Molecular identification and characterization of two rubber dandelion amalgaviruses

The Amalgaviridae family is composed of persistent viruses that share the genome architecture of Totiviridae and gene evolutionary resemblance to Partitiviridae. A single Amalgavirus genus has been assigned to this family, presenting only four recognized species, corresponding to plant infecting viruses with dsRNA monopartite genomes of ca. 3.4 kb. Here, we present the genomic identification and characterization of two novel viruses detected in rubber dandelion (Taraxacum kok-saghyz). The sequenced isolates presented genomes of 3,409 and 3,413 nt long, including two partially overlapping ORFs encoding a putative coat protein and an RNA-dependent RNA polymerase (RdRP). Phylogenetic insights based on the detected virus sequences suggest them to be members of two new species within the Amalgavirus genus. Multiple independent RNAseq data suggest that the identified viruses have a dynamic distribution and low relative RNA levels in infected plants. Virus presence was not associated with any apparent symptoms on the plant hosts. We propose the names rubber dandelion latent virus 1 & 2 to the detected amalgaviruses; the first viruses to be associated to this emergent and sustainable natural rubber crop.Fil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Zinan Luo. Ohio State University. Department of Horticulture and Crop Science; Estados UnidosFil: Iaffaldano, Brian J. Ohio State University. Department of Horticulture and Crop Science; Estados UnidosFil: Xiaofeng Zhuang. Ohio State University. Department of Horticulture and Crop Science; Estados UnidosFil: Cornish, Katrina. Ohio State University. Department of Horticulture and Crop Science; Estados Unido

The physio-biochemical characterization reflected different calcium utilization efficiency between the sensitive and tolerant peanut accessions under calcium deficiency

Peanut yield in southern China is usually limited by calcium deficiency in soil. Most previous studies have found that small-seed varieties showed higher tolerance than large-seed varieties (e.g. Virginia type) under calcium deficiency, however, our preliminary research found that sensitive varieties also existed in small-seed counterparts. Few studies have been conducted to characterize low-calcium tolerance among small-seed germplasms with genetic diversity, and the differences in physiological characteristics between sensitive and tolerant varieties has not been reported yet. Thus, in order to better understand such differences, the current study firstly collected and characterized a diversity germplasm panel consisting of 50 small-seed peanut genotypes via a 2-year field trial, followed by the physiological characterization in sensitive (HN032) and tolerant (HN035) peanut genotypes under calcium deficiency. As a result, the adverse effects brought by calcium deficiency on calcium uptake and distribution in HN032 was much larger than HN035. In details, calcium uptake in the aboveground part (leaves and stems) was reduced by 16.17% and 33.66%, while in the underground part (roots and pods), it was reduced by 13.69% and 68.09% under calcium deficiency for HN035 and HN032, respectively; The calcium distribution rate in the pods of HN035 was 2.74 times higher than HN032. The utilization efficiency of calcium in the pods of HN035 was 1.68 and 1.37 times than that of HN032 under calcium deficiency and sufficiency, respectively. In addition, under calcium deficiency conditions, the activities of antioxidant enzymes SOD, POD, and CAT, as well as the MDA content, were significantly increased in the leaves of HN032, peanut yield was significantly reduced by 22.75%. However, there were no significant changes in the activities of antioxidant enzymes, MDA content, and peanut yield in HN035. Therefore, higher calcium absorption and utilization efficiency may be the key factors maintaining peanut yield in calcium-deficient conditions for tolerant genotypes. This study lays a solid foundation for selecting low-calcium tolerant varieties in future peanut breeding

Dynamic polarization attractors of dissipative solitons from carbon nanotube mode-locked Er-doped laser

We report experimental observation of polarization attractors in the form of vector dissipative solitons from a carbon nanotube mode locked fiber laser. At a time scale of 14-14,000 roundtrips, the typical polarization locked vector solitons, and other appealing attractors are shown. In addition, we observe the vector dissipative solitons operated in dual-wavelength regime with central wavelength of 1533 and 1557 nm which can be related to a fixed point polarization attractor. The results unveiled complex oscillatory behavior of dissipative solitons in the polarization domain which may help understand laser physics, nonlinear optics. The demonstrated work may underpin a new type of high energy laser source leading to possible applications in nanoparticle manipulation, micromachining, spectroscopy etc

Genetic Diversity and Population Structure of a Camelina sativa Spring Panel

There is a need to explore renewable alternatives (e.g., biofuels) that can produce energy sources to help reduce the reliance on fossil oils. In addition, the consumption of fossil oils adversely affects the environment and human health via the generation of waste water, greenhouse gases, and waste solids. Camelina sativa, originated from southeastern Europe and southwestern Asia, is being re-embraced as an industrial oilseed crop due to its high seed oil content (36–47%) and high unsaturated fatty acid composition (\u3e90%), which are suitable for jet fuel, biodiesel, high-value lubricants and animal feed. C. sativa’s agronomic advantages include short time to maturation, low water and nutrient requirements, adaptability to adverse environmental conditions and resistance to common pests and pathogens. These characteristics make it an ideal crop for sustainable agricultural systems and regions of marginal land. However, the lack of genetic and genomic resources has slowed the enhancement of this emerging oilseed crop and exploration of its full agronomic and breeding potential. Here, a core of 213 spring C. sativa accessions was collected and genotyped. The genotypic data was used to characterize genetic diversity and population structure to infer how natural selection and plant breeding may have affected the formation and differentiation within the C. sativa natural populations, and how the genetic diversity of this species can be used in future breeding efforts. A total of 6,192 high-quality single nucleotide polymorphisms (SNPs) were identified using genotypingby- sequencing (GBS) technology. The average polymorphism information content (PIC) value of 0.29 indicate moderate genetic diversity for the C. sativa spring panel evaluated in this report. Population structure and principal coordinates analyses (PCoA) based on SNPs revealed two distinct subpopulations. Sub-population 1 (POP1) contains accessions that mainly originated from Germany while the majority of POP2 accessions (\u3e75%) were collected from Eastern Europe. Analysis of molecular variance (AMOVA) identified 4% variance among and 96% variance within subpopulations, indicating a hig

Genetic Diversity and Population Structure of a Camelina sativa Spring Panel

There is a need to explore renewable alternatives (e.g., biofuels) that can produce energy sources to help reduce the reliance on fossil oils. In addition, the consumption of fossil oils adversely affects the environment and human health via the generation of waste water, greenhouse gases, and waste solids. Camelina sativa, originated from southeastern Europe and southwestern Asia, is being re-embraced as an industrial oilseed crop due to its high seed oil content (36–47%) and high unsaturated fatty acid composition (>90%), which are suitable for jet fuel, biodiesel, high-value lubricants and animal feed. C. sativa’s agronomic advantages include short time to maturation, low water and nutrient requirements, adaptability to adverse environmental conditions and resistance to common pests and pathogens. These characteristics make it an ideal crop for sustainable agricultural systems and regions of marginal land. However, the lack of genetic and genomic resources has slowed the enhancement of this emerging oilseed crop and exploration of its full agronomic and breeding potential. Here, a core of 213 spring C. sativa accessions was collected and genotyped. The genotypic data was used to characterize genetic diversity and population structure to infer how natural selection and plant breeding may have affected the formation and differentiation within the C. sativa natural populations, and how the genetic diversity of this species can be used in future breeding efforts. A total of 6,192 high-quality single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing (GBS) technology. The average polymorphism information content (PIC) value of 0.29 indicate moderate genetic diversity for the C. sativa spring panel evaluated in this report. Population structure and principal coordinates analyses (PCoA) based on SNPs revealed two distinct subpopulations. Sub-population 1 (POP1) contains accessions that mainly originated from Germany while the majority of POP2 accessions (>75%) were collected from Eastern Europe. Analysis of molecular variance (AMOVA) identified 4% variance among and 96% variance within subpopulations, indicating a high gene exchange (or low genetic differentiation) between the two subpopulations. These findings provide important information for future allele/gene identification using genome-wide association studies (GWAS) and marker-assisted selection (MAS) to enhance genetic gain in C. sativa breeding programs

Pump-controlled wavelength switchable dissipative soliton mode-locked Yb-doped fiber laser using a 45° tilted fiber grating

We demonstrate a pump-controlled wavelength switchable Yb-doped fiber laser (YDFL) by nonlinear polarization rotation (NPR) for the first time. The polarizer replaced by a 45° tilted fiber grating (45°-TFG) combines with a section of polarization maintaining fiber (PMF) to form a fiber-based birefringent filter. Stable dissipative soliton (DS) with center wavelength of 1068.39 nm is generated under the mode-locked threshold of 277 mW. The operating wavelength switching between 1046.51 nm and 1067.90 nm can be realized via increasing the pump power simply while keeping the polarization controllers (PCs) in a fixed state. The laser maintains stable mode-locking operation at each wavelength, which can be regarded as a type of multi-wavelength ultrafast light source with precise control and integration potential

Genome-Wide Association Study (GWAS) Analysis of Camelina Seedling Germination under Salt Stress Condition

Camelina sativa is an important renewable oilseed crop for biofuel and feedstock that can relieve the reliance on petroleum-derived oils and reduce greenhouse gases and waste solids resulting from petroleum-derived oils consumption. C. sativa has recently seen revived attention due to its high oil content, high omega-3 unsaturated fatty acids, short life cycle, broader regional adaptation, and low-input agronomic requirements. However, abiotic stress such as salinity stress has imposed threatens on plant photosynthesis and growth by reducing water availability or osmotic stress, ion (Na+ and Cl−) toxicity, nutritional disorders and oxidative stress yield. There still remains much to know for the molecular mechanisms underlying these effects. In this study, a preliminary study applying 10 C. sativa cultivars to be treated under a gradient NaCl concentrations ranging from 0–250 mM and found that 100 mM was the optimal NaCl concentration to effectively differentiate phenotypic performance among different genotypes. Then, a spring panel consisting of 211 C. sativa accessions were germinated under 100 mM NaCl concentration. Six seedling germination traits, including germination rate at two stages (5-day and 9-day seedling stages), germination index, dry and fresh weight, and dry/fresh ratio, were measured. Significant correlations were found between the germination rate at two stages as well as plant biomass traits. Combining the phenotypic data and previously obtained genotypic data, a total of 17 significant trait-associated single nucleotide polymorphisms (SNPs) for the germination rate at the two stages and dry weight were identified from genome-wide association analysis (GWAS). These SNPs are located on putative candidate genes controlling plant root development by synergistically mediating phosphate metabolism, signal transduction and cell membrane activities. These identified SNPs could provide a foundation for future molecular breeding efforts aimed at improved salt tolerance in C. sativa

Genome-wide association study (GWAS) of leaf cuticular wax components in Camelina sativa identifies genetic loci related to intracellular wax transport

Abstract Background It is important to explore renewable alternatives (e.g. biofuels) that can produce energy sources to help reduce reliance on fossil oils, and reduce greenhouse gases and waste solids resulted from fossil oils consumption. Camelina sativa is an oilseed crop which has received increasing attention due to its short life cycle, broader adaptation regions, high oil content, high level of omega-3 unsaturated fatty acids, and low-input requirements in agriculture practices. To expand its Camelina production areas into arid regions, there is a need to breed for new drought-tolerant cultivars. Leaf cuticular wax is known to facilitate plant development and growth under water-limited conditions. Dissecting the genetic loci underlying leaf cuticular waxes is important to breed for cultivars with improved drought tolerance. Results Here we combined phenotypic data and single nucleotide polymorphism (SNP) data from a spring C. sativa diversity panel using genotyping-by-sequencing (GBS) technology, to perform a large-scale genome-wide association study (GWAS) on leaf wax compositions. A total of 42 SNP markers were significantly associated with 15 leaf wax traits including major wax components such as total primary alcohols, total alkanes, and total wax esters as well as their constituents. The vast majority of significant SNPs were associated with long-chain carbon monomers (carbon chain length longer than C28), indicating the important effects of long-chain carbon monomers on leaf total wax biosynthesis. These SNP markers are located on genes directly or indirectly related to wax biosynthesis such as maintaining endoplasmic reticulum (ER) morphology and enabling normal wax secretion from ER to plasma membrane or Golgi network-mediated transport. Conclusions These loci could potentially serve as candidates for the genetic control involved in intracellular wax transport that might directly or indirectly facilitate leaf wax accumulation in C. sativa and can be used in future marker-assisted selection (MAS) to breed for the cultivars with high wax content to improve drought tolerance

Genetic Diversity and Population Structure of a Camelina sativa Spring Panel

There is a need to explore renewable alternatives (e.g., biofuels) that can produce energy sources to help reduce the reliance on fossil oils. In addition, the consumption of fossil oils adversely affects the environment and human health via the generation of waste water, greenhouse gases, and waste solids. Camelina sativa, originated from southeastern Europe and southwestern Asia, is being re-embraced as an industrial oilseed crop due to its high seed oil content (36–47%) and high unsaturated fatty acid composition (\u3e90%), which are suitable for jet fuel, biodiesel, high-value lubricants and animal feed. C. sativa’s agronomic advantages include short time to maturation, low water and nutrient requirements, adaptability to adverse environmental conditions and resistance to common pests and pathogens. These characteristics make it an ideal crop for sustainable agricultural systems and regions of marginal land. However, the lack of genetic and genomic resources has slowed the enhancement of this emerging oilseed crop and exploration of its full agronomic and breeding potential. Here, a core of 213 spring C. sativa accessions was collected and genotyped. The genotypic data was used to characterize genetic diversity and population structure to infer how natural selection and plant breeding may have affected the formation and differentiation within the C. sativa natural populations, and how the genetic diversity of this species can be used in future breeding efforts. A total of 6,192 high-quality single nucleotide polymorphisms (SNPs) were identified using genotypingby- sequencing (GBS) technology. The average polymorphism information content (PIC) value of 0.29 indicate moderate genetic diversity for the C. sativa spring panel evaluated in this report. Population structure and principal coordinates analyses (PCoA) based on SNPs revealed two distinct subpopulations. Sub-population 1 (POP1) contains accessions that mainly originated from Germany while the majority of POP2 accessions (\u3e75%) were collected from Eastern Europe. Analysis of molecular variance (AMOVA) identified 4% variance among and 96% variance within subpopulations, indicating a hig