Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus)

BACKGROUND

Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species.

RESULTS

Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process.

CONCLUSIONS

We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.

Morphological and Molecular Characterization of Bacterial Pathogens Associated with Leaf Mottle of Sunflower in Northern Kazakhstan

Leaf mottle is a serious disease in the common sunflower (Helianthus annuus L.), which affects plant growth and development and seed quality and yield. Over the past few years, the North Kazakhstan region, a sunflower-producing area in Kazakhstan, has been seriously affected by leaf mottle. Since 2021, symptomatic leaves have been collected from production areas of this base to determine the pathogens causing sunflower foliar diseases. One hundred bacterial strains were isolated, and two genera and five species were identified based on morphological characteristics, molecular genetics, and phylogenetic analysis (16S gene region). The genus Bacillus was represented by four species: Bacillus subtilis, B. megaterium, B. amyloliquefaciens, and B. flexus. The genus Paenibacillus was represented by one species, P. peoriae. Pathogenicity experiments showed that B. subtilis, B. megaterium, B. flexus, and P. peoriae could cause leaf mottle disease symptoms. However, disease symptoms caused by B. flexus were highly similar to those observed on infected leaves under natural conditions in the field. Therefore, these bacterial isolates were found to be the primary pathogens causing sunflower leaf mottle, and B. flexus was the most common and virulent pathogen in this study. In addition, this is the first report of B. megaterium, B. flexus, and P. peoriae as pathogens associated with sunflower leaf mottle in Kazakhstan.

Genome-Wide Association Mapping in Sunflower (Helianthus annuus) Reveals Common Loci and Putative Candidate Genes for Resistance to Diaporthe gulyae and D. helianthi Causing Phomopsis Stem Canker

Diaporthe gulyae and D. helianthi cause Phomopsis stem canker of sunflower (Helianthus annuus L.) in the United States. Because Phomopsis stem canker did not gain importance until the disease epidemic in 2010, limited studies were conducted to understand the genetic basis of sunflower resistance to D. gulyae and D. helianthi. The objectives of this study were to evaluate the United States Department of Agriculture cultivated accessions for resistance to D. gulyae and D. helianthi as well as to utilize genome-wide association studies (GWAS) to identify quantitative trait loci (QTLs) and putative candidate genes underlying those loci common to both organisms. For each fungus, 213 accessions were screened in a complete randomized design in the greenhouse and the experiment was repeated once. Six plants per accession were inoculated with a single isolate of D. gulyae or D. helianthi at four to six true leaves using the mycelium-contact inoculation method. At 15 days (D. gulyae) and 30 days (D. helianthi) postinoculation, accessions were evaluated for disease severity and compared with the susceptible confection inbred PI 552934. GWAS identified 28 QTLs common to the two fungi, and 24 genes overlapped close to these QTLs. Additionally, it was observed that the resistance QTLs derived mainly from landraces rather than from wild species. Seventeen putative candidate genes associated with resistance to D. gulyae or D. helianthi were identified that may be related to plant-pathogen interactions. These findings advanced our understanding of the genetic basis of resistance to D. gulyae and D. helianthi and will help develop resources for genomics-assisted breeding.

Application of malrstone-based conditioner and plantation of Jerusalem artichoke improved properties of saline-alkaline soil in Inner Mongolia

Soil salinization is a critical environmental issue restricting agricultural production. Inner Mongolia is one of the areas with severe land salinization in China. This study aimed to investigate the effects of conditioning agent (containing marlstone and a range of enzymes) and cultivating Jerusalem artichoke on saline soils in Inner Mongolia. The effects of conditioner (0, 0.06 and 0.18 kg/m²) on soil physical, chemical and biological properties, including soil carbon fractions and microbiota in saline soils planted with Jerusalem artichoke, were characterized. The results showed that soil salinity was reduced significantly after cultivating Jerusalem artichoke and declined also after the conditioner addition. The application of conditioner increased the content of DOC (dissolved organic carbon), HFOC (heavy fraction organic carbon) and the content of aggregates >0.25 mm compared to the soil planted with Jerusalem artichoke alone. The relative abundance of halophilic bacteria such as Thioalkalivibrio and Thiohalobacter was greater in the CK (non-treated control). By contrast, the relative abundance of microorganisms with the carbon assimilation and nitrogen fixation capacities, such as Cyanobacteria and Rhodovulum, was greater in the conditioner-treated and Jerusalem artichoke-planted treatments. The planting of Jerusalem artichoke reduced soil salinity, increased soil organic carbon fractions, improved soil structure, and altered the soil microbial community, with the application of the conditioning agent enhancing these positive changes. The co-occurrence network structure of "Jerusalem artichoke-conditioner-saline soil-soil microorganism" was established, which provided scientific basis for Jerusalem artichoke-conditioner to improve saline soil.

Multiple Species of Asteraceae Plants Are Susceptible to Root Infection by the Necrotrophic Fungal Pathogen Sclerotinia sclerotiorum

The necrotrophic fungal pathogen Sclerotinia sclerotiorum can cause disease on numerous plant species, including many important crops. Most S. sclerotiorum-incited diseases of crop plants are initiated by airborne ascospores produced when fungal sclerotia germinate to form spore-bearing apothecia. However, basal stalk rot of sunflower occurs when S. sclerotiorum sclerotia germinate to form mycelia within the soil, which subsequently invade sunflower roots. To determine whether other plant species in the Asteraceae family are susceptible to root infection by S. sclerotiorum, cultivated sunflower (Helianthus annuus L.) and seven other Asteraceae species were evaluated for S. sclerotiorum root infection by inoculation with either sclerotia or mycelial inoculum. Additionally, root susceptibility of sunflower was compared with that of dry edible bean and canola, two plant species susceptible to S. sclerotiorum but not known to display root-initiated infections. Results indicated that multiple Asteraceae family plants are susceptible to S. sclerotiorum root infection after inoculation with either sclerotia or mycelium. These observations expand the range of plant hosts susceptible to S. sclerotiorum root infection, elucidate differences in root inoculation methodology, and emphasize the importance of soilborne infection to Asteraceae crop and weed species.

Antimicrobial Activity of Sunflower (Helianthus annuus) Seed for Household Domestic Water Treatment in Buhera District, Zimbabwe

Various plants have been used by humans for a very long time, and the uses vary, including food, medicine, toothpaste, dyes, food preservatives, water treatment, and beer brewing, among others. For food preservation and water treatment, the plant must have antimicrobial properties which are biocidal. For this research, extracts were obtained from sunflower (Helianthus annuus) seeds. The extracts were assessed for the presence of antimicrobial properties against three groups of bacteria, including faecal coliforms, total coliforms, and Escherichia coli (E. coli). Dosages of ground sunflower seeds ranging from 0.5 g to 4 g were administered to the three bacterial species and their susceptibilities to the antimicrobial agents were measured and recorded. The results indicate the presence of antimicrobial properties in sunflower. The antimicrobial activities were more effective on E. coli, with an average zone of inhibition of 12 mm with a 3 g dosage of sunflower seed extract. This was followed by total coliforms (11 mm) and lastly faecal coliforms (11 mm). These findings suggested that sunflower seeds proved to be potentially effective in treating water against microbial contaminants.

