. The genome was assembled into 1377 scaffolds spanning 547.76 Mb (N50 = 55.14 Mb, L50 = 5), with 94% comprised in nine chromosome-scale scaffolds and 93.9% Benchmarking Universal Single-Copy Orthologs genes identified as single copy and 3.4% as duplicated. A high degree of synteny, with minor and mostly telomeric rearrangements, was found when comparing this taxon with the previously reported genome of South American C. pallidicaule and the A-subgenome chromosomes of C. quinoa. Phylogenetic analysis was performed using 10,588 single-nucleotide polymorphisms generated by resequencing a panel of 41 New World AA diploid accessions and the Eurasian H-genome diploid Chenopodium vulvaria, along with three AABB tetraploids previously sequenced. Phylogenetic analysis of these 32 taxa positioned the psammophyte Chenopodium subglabrum on the branch containing A-genome sequences from the ATGC. We also present evidence for long-range dispersal of Chenopodium diploids between North and South America.
UNLABELLED: The diversity in human diets that can be reached by proper use of different crops and varieties, including some underutilized ones, is a potentially powerful strategy to ensure food security and prevent serious health problems caused by current diets that are often not fulfilling nutritional requirements. In the framework of this research, the content of tocopherols and tocotrienols, thiamine, riboflavin, pyridoxine, and superoxide dismutase in nine varieties of quinoa, both colored and nonpigmented, obtained from 4 different countries, was investigated and compared to the content of the same vitamins and antioxidants in barley and wheat, both colored and nonpigmented, cultivated in the same experimental field. The aim of this work was to create a crop diversity strategy and encourage the consumption of underutilized crops to ensure that the human diet fulfills nutritional requirements. The contents of vitamin B1, B2, B6, tocopherol, and tocotrienol isomers and superoxide dismutase were determined via HPLC; imaging techniques were used to evaluate the seed color. Quinoa grains had the greatest concentration of tocopherol isomers and activity, represented mainly by α-tocopherol and γ-tocopherol. Wheat and barley seeds had substantial concentrations of tocopherols and tocotrienols. The concentration of riboflavin was greater in barley and wheat than in quinoa, the concentrations of pyridoxine and thiamine were variety-dependent in all grains. Quinoa grains had greater concentration of superoxide dismutase compared to wheat and barley. The richness of each variety and crop should be recognized and used integrally to improve the diet quality. PRACTICAL APPLICATION: Nutritional potential of crops was evaluated from the viewpoint of selected vitamins and antioxidants to create a well-balanced diet. Combined use of both traditional (wheat, barley) and underutilized crops (quinoa) is recommended. HPLC methods and image analysis were successfully used as viable tools for food quality determination.
- Klíčová slova
- antioxidant compounds, barley, quinoa, vitamins, wheat,
- MeSH
- alfa-tokoferol analýza MeSH
- antioxidancia analýza MeSH
- Chenopodium quinoa chemie MeSH
- ječmen (rod) chemie MeSH
- lidé MeSH
- nutriční hodnota MeSH
- pšenice chemie MeSH
- semena rostlinná chemie MeSH
- thiamin analýza MeSH
- tokoferoly analýza MeSH
- tokotrienoly analýza MeSH
- vitamin A analýza MeSH
- vitamin E analýza MeSH
- vitaminy analýza MeSH
- zemědělské plodiny MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- alfa-tokoferol MeSH
- antioxidancia MeSH
- thiamin MeSH
- tokoferoly MeSH
- tokotrienoly MeSH
- vitamin A MeSH
- vitamin E MeSH
- vitaminy MeSH
Seed germination is critical for successful crop production and this growth stage can be very sensitive to salt stress depending on the plant's tolerance mechanisms. The pretreatment of Chenopodium quinoa (quinoa) seeds with CaCl2, H2O2 and sodium nitroprusside (SNP) limited the adverse effect of salt stress on seed germination. The pre-treated seeds showed a significant increase in germination rate, relative germination rate and germination index while the mean germination time was significantly reduced under both optimal and stress conditions. In parallel with seed germination, the negative effect of salt stress on the activity of α-amylase and β-amylase was reduced in pre-treated seeds. The amylase enzymes are responsible for starch hydrolysis, so the reduction of amylase activity by salt stress resulted in higher starch content in the seeds and lower concentrations of water-soluble sugars such as glucose. Pretreatment stimulated amylase activity resulting in starch breakdown and increased content of water-soluble sugars in the salt-stressed seeds. Protein and amino acid contents were significantly enhanced in salt-stressed seeds, which were highlighted in pre-treated seeds. The findings of this study demonstrate that pretreatment of quinoa seeds with CaCl2, H2O2 and SNP at 5, 5 and 0.2 mM, respectively, concentration to achieve rapid germination at high levels under optimal and salt-stress conditions.