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

Agrochemical applications on farmland aim to enhance crop yield; however, the consequence of biodiversity loss has caused a reduction in ecological functions. The positive endosphere interactions and crop rotation systems may function in restoring a stable ecosystem. Employing culture-independent techniques will help access the total bacteria community in the sunflower endosphere. Limited information is available on the bacteria diversity in sunflower plants cultivated under different agricultural practices. Hence, this study was designed to investigate the endophytic bacterial community structure of sunflower at the growing stage. Plant root and stem samples were sourced from two locations (Itsoseng and Lichtenburg), for DNA extraction and sequenced on the Illumina Miseq platform. The sequence dataset was analyzed using online bioinformatics tools. Saccharibacteria and Acidobacteria were dominant in plant roots, while the stem is dominated by Proteobacteria, Bacteriodetes, and Gemmatimonadetes across the sites. Bacterial genera, Acidovorax, Flavobacterium, Hydrogenophaga, and Burkholderia-Paraburkhoderia were found dominant in the root, while the stem is dominated by Streptomyces. The diverse bacterial community structure at phyla and class levels were significantly different in plant organs across the sites. The influence of soil physical and chemical parameters analyzed was observed to induce bacterial distribution across the sites. This study provides information on the dominant bacteria community structure in sunflowers at the growing stage and their predictive functions, which suggest their future exploration as bioinoculants for improved agricultural yields.

Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome

Sunflowers (Helianthus annuus L.) are susceptible to multiple diseases in field production. In this study, we collected diseased sunflower leaves in fields located in South Dakota, USA, for virome investigation. The leaves showed visible symptoms on the foliage, indicating phomopsis and rust infections. To identify the viruses potentially associated with the disease diagnosed, symptomatic leaves were obtained from diseased plants. Total RNA was extracted corresponding to each disease diagnosed to generate libraries for paired-end high throughput sequencing. Short sequencing reads were assembled de novo and the contigs with similarities to viruses were identified by aligning against a custom protein database. We report the discovery of two novel mitoviruses, four novel partitiviruses, one novel victorivirus, and nine novel totiviruses based on similarities to RNA-dependent RNA polymerases and capsid proteins. Contigs similar to bean yellow mosaic virus and Sclerotinia sclerotiorum hypovirulence-associated DNA virus were also detected. To the best of our knowledge, this is the first report of direct metatranscriptomics discovery of viruses associated with fungal infections of sunflowers bypassing culturing. These newly discovered viruses represent a natural genetic resource from which we can further develop potential biopesticide to control sunflower diseases.

Role of PGPR on the physiology of sunflower irrigated with produced water containing high total dissolved solids (TDS) and its residual effects on soil fertility

The present study was conducted to evaluate the bioremediation potential of plant growth-promoting rhizobacteria (PGPR) PGPR isolates from high total dissolved solids (TDS) bearing produced water on the water quality, soil physicochemical properties and growth and physiology of sunflower irrigated with high TDS bearing produced water having salinity level 130 times higher above seawater and also containing traces of oil and grease. Seeds of sunflower hybrid Parsun 3 were soaked for 3-4 h prior to sowing in 72 h old culture of PGPR strains W1 and W2 isolated from high TDS bearing polluted water. The control plants were irrigated with 90% diluted TDS water supplemented with 5 ml LB media. Whereas, the inoculated plants were irrigated with 90% diluted TDS water supplemented with 5 ml PGPR inocula.in LB media. The plants were grown under natural conditions. The 16S rRNA sequence analyses identified the isolate W1 bearing 100% similarity with the plant growth-promoting rhizobacteria (PGPR) Ralstonia pickettii and W2 bearing 99.7% similarity with Brevibacillus invocatus. Both the isolate were catalase and oxidase positive. The Ralstonia pickettii and Brevibacillus invocatus treatments decreased the EC and TDS values significantly such that the EC and TDS values of 90% diluted TDS water were 29 times and 19 times higher than tap water. Sodium adsorption ratio (SAR), organic matter, nitrogen, potassium, magnesium and carbon content were 1.96, 1.10, 2.28 1.20, 6.63 and 1.00 times greater than control in the rhizosphere soil of Ralstonia pickettii inoculated plants irrigated with high TDS bearing water There were significant increases in plant growth, sugar, flavonoids and phenolics, chlorophyll b, total chlorophyll, carotenoids content and activities of superoxide dismutase, catalase and peroxidase in plants inoculated with Ralstonia pickettii and Brevibacillus invocatus. The flavonoids, phenolics and proline contents were 0.54, 0.72 and 0.30 times higher in Ralstonia pickettii inoculated plants. Shoot/root dry weight ratio was about (50%) lower than control in Ralstonia pickettii and Brevibacillus invocatus treatments. Ralstonia pickettii was more effective than Brevibacillus invocatus to combat oxidative and osmotic stresses. It is inferred that the high TDS bearing produced water from oil factory harbor Plant growth-promoting rhizobacteria (PGPR) having the potential to combat high salinity stress in plants when used as bioinoculant. The broth culture containing the bacteria may be supplemented with the saline water used for irrigation as it provides nutrients for the growth and proliferation of bacteria present in the saline water and hence the synergistic action of bacterial inocula with the indigenous bacteria present in saline water may better alleviate osmotic and oxidative stresses of plants encountered under salinity stress. The residual effect of Ralstonia pickettii on organic matter and Ca, Mg, K and P content of the rhizosphere soil was notably higher for succeeding crops. Novelty statement This is the first report demonstrating that rhizobacteria can proliferate in water containing salinity higher above seawater in addition to oil grease and TSS. Their efficiency to reduce TDS can be augmented by an exogenous supply of LB broth culture of PGPR isolated from the polluted water. These indigenous rhizobacteria when used as bioinoculant on the plant can act as plant growth promoters as well as bioremediation of salinity effects.

Discovery and mapping of two new rust resistance genes, R17 and R18, in sunflower using genotyping by sequencing

Discovery of two rust resistance genes, R₁₇ and R₁₈, from the sunflower lines introduced from South Africa and genetic mapping of them to sunflower chromosome 13. Rust, caused by the fungus Puccinia helianthi Schw., is one of the most serious diseases of sunflower in the world. The rapid changes that occur in the virulence characteristics of pathogen populations present a continuous threat to the effectiveness of existing rust-resistant hybrids. Thus, there is a continued need for the characterization of genetically diverse sources of rust resistance. In this study, we report to identify two new rust resistance genes, R₁₇ and R₁₈, from the sunflower lines, KP193 and KP199, introduced from South Africa. The inheritance of rust resistance was investigated in both lines using two mapping populations developed by crossing the resistant plants selected from KP193 and KP199 with a common susceptible parent HA 89. The F₂ populations were first genotyped using genotyping by sequencing for mapping of the rust genes and further saturated with markers in the target region. Molecular mapping positioned the two genes at the lower end of sunflower chromosome 13 within a large gene cluster. Two co-segregating SNP markers, SFW01497 and SFW08875, were distal to R₁₇ at a 1.9 cM genetic distance, and a cluster of five co-segregating SNPs was proximal to R₁₇ at 0.7 cM. R₁₈ co-segregated with the SNP marker SFW04317 and was proximal to two cosegregating SNPs, SFW01497 and SFW05453, at 1.9 cM. These maps provide markers for stacking R₁₇ or R₁₈ with other broadly effective rust resistance genes to extend the durability of rust resistance. The relationship of the six rust resistance genes in the cluster was discussed.

Genetic loci underlying quantitative resistance to necrotrophic pathogens Sclerotinia and Diaporthe (Phomopsis), and correlated resistance to both pathogens

We provide results rooted in quantitative genetics, which combined with knowledge of candidate gene function, helps us to better understand the resistance to two major necrotrophic pathogens of sunflower. Necrotrophic pathogens can avoid or even benefit from plant defenses used against biotrophic pathogens, and thus represent a distinct challenge to plant populations in natural and agricultural systems. Sclerotinia and Phomopsis/Diaporthe are detrimental pathogens for many dicotyledonous plants, including many economically important plants. With no well-established methods to prevent infection in susceptible plants, host-plant resistance is currently the most effective strategy. Despite knowledge of a moderate, positive correlation in resistance to the two diseases in sunflower, detailed analysis of the genetics, in the same populations, has not been conducted. We present results of genome-wide analysis of resistance to both pathogens in a diversity panel of 218 domesticated sunflower genotypes of worldwide origin. We identified 14 Sclerotinia head rot and 7 Phomopsis stem canker unique QTLs, plus 1 co-located QTL for both traits, and observed extensive patterns of linkage disequilibrium between sites for both traits. Most QTLs contained one credible candidate gene, and gene families were common for the two disease resistance traits. These results suggest there has been strong, simultaneous selection for resistance to these two diseases and that a generalized mechanism for defense against these necrotrophic pathogens exists.

Investigation of factors affecting phytoremediation of multi-elements polluted calcareous soil using Taguchi optimization

Growing environmental concern regarding multi elements-contaminated soils reveals the necessity of paying more attention to environmentally friendly remediation techniques such as phytoremediation. A large number of factors influences phytoremediation of potentially toxic elements (PTEs) and investigation on a variety of these factors need appropriate statistical approaches such as "Taguchi optimization" which effectively decreases time and cost of experiments. In the present study, based on the Taguchi optimization method, the effects of several biological (plant type and mycorrhizal fungi (AMF)) and chemical (chelating agents, surfactants and organic acids) factors, on the phytoremediation of soils contaminated with zinc (Zn), lead (Pb), cadmium (Cd) and nickel (Ni) were investigated. The goal was to find out the most effective factors as well as the best level for each factor. The values of dry weights in roots and aerial parts of the studied plants were in orders of maize > sorghum > sunflower and sorghum > maize > sunflower, respectively. AMF was the main factor in increasing dry weight of shoots. Inoculation of AMF caused increases in root and shoot uptake of some PTEs. RESULTS: showed that phytoremediation of PTEs is element-dependent; as Zn showed the highest translocation factor (TF) and bioconcentration factor (BCF) values, while Ni showed the lowest ones and the intermediate values belonged to Pb and Cd. These results show the diverse distribution of elements in plant parts, as Zn and Ni were mostly accumulated in shoot and root, respectively. Although different factors caused impacts on phytoremediation criteria, the role of plant type in the phytoremediation of PTEs was at the first rank. Mean TF of PTEs in sunflower was 6.3 times that of maize. Sunflower showed high TF value for the four elements and translocated most of the PTEs from root to the aerial parts demonstrating phytoextraction as the main mechanism in this plant. Maize and sorghum, however, showed low TF and accumulated most of PTEs in their roots revealing phytostabilization as the main mechanism. In general, it can be concluded that plant type was the most influential factor in the phytoremediation of PTEs followed by EDTA and AMF. Taguchi optimization revealed the appropriateness and significance of different chemical and biological treatments on phytoremediation criteria of different elements.

Spatially explicit depiction of a floral epiphytic bacterial community reveals role for environmental filtering within petals

The microbiome of flowers (anthosphere) is an understudied compartment of the plant microbiome. Within the flower, petals represent a heterogeneous environment for microbes in terms of resources and environmental stress. Yet, little is known of drivers of structure and function of the epiphytic microbial community at the within-petal scale. We characterized the petal microbiome in two co-flowering plants that differ in the pattern of ultraviolet (UV) absorption along their petals. Bacterial communities were similar between plant hosts, with only rare phylogenetically distant species contributing to differences. The epiphyte community was highly culturable (75% of families) lending confidence in the spatially explicit isolation and characterization of bacteria. In one host, petals were heterogeneous in UV absorption along their length, and in these, there was a negative relationship between growth rate and position on the petal, as well as lower UV tolerance in strains isolated from the UV-absorbing base than from UV reflecting tip. A similar pattern was not seen in microbes isolated from a second host whose petals had uniform patterning along their length. Across strains, the variation in carbon usage and chemical tolerance followed common phylogenetic patterns. This work highlights the value of petals for spatially explicit explorations of bacteria of the anthosphere.

High-Density Mapping and Candidate Gene Analysis of Pl18 and Pl20 in Sunflower by Whole-Genome Resequencing

Downy mildew (DM) is one of the severe biotic threats to sunflower production worldwide. The inciting pathogen, Plasmopara halstedii, could overwinter in the field for years, creating a persistent threat to sunflower. The dominant genes Pl18 and Pl20 conferring resistance to known DM races have been previously mapped to 1.5 and 1.8 cM intervals on sunflower chromosomes 2 and 8, respectively. Utilizing a whole-genome resequencing strategy combined with reference sequence-based chromosome walking and high-density mapping in the present study, Pl18 was placed in a 0.7 cM interval on chromosome 2. A candidate gene HanXRQChr02g0048181 for Pl18 was identified from the XRQ reference genome and predicted to encode a protein with typical NLR domains for disease resistance. The Pl20 gene was placed in a 0.2 cM interval on chromosome 8. The putative gene with the NLR domain for Pl20, HanXRQChr08g0210051, was identified within the Pl20 interval. SNP markers closely linked to Pl18 and Pl20 were evaluated with 96 diverse sunflower lines, and a total of 13 diagnostic markers for Pl18 and four for Pl20 were identified. These markers will facilitate to transfer these new genes to elite sunflower lines and to pyramid these genes with broad-spectrum DM resistance in sunflower breeding.

Phytohormones producing rhizobacterium alleviates chromium toxicity in Helianthus annuus L. by reducing chromate uptake and strengthening antioxidant system

Contamination of agricultural land with heavy metal is a serious biological and environmental issue. Such threat can be challenged by exploring the plant symbiotic microbes that can improve plant growth through phyto-hormones secretion and chromate chelation. In the current study, chromate resistant rhizospheric Staphylococcus arlettae strain MT4 was isolated from the rhizosphere of Malvestrum tricuspadatum L. The strain showed potential to secrete phytohormones and plant growth promoting secondary metabolites under induced chromate stress, making it a best suitable candidate in chromate stress alleviation. Moreover, the rhizobacterium MT4 significantly promoted the net assimilation and relative growth rate of sunflower grown in the presence of chromate (100 ppm). Chromate stress alleviation strategy of MT4 strain was three-fold. MT4 alleviated chromate stress and promoted the sunflower growth by suppressing the chromate intake by the host, modulating phytohormones and strengthening of the host's antioxidant system. The improved antioxidant system was confirmed by noticing lower ROS accumulation and improved ROS scavenging, lower peroxidase activity and higher accumulation of phenols and flavonoids.

Biofilm forming rhizobacteria enhance growth and salt tolerance in sunflower plants by stimulating antioxidant enzymes activity

Salinity stress is one of the major environmental stresses that impose global socio-economic impacts, as well as hindering crop productivity. Halotolerant plant growth-promoting rhizobacteria (PGPR) having potential to cope with salinity stress can be employed to counter this issue in eco-friendly way. In the present investigation, halotolerant PGPR strains, AP6 and PB5, were isolated from saline soil and characterized for their biochemical, molecular and physiological traits. Sequencing of 16 S rRNA gene and comparative analysis confirmed the taxonomic affiliation of AP6 with Bacillus licheniformis and PB5 with Pseudomonas plecoglossicida. The study was carried out in pots with different levels of induced soil salinity viz. 0, 5, 10 and 15 dSm^-1 to evaluate the potential of bacterial inoculants in counteracting salinity stress in sunflower at different plant growth stages (30, 45 and 60 days after sowing). Both the bacterial inoculants were capable of producing indole acetic acid and biofilm, solubilizing inorganic rock phosphate, and also expressed ACC deaminase activity. The PGPR inoculated plants showed significantly higher fresh and dry biomass, plant height, root length and yield plant^-1. Ameliorative significance of applied bacterial inoculants was also evidenced by mitigating oxidative stress through upregulation of catalase (CAT), superoxide dismutase (SOD) and guaiacol peroxidase (GPX) antioxidant enzymes. Increase in photosynthetic pigments, gas exchange activities and nutrient uptake are crucial salt stress adaptations, which were enhanced with the inoculation of salt tolerant biofilm producing PGPR in sunflower plants. Although increase in salinity stress levels has gradually decreased the plant's output compared to non-salinized plants, the plants inoculated with PGPR confronted salinity stress in much better way than uninoculated plants. Owing to the wide action spectrum of these bacterial inoculants, it was concluded that these biofilm PGPR could serve as effective bioinoculants and salinity stress alleviator for sunflower (oil seed crop) by increasing crop productivity in marginalized agricultural systems.

Arbuscular mycorrhizal fungi alleviate Fe-deficiency symptoms in sunflower by increasing iron uptake and its availability along with antioxidant defense

Iron (Fe)-deficiency causes chlorosis and growth inhibition in sunflower, an important commercial crop. This study examines whether and how arbuscular mycorrhizal fungi (AMF) ameliorate Fe-deficiency symptoms in Fe-deficiency sensitive sunflower plants. AMF supplementation showed a significant improvement in plant biomass, chlorophyll score, Fv/Fm (quantum efficiency of photosystem II), and Pi_ABS (photosynthesis performance index), suggesting its beneficial effect under Fe deficiency. This AM-driven amelioration of Fe deficiency was further supported by the improvement of biochemical stress indicators, such as cell death, electrolyte leakage, superoxide anion, and hydrogen peroxide. In this study, the AMF supplementations resulted in significant improvement in Fe as well as Zn concentrations in root and shoot of sunflower under Fe deficiency. One of the primary Strategy-I responses, ferric reductase activity along with the expression of its respective gene (HaFRO1), significantly increased in roots due to AMF ensuring Fe availability in the rhizosphere under Fe deficiency. Our qPCR analysis also showed a significant upregulation of HaIRT1, HaNramp1, and HaZIP1 in roots of sunflower in the presence of AMF, suggesting that Fe and Zn transporters are concurrently involved with AMF-mediated alleviation of Fe deficiency. Further, AMF accelerates the activities of CAT and SOD, predominantly in roots to protect sunflower plants from Fe-deficiency reactive oxygen species (ROS). This study unveils the mechanistic basis of AMF to limit Fe deficiency retardation in sunflower.

Rhizophagus irregularis and Rhizoctonia solani Differentially Elicit Systemic Transcriptional Expression of Polyphenol Biosynthetic Pathways Genes in Sunflower

Plant roots are exposed to penetration by different biotrophic and necrotrophic fungi. However, plant immune responses vary, depending on the root-penetrating fungus. Using qRT-PCR, changes over time in the systemic transcriptional expression of the polyphenol biosynthesis-related genes were investigated in sunflower plants in response to colonization with Rhizophagus irregularis and/or infection with Rhizoctonia solani. The results demonstrated that both fungi systemically induced the transcriptional expression of most of the addressed genes at varying degrees. However, the inducing effect differed according to the treatment type, plant organ, targeted gene, and time stage. The inducing effect of R. irregularis was more prevalent than R. solani in the early stages. In general, the dual treatment showed a superior inducing effect over the single treatments at most of the time. The hierarchical clustering analysis showed that cinnamate-4-hydroxylase was the master expressed gene along the studied time period. The cell wall lignification was the main plant-defensive-mechanism induced. In addition, accumulations of chlorogenic acid, flavonoids, and anthocyanins were also triggered. Moreover, colonization with R. irregularis improved the plant growth and reduced the disease severity. We can conclude that the proactive, rather than curative, colonization with R. irregularis is of great importance, owing to their protective and growth-promoting roles, even if no infection occurred.

Arbuscular mycorrhiza and environmentally biochemicals enhance the nutritional status of Helianthus tuberosus and induce its resistance against Sclerotium rolfsii

Chemical fungicides are effective tools in controlling plant pathogens; however, these chemicals can, on the other hand, distress the ecosystem. Accordingly, the current research investigates the potentiality of substituting traditional chemical fungicides by inducing plant resistance against infection with soil-born pathogens i.e. Sclerotium rolfsii in the presence of mycorrhizae (AMF) as plant inoculants and one of the following amendments: humic acid, sulphex (a mixture of canola oil and diluted sulphuric acid) and paclobutrazol (ABZ). To attain the abovementioned objective, a field (mildly infected with S. rolfsii) was cultivated with Helianthus tuberosus (a perennial plant belongs to the Asteraceae family) for two successive seasons (2014 and 2015) and the above-mentioned treatments were tested for their feasibilities in controlling S. rolfsii infection against the chemical fungicide "Vitavax-200" either solely or in combinations in a complete randomized block design. Inoculating plants with AMF or amending soils with either humic acid, Sulphex or ABZ solely increased significantly the activities of plant defense enzymes by approximately 1.5-2.1 folds higher than the control treatment. These treatments also improved NPK availability in soil and; hence, increased their contents within plant tubers. Consequently, these treatments decreased the disease incidence and severity caused by S. rolfsii while improved shoot biomass and tuber yield. In spite of that, these results stood below the prospective of the fungicide treatment. The integrated treatments i.e. "humic acid + AMF", "Sulphex + AMF" and "ABZ + AMF" caused further significant improvements in both NPK availabilities in soil and plant areal bio-masses. This probably induced further plant resistance against the investigated soil-borne pathogen while recorded insignificant variations in disease incidence and severity when compared with the fungicide treatment. Moreover, the integrated treatments increased the tuber yields beyond those attained for the fungicide treatment. Accordingly, such integrated strategies can completely substitute the chemical fungicides; thus, minimize their negative impacts on the ecosystem.

Marker-Assisted Gene Pyramiding and the Reliability of Using SNP Markers Located in the Recombination Suppressed Regions of Sunflower (Helianthus annuus L.)

Rust caused by the fungus Puccinia helianthi and downy mildew (DM) caused by the obligate pathogen Plasmopara halstedii are two of the most globally important sunflower diseases. Resistance to rust and DM is controlled by race-specific single dominant genes. The present study aimed at pyramiding rust resistance genes combined with a DM resistance gene, using molecular markers. Four rust resistant lines, HA-R3 (carrying the R₄ gene), HA-R2 (R₅), HA-R8 (R₁₅), and RHA 397 (R_13b), were each crossed with a common line, RHA 464, carrying a rust gene R₁₂ and a DM gene Pl_Arg. An additional cross was made between HA-R8 and RHA 397. Co-dominant simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers linked to the target genes were used to discriminate between homozygotes and heterozygotes in F₂ populations. Five pyramids with different combinations of rust resistance genes were selected in the homozygous condition through marker-assisted selection, and three of them were combined with a DM resistance gene Pl_Arg: R₄/R₁₂/Pl_Arg, R₅/R₁₂/Pl_Arg, R_13b/R₁₂/Pl_Arg, R₁₅/R₁₂, and R_13b/R₁₅. The pyramiding lines with the stacking of two rust and one DM genes were resistant to all known races of North American sunflower rust and all known races of the pathogen causing DM, potentially providing multiple and durable resistance to both rust and DM. A cluster of 12 SNP markers spanning a region of 34.5 Mb on chromosome 1, which co-segregate with Pl_Arg, were tested in four populations. Use of those markers, located in a recombination suppressed region in marker selection, is discussed.

Verticillium isaacii is a Pathogen and Endophyte of Potato and Sunflower in the Columbia Basin of Washington

The objective of this research was to test the hypothesis that Verticillium isaacii causes diseases of sunflower and potato plants. Two sunflower genotypes and one potato cultivar were inoculated with five V. isaacii isolates and three pathogenic V. dahliae isolates. Biomass, disease expression, and stem colonization were quantified. Overt wilt symptoms were observed on both sunflower genotypes and potato plants inoculated with a subset of the V. isaacii isolates. Biomass of both sunflower genotypes was not affected by V. isaacii infection. Tuber yields either decreased in response to infection by one V. isaacii isolate or were not affected by infection. Stems of sunflower and potato plants were infected by at least four of the five V. isaacii isolates. A new disease of sunflower and potato is documented. Evidence that V. isaacii exhibits different lifestyles including pathogenicity and endophytism is presented. Finally, this research documents variation in fungal lifestyles that can exist in samples from a single field.

Potential of plant beneficial bacteria and arbuscular mycorrhizal fungi in phytoremediation of metal-contaminated saline soils

Phytoremediation has been considered as a promising technique to decontaminate polluted soils. However, climatic stress particularly salinity, is a potential threat to soil properties and plant growth, thus restricting the employment of this technology. The aim of this study was to access the impact of microbial inoculation on phytoremediation of nickel (Ni) contaminated saline soils using Helianthus annuus. Salt resistant plant beneficial bacterium (PBB) Pseudomonas libanensis TR1 and arbuscular mycorrhizal fungus (AMF) Claroideoglomus claroideum BEG210 were used. Inoculation of P. libanensis alone or in combination with C. claroideum significantly enhanced plant growth, changed physiological status (e.g. electrolyte leakage, chlorophyll, proline and malondialdehyde contents) as well as Ni and sodium (Na⁺) accumulation potential (e.g. uptake and translocation factor of Ni and Na⁺) of H. annuus under Ni and salinity stress either alone or in combination. These results revealed that bioaugmentation of microbial strains may serve as a preferred strategy for improving phytoremediation of metal-polluted saline soils.

The effect of Cu-resistant plant growth-promoting rhizobacteria and EDTA on phytoremediation efficiency of plants in a Cu-contaminated soil

Remediation of heavy metal-contaminated soils is essential for safe agricultural or urban land use, and phytoremediation is among the most effective methods. The success of phytoremediation relies on the size of the plant biomass and bioavailability of the metal for plant uptake. This research was carried out to determine the effect of Ethylenediaminetetraacetic acid (EDTA) ligand and Cu-resistant plant growth-promoting rhizobacteria (PGPR) on phytoremediation efficiency of selected plants as well as fractionation and bioavailability of copper (Cu) in a contaminated soil. The test conditions included three plant species (maize: Zea mays L., sunflower: Helianthus annuus L., and pumpkin: Cucurbita pepo L.) and six treatments, comprising two PGPR strains (Pseudomonas cedrina K4 and Stenotrophomonas sp. A22), two PGPR strains with EDTA, EDTA, and control (without PGPR and EDTA). The combination of EDTA and PGPR enhanced the Cu concentration in both shoot and root tissues and increased the plant biomass. The Cu specific uptake was at a maximum level in the shoots of pumpkin plants when treated with the PGPR strain K4 + EDTA (202 μg pot^-1), and the minimum amount of Cu was recorded for sunflower with no PGPR or EDTA addition (29.6 μg pot^-1). The result of the PGPR-EDTA treatments showed that the combined application of EDTA and PGPR increased the shoot Cu-specific uptake approximately fourfold in pumpkin. Pumpkin with the highest shoot Cu specific uptake and maize with the highest root Cu specific uptake were the most effective plants in phytoextraction and phytostabilization, respectively. The effectiveness of different PGPR-EDTA treatments in increasing Cu specific uptake by crop plants was assessed by measuring the amount of Cu extracted from the rhizosphere soil adhering to the roots of crop species, by the use of the single extractants Diethylenetriamine pentaacetic acid (DTPA), H₂O, NH₄NO₃, and NH₄OAc. PGPR-EDTA treatments increased the amount of water-extractable Cu from rhizosphere soils more than ten times that of the control. The combined application of the EDTA and PGPR reduced the carbonated Fe and Mn oxide-bound Cu in the contaminated soil, and increased the soluble and exchangeable concentration of Cu. Pumpkin, with high shoot biomass and the highest shoot Cu specific uptake was found to be the most effective field crop in phytoextraction of Cu from the contaminated soil. The results of this pot study demonstrated that the EDTA+PGPR treatment could play an important role in increasing the Cu bioavailability and specific uptake by plants, and thus increasing the phytoremediation efficiency of plants in Cu-contaminated areas.

Novel synergistic fungicidal mixtures of oxathiapiprolin protect sunflower seeds from downy mildew caused by Plasmopara halstedii

Plenaris (oxathiapiprolin) applied to sunflower seedlings was highly effective in controlling downy mildew incited by the oomycete Plasmopara halstedii. In vitro assays revealed strong suppression of zoospore release and cystospore germination of P.halstedii by Plenaris. Bion (acibenzolar-S-methyl) and Apron (mefenoxam) were partially effective when used singly, but performed synergistically when mixed with Plenaris. Seed treatment (coating) with Plenaris provided dose-dependent control of the disease whereas Bion and Apron provided partial or poor control. However, seeds treated with mixtures containing reduced rates of Plenaris and full rates of Bion and/or Apron provided complete control of the disease due to the synergistic interaction between these components. Such mixtures should be used for seed treatment in the field to minimize selection pressure imposed on the pathogen.

A comparative evaluation towards the potential of Klebsiella sp. and Enterobacter sp. in plant growth promotion, oxidative stress tolerance and chromium uptake in Helianthus annuus (L.)

Prevalence of metal pollutants exerts negative effects on human health and environment, thus propounding an urgent need for a safer substitute. This study was conducted to compare the chromium bioremediation and plant growth promotion ability of two bacterial strains, Klebsiella sp. strain CPSB4 (MH266218) and Enterobacter sp. strain CPSB49 (MH532567), isolated from the rhizospheric soils. A pot scale experiment was setup with Helianthus annuus (L.) as a test plant to compare the efficiency of both isolates in enhancement of plant growth, nutrients uptake, anti-oxidative enzymes production, lipid peroxidation, and chromium bioremediation. Inoculation of strains, CPSB4 and CPSB49 enhanced plant biomass, plant growth, nutrient uptake, anti-oxidative enzymes, and chromium bioremediation, while reduction in lipid peroxidation was observed compared to uninoculated control under chromium stress. The maximum increase in plant growth and nutrient uptake was found in treatments inoculated with CPSB49, while maximum chromium uptake by sunflower was observed in treatments inoculated with CPSB4. Moreover, an increase in anti-oxidative enzyme production and decrease in lipid peroxidation was observed on inoculation of the selected strains. Thus, the strains Klebsiella sp. and Enterobacter sp. can be effectively used in chromium bioremediation and plant growth promotion under chromium stress conditions.

Diversification of the downy mildew resistance gene pool by introgression of a new gene, Pl35, from wild Helianthus argophyllus into oilseed and confection sunflowers (Helianthus annuus L.)

We have mapped a new downy mildew resistance gene, Pl₃₅, derived from wild Helianthus argophyllus to sunflower linkage group 1. New germplasms incorporating the Pl₃₅ gene were developed for both oilseed and confection sunflower Sunflower downy mildew (DM), caused by the oomycete pathogen Plasmopara halstedii, is an economically important and widespread sunflower disease worldwide. Non-race-specific resistance is not available in sunflower, and breeding for DM resistance relies on race-specific resistance to control this disease. The discovery of the novel DM resistance genes is a long-term task due to the highly virulent and aggressive nature of the P. halstedii pathogen, which reduces the effectiveness of resistance genes. The objectives of this study were to: (1) transfer DM resistance from a wild sunflower species Helianthus argophyllus (PI 494576) into cultivated sunflowers; (2) map the resistance gene; and (3) develop diagnostic single-nucleotide polymorphism (SNP) markers for efficient targeting of the gene in breeding programs. The H. argophyllus accession PI 494576 previously identified with resistance to the most virulent P. halstedii race 777 was crossed with oilseed and confection sunflower in 2012. Molecular mapping using the BC₂F₂ and BC₂F₃ populations derived from the cross CONFSCLB1/PI 494576 located a new resistance gene Pl₃₅ on linkage group 1 of the sunflower genome. The new gene Pl₃₅ was successfully transferred from PI 494576 into cultivated sunflowers. SNP markers flanking Pl₃₅ were surveyed in a validation panel of 548 diversified sunflower lines collected globally. Eleven SNP markers were found to be diagnostic for Pl₃₅ SNP alleles, with four co-segregating with Pl₃₅. The developed oilseed and confection germplasms with diagnostic SNP markers for Pl₃₅ will be very useful resources for breeding of DM resistance in sunflower.

Photomorphogenesis of the root system in developing sunflower seedlings: a role for sucrose

The domestic sunflower (Helianthus annuus L. cv. 'Giganteus') has been used since the 19th century as a model plant for the study of seedling development in darkness and white light (WL) (scoto- versus photomorphogenesis). However, most pertinent studies have focused on the developmental patterns of the hypocotyl and cotyledons, whereas the root system has been largely ignored. In this study, we analysed entire sunflower seedlings (root and shoot) and quantified organ development in the above- and belowground parts of the organism under natural (non-sterile) conditions. We document that seedlings, raised in moist vermiculite, are covered with methylobacteria, microbes that are known to promote root development in Arabidopsis. Quantitative data revealed that during photomorphogenesis in WL, the root system expands by 90%, whereas stem elongation is inhibited, and hook opening/cotyledon expansion occurs. Root morphogenesis may be mediated via imported sucrose provided by the green, photosynthetically active cotyledons. This hypothesis is supported by the documented effect of sucrose on the induction of lateral root initials in sunflower cuttings. Under these experimental conditions, phytohormones (auxin, cytokinin, brassinolide) exerted little effect on root and cotyledon expansion, and no hormone-induced initiation of lateral roots was observed. It is concluded that sucrose not only acts as an energy source to fuel cell metabolism but is also a shoot-derived signalling molecule that triggers root morphogenesis.

Photomorphogenesis of the root system in developing sunflower seedlings: a role for sucrose

The domestic sunflower (Helianthus annuus L. cv. 'Giganteus') has been used since the 19th century as a model plant for the study of seedling development in darkness and white light (WL) (scoto- versus photomorphogenesis). However, most pertinent studies have focused on the developmental patterns of the hypocotyl and cotyledons, whereas the root system has been largely ignored. In this study, we analysed entire sunflower seedlings (root and shoot) and quantified organ development in the above- and belowground parts of the organism under natural (non-sterile) conditions. We document that seedlings, raised in moist vermiculite, are covered with methylobacteria, microbes that are known to promote root development in Arabidopsis. Quantitative data revealed that during photomorphogenesis in WL, the root system expands by 90%, whereas stem elongation is inhibited, and hook opening/cotyledon expansion occurs. Root morphogenesis may be mediated via imported sucrose provided by the green, photosynthetically active cotyledons. This hypothesis is supported by the documented effect of sucrose on the induction of lateral root initials in sunflower cuttings. Under these experimental conditions, phytohormones (auxin, cytokinin, brassinolide) exerted little effect on root and cotyledon expansion, and no hormone-induced initiation of lateral roots was observed. It is concluded that sucrose not only acts as an energy source to fuel cell metabolism but is also a shoot-derived signalling molecule that triggers root morphogenesis.

Introgression and monitoring of wild Helianthus praecox alien segments associated with Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing

Sclerotinia basal stalk rot (BSR) and downy mildew are major diseases of sunflowers worldwide. Breeding for BSR resistance traditionally relies upon cultivated sunflower germplasm that has only partial resistance thus lacking an effective resistance against the pathogen. In this study, we report the transfer of BSR resistance from sunflower wild species, Helianthus praecox, into cultivated sunflower and molecular assessment of the introgressed segments potentially associated with BSR resistance using the genotyping-by-sequencing (GBS) approach. Eight highly BSR-resistant H. praecox introgression lines (ILs), H.pra 1 to H.pra 8, were developed. The mean BSR disease incidence (DI) for H.pra 1 to H.pra 8 across environments for four years ranged from 1.2 to 11.1%, while DI of Cargill 270 (susceptible check), HA 89 (recurrent parent), HA 441 and Croplan 305 (resistant checks) was 36.1, 31.0, 19.5, and 11.6%, respectively. Molecular assessment using GBS detected the presence of H. praecox chromosome segments in chromosomes 1, 8, 10, 11, and 14 of the ILs. Both shared and unique polymorphic SNP loci were detected throughout the entire genomes of the ILs, suggesting the successful transfer of common and novel introgression regions that are potentially associated with BSR resistance. Downy mildew (DM) disease screening and molecular tests revealed that a DM resistance gene, Pl₁₇, derived from one of the inbred parent HA 458 was present in four ILs. Introgression germplasms possessing resistance to both Sclerotinia BSR and DM will extend the useful diversity of the primary gene pool in the fight against two destructive sunflower diseases.

Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii

Over the last 40 years, new sunflower downy mildew isolates (Plasmopara halstedii) have overcome major gene resistances in sunflower, requiring the identification of additional and possibly more durable broad-spectrum resistances. Here, 354 RXLR effectors defined in silico from our new genomic data were classified in a network of 40 connected components sharing conserved protein domains. Among 205 RXLR effector genes encoding conserved proteins in 17 P. halstedii pathotypes of varying virulence, we selected 30 effectors that were expressed during plant infection as potentially essential genes to target broad-spectrum resistance in sunflower. The transient expression of the 30 core effectors in sunflower and in Nicotiana benthamiana leaves revealed a wide diversity of targeted subcellular compartments, including organelles not so far shown to be targeted by oomycete effectors such as chloroplasts and processing bodies. More than half of the 30 core effectors were able to suppress pattern-triggered immunity in N. benthamiana, and five of these induced hypersensitive responses (HR) in sunflower broad-spectrum resistant lines. HR triggered by PhRXLRC01 co-segregated with Pl22 resistance in F3 populations and both traits localized in 1.7 Mb on chromosome 13 of the sunflower genome. Pl22 resistance was physically mapped on the sunflower genome recently sequenced, unlike all the other downy mildew resistances published so far. PhRXLRC01 and Pl22 are proposed as an avirulence/resistance gene couple not previously described in sunflower. Core effector recognition is a successful strategy to accelerate broad-spectrum resistance gene identification in complex crop genomes such as sunflower.

Effect of endosulfan tolerant bacterial isolates (Delftia lacustris IITISM30 and Klebsiella aerogenes IITISM42) with Helianthus annuus on remediation of endosulfan from contaminated soil

Endosulfan contaminated soil has become an important risk to the environment and human health worldwide. In the present study, endosulfan tolerant bacterial strain Delftia lacustris IITISM30 and Klebsiella aerogenes IITISM42 were isolated from pesticide stressed agricultural soil and tested for plant growth promoting activities. A pot experiment was performed using Helianthus annuus, grown in soil supplemented with endosulfan and inoculated with pure and consortium of bacterial strain IITISM30 and IITISM42. Inoculation increased plant biomass production and endosulfan degradation, maximum degradation (90% at 5 mg kg^-1 of soil) was observed by inoculation with a consortium of bacterial strain IITISM30 and IITISM42. Moreover, there was significantly less endosulfan accumulation was observed in roots and shoots of bacterial inoculated plants as compared to uninoculated plants. Decrease in production of malonialdehyde (MDA) was noticed on inoculation of a bacterial strain. The study demonstrated that inoculation of a consortium of endosulfan tolerant plant growth promoting bacterial isolates could more effectively remediate endosulfan contaminated soils and decrease endosulfan residues in plants, than individual strains. Moreover, it revealed that combined use of H. annuus and endosulfan tolerant bacterial isolates IITISM30 and IITISM42 has great potential for remediating endosulfan contaminated soil.

Selection of reference genes for quantitative real-time PCR normalization in the plant pathogen Puccinia helianthi Schw

BACKGROUND

Real-time RT-PCR has become a common and robust technique to detect and quantify low-abundance mRNA expression and is a prefered tool when examining fungal gene expression in infected host tissues. However, correct evaluation of gene expression data requires accurate and reliable normalization against a reference transcript. Thus, the identification of reference genes with stable expression during different conditions is of paramount importance. Here, we present a study where in vitro and in planta experiments were used to validate the expression stability of reference gene candidates of Puccinia helianthi Schw., an obligate pathogen that causes rust in sunflower (Helianthus annuus).

RESULTS

Eleven reference genes of P. helianthi were validated at different growth stages. Excel-based software geNorm, BestKeeper and NormFinder were used to evaluate the reference gene transcript stabilities. Of eleven reference gene candidates tested, three were stably expressed in urediniospores, germinating growth stage and in planta. Two of these genes (UBC, EF2), encoding ubiquitin-conjugating enzyme and elongation factor 2, proved to be the most stable set of reference genes under the experimental conditions used.

CONCLUSION

We found that UBC and EF2 are suitable candidates for for the standardization of gene expression studies in the plant pathogen P. helianthi and potentially other related pathogens.

Endophytic bacterial communities in peels and pulp of five root vegetables

Plants contain endophytic bacteria, whose communities both influence plant growth and can be an important source of probiotics. Here we used deep sequencing of a 16S rRNA gene fragment and bacterial cultivation to independently characterize the microbiomes of five plant species from divergent taxonomic orders—potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), neep (Brassica napus spp. napobrassica), and topinambur (Helianthus tuberosus). We found that both species richness and diversity tend to be higher in the peel, where Alphaproteobacteria and Actinobacteria dominate, while Gammaproteobacteria and Firmicutes dominate in the pulp. A statistical analysis revealed that the main characteristic features of the microbiomes of plant species originate from the peel microbiomes. Topinambur pulp displayed an interesting characteristic feature: it contained up to 10⁸ CFUs of lactic acid bacteria, suggesting its use as a source of probiotic bacteria. We also detected Listeria sp., in topinambur pulps, however, the 16S rRNA gene fragment is unable to distinguish between pathogenic versus non-pathogenic species, so the evaluation of this potential health risk is left to a future study.

A Reduced Phosphorus Application Rate Using a Mycorrhizal Plant as the Preceding Crop Maintains Soybean Seeds' Nutritional Quality

We tested whether introducing an arbuscular mycorrhizal fungi (AMF)-host plant with a reduced P application rate could maintain soybean seeds' nutrient quality. The dynamic variation of 14 nutrients was analyzed in source and sink organs during the seed-filling stage. The AMF-host and non-AMF-host plants, sunflower and mustard, were grown as preceding crops (PCs). Soybeans, the succeeding crops, were planted with three different phosphorus levels, namely, 0, 50, and 150 kg P2O5 ha-1. The results showed that the AMF-host PC with a reduced P application rate maintained the seed's yield and nutrients quality. During the seed-filling stage, the AMF-host PC with a reduced P application rate increased the uptake of most nutrients compared to the non-AMF-host PC, and improved the remobilization efficiency of all nutrients except Mn, Fe, and Se, compared to the optimal P application rate. These results could help improve the utilization efficiency of P fertilizers and protect soybeans' nutritional value.

Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance

Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.

Impact of pyrometallurgical slags on sunflower growth, metal accumulation and rhizosphere microbial communities

Metallurgical exploitation originates metal-rich by-products termed slags, which are often disposed in the environment being a source of heavy metal pollution. Despite the environmental risk that this may pose for living organisms, little is known about the impact of slags on biotic components of the ecosystem like plants and rhizosphere microbial communities. In this study, metal-rich (Cu, Pb, Zn) granulated slags (GS) derived from Cu production process, were used for a leaching test in the presence of the soil pore solution, showing that soil solution enhanced the release of Cu from GS. A pot experiment was conducted using as growing substrate for sunflower (Helianthus annuus) a 50% w/w mix of an agricultural soil and GS. Bioavailability of metals in soil was, in increasing order: Pb < Zn < Cu. Sunflower was able to grow in the presence of GS and accumulated metals preferentially in above-ground tissues. Microbial diversity was assessed in rhizosphere and bulk soil using community level physiological profiling (CLPP) and 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) analyses, which demonstrated a shift in the diversity of microbial communities induced by GS. Overall, these results suggest that metallurgical wastes should not be considered inert when dumped in the soil. Implications from this study are expected to contribute to the development of sustainable practices for the management of pyrometallurgical slags, possibly involving a phytomanagement approach.

The Colonization Process of Sunflower by a Green Fluorescent Protein-Tagged Isolate of Verticillium dahliae and its Seed Transmission

Sunflower Verticillium wilt is a widespread and destructive disease caused by the soilborne pathogen Verticillium dahliae. To better understand the process of infection and seed transmission of the fungus, sunflower roots were inoculated with a V. dahliae strain (VdBM9-6) labeled with green fluorescent protein (GFP) and monitored microscopically. After 24 to 96 h postinoculation (hpi), conidia germinated and developed into mycelium on root hairs, elongation zones, and caps of lateral roots. Mycelium colonized vascular bundles of lateral roots and taproots at 7 days postinoculation (dpi). At 10 weeks postinoculation (wpi), the epidermal cells, cortical tissues, and vascular elements of stem, petiole, and leaf veins were colonized by mycelium. By 12 wpi, strong GFP signals were detected not only on different tissues of inflorescence but also on testa of seed and a small fraction of pollen grains. A GFP signal was not observed on cotyledon tissues in the seed. Additionally, the colonization of V. dahliae on testa was also confirmed with MNP-10 selection medium, indicating that the testa of seed is the main carrier for the long distance transmission of sunflower yellow wilt.

High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15 , in sunflower (Helianthus annuus L.)

A novel rust resistance gene, R ₁₅ , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R ₁₅ were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance. The inbred line HA-R8 carries a gene conferring resistance to all known races of the rust pathogen in North America and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments of 140 F₂ individuals derived from a cross of HA 89 with HA-R8, rust resistance in the population was found to be conferred by a single dominant gene (R ₁₅ ) originating from HA-R8. Genotypic analysis with the currently available SSR markers failed to find any association between rust resistance and any markers. Therefore, we used genotyping-by-sequencing (GBS) analysis to achieve better genomic coverage. The GBS data showed that R ₁₅ was located at the top end of linkage group (LG) 8. Saturation with 71 previously mapped SNP markers selected within this region further showed that it was located in a resistance gene cluster on LG8, and mapped to a 1.0-cM region between three co-segregating SNP makers SFW01920, SFW00128, and SFW05824 as well as the NSA_008457 SNP marker. These closely linked markers will facilitate marker-assisted selection and breeding in sunflower