- Klíčová slova
- Amino acids, Amylase, Carbohydrates, Proteins, Salt tolerance, Seed germination,
- MeSH
- Chenopodium quinoa účinky léků fyziologie MeSH
- chlorid vápenatý farmakologie MeSH
- klíčení * MeSH
- nitroprusid farmakologie MeSH
- oxid dusnatý metabolismus MeSH
- peroxid vodíku metabolismus farmakologie MeSH
- semena rostlinná účinky léků fyziologie MeSH
- soli MeSH
- solný stres * MeSH
- vápník metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- chlorid vápenatý MeSH
- nitroprusid MeSH
- oxid dusnatý MeSH
- peroxid vodíku MeSH
- soli MeSH
- vápník MeSH
Quinoa displays huge genetic variability and adaptability to distinct climatic conditions. Quinoa seeds are a good source of nutrients; however, the overall nutritional composition and nutrient content is influenced by numerous factors. This study focused on the nutritional and morphologic evaluation of various quinoa genotypes grown in the Czech Republic. Significant differences between years were observed for morphological traits (plant height, inflorescence length, weight of thousand seeds). The weather conditions in the year 2018 were favorable for all the morphological traits. The protein content of quinoa accessions ranged between 13.44 and 20.01% and it was positively correlated to mauritianin. Total phenolic content varied greatly from year to year, while the antioxidant activity remained relatively stable. The most abundant phenolic compounds were the flavonoids miquelianin, rutin, and isoquercetin. Isoquercetin, quercetin, and N-feruoloyl octopamine showed the highest stability under variable weather conditions in the analyzed years. A total of six compounds were detected and quantified in quinoa for the first time. Most varieties performed well under Central European conditions and can be considered a good source of nutrients and bioactive compounds. These data can be used as a source of information for plant breeders aiming to improve the quality traits of quinoa.
- Klíčová slova
- Chenopodium, breeding, mass spectrometry, phenolic compounds, protein, quinoa,
- Publikační typ
- časopisecké články MeSH
Quinoa has been identified as a climate-resilient crop that can overcome unfavorable conditions. This study explores the photochemical efficiency of quinoa compared to maize subjected to drought stress. The JIP-test was used to assess the photochemical efficiency of both crops. Proline content, leaf water potential, and membrane leakage were also determined. The maximum photochemical efficiency (Fv/Fm) did not change for quinoa and maize under moderate stress. However, severe drought conditions resulted in a decline in Fv/Fm in maize but not quinoa. Furthermore, the PSII performance index (PIABS,total) declined steadily in maize soon after the onset of drought stress. The decline in the PIABS,total values for quinoa was only observed after a period of severe drought stress. Membrane leakage was also more prevalent in the maize plants, while quinoa had higher proline contents. This study concluded that both quinoa and maize maintained PSII structure and function under moderate drought conditions. However, only quinoa maintained PSII structure and function under severe drought conditions.
- Klíčová slova
- drought, leaf water potential, membrane leakage, performance index, photosynthesis, quantum yield,
- Publikační typ
- časopisecké články MeSH
One of the major challenges in agriculture is to ensure sufficient and healthy food availability for the increasing world population in near future. This requires maintaining sustainable cultivation of crop plants under varying environmental stresses. Among these stresses, salinity is the second most abundant threat worldwide after drought. One of the promising strategies to mitigate salinity stress is to cultivate halotolerant crops such as quinoa. Under high salinity, performance can be improved by plant growth promoting bacteria (PGPB). Among PGPB, endophytic bacteria are considered better in stimulating plant growth compared to rhizosphere bacteria because of their ability to colonize both in plant rhizosphere and plant interior. Therefore, in the current study, a pot experiment was conducted in a controlled greenhouse to investigate the effects of endophytic bacteria i.e., Burkholderia phytofirmans PsJN on improving growth, physiology and yield of quinoa under salinity stress. At six leaves stage, plants were irrigated with saline water having either 0 (control) or 400 mM NaCl. The results indicated that plants inoculated with PsJN mitigated the negative effects of salinity on quinoa resulting in increased shoot biomass, grain weight and grain yield by 12%, 18% and 41% respectively, over un-inoculated control. Moreover, inoculation with PsJN improved osmotic adjustment and ion homeostasis ability. In addition, leaves were also characterized for five key reactive oxygen species (ROS) scavenging enzyme in response to PsJN treatment. This showed higher activity of catalase (CAT) and dehydroascobate reductase (DHAR) in PsJN-treated plants. These findings suggest that inoculation of quinoa seeds with Burkholderia phytofirmans PsJN could be used for stimulating growth and yield of quinoa in highly salt-affected soils.
- Klíčová slova
- Endophytic bacteria, Plant growth promoting bacteria (PGPB),
- Publikační typ
- časopisecké články MeSH
Triple gene block (TGB) sequences derived from isolates of ordinary Potato virus S (PVS-O) and Chenopodium-systemic (PVS-CS) were analyzed. Although the TGB sequences did not reveal any specific difference within the 7K protein, some specific differences within the 25K and 12K ORFs were found. In order to investigate a possible functional divergence of PVS-O and PVS-CS TGB variants, these genes were propagated in chimeric Potato virus X (PVX). Both PVS TGB variants partly complemented PVX TGB in Nicotiana benthamiana. The recombinant viruses multiplied to lower titer than the wild-type PVX in N. benthamiana showed attenuated symptoms. Whereas the recombinant PVX variants were also propagated systemically in Nicotiana glutinosa, Celosia argentea, Nicotiana occidentalis and chimeric PVX bearing TGB from PVS-O in Solanum lycopersicum, neither were propagated systemically in Chenopodium quinoa nor in Nicotiana tabacum cv. Samsun nn and the PVX-resistant Solanum tuberosum cv. Szignal. The potential for recombinant viruses to be transmitted by the aphid Myzus persicae was investigated. Aphid transmission in the recombinant virus was obtained by replacing PVX TGB by TGB from the PVS-CS isolate. These results show the potential function of Carlavirus TGB in aphid transmissibility and underlines the possible biological risks from certain recombinant virus variants.
- MeSH
- Carlavirus genetika patogenita MeSH
- Celosia virologie MeSH
- Chenopodium quinoa virologie MeSH
- faktory virulence genetika fyziologie MeSH
- molekulární sekvence - údaje MeSH
- mšice virologie MeSH
- nemoci rostlin virologie MeSH
- sekvence aminokyselin MeSH
- sekvenční homologie aminokyselin MeSH
- shluková analýza MeSH
- Solanum lycopersicum virologie MeSH
- tabák virologie MeSH
- testy genetické komplementace MeSH
- virové proteiny genetika fyziologie MeSH
- virulence MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- faktory virulence MeSH
- virové proteiny MeSH
Plants of the genus Pleione, originating from hobby growers in the Netherlands and in the Czech Republic, were conspicuous for viral infection, showing symptoms of leaf mosaic or flower breaking. Using Sanger and high throughput sequencing, the full genome sequence of a novel potyvirus was obtained from sequencing data. The genome sequence was annotated and compared to the genome of other potyviruses. The virus was experimentally transmitted by aphids into Pleione and Chenopodium quinoa plants. The name Pleione flower breaking virus (PlFBV) was suggested for the new virus. The presence of the virus was confirmed using RT-PCR, with newly designed primers targeting this new species. The incidence of the virus was contrasted between both countries and might have been influenced by the growth conditions and the exposure of the plants to aphids.
- Klíčová slova
- Aphid transmission, Electron microscopy, High-throughput sequencing, Next generation sequencing, Pleione flower breaking virus, Potyvirus,
- MeSH
- anotace sekvence MeSH
- Chenopodium quinoa virologie MeSH
- hmyz - vektory MeSH
- incidence MeSH
- mšice MeSH
- nemoci rostlin virologie MeSH
- Orchidaceae virologie MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- Potyvirus klasifikace genetika izolace a purifikace MeSH
- přenos infekční nemoci MeSH
- sekvenční analýza DNA MeSH
- sekvenování celého genomu MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
- Nizozemsko MeSH
The bacterial strain SECRCQ15T was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15T, we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15T genome. We also found that singletons of F. quinoae SECRCQ15T are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.
- Klíčová slova
- Ferdinandcohnia quinoae, Adaptation, Comparative genomics, Microbial ecology, Quinoa, Speciation,
- MeSH
- DNA bakterií genetika MeSH
- fylogeneze MeSH
- mastné kyseliny * MeSH
- RNA ribozomální 16S genetika MeSH
- rostliny * genetika MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA bakterií MeSH
- mastné kyseliny * MeSH
- RNA ribozomální 16S MeSH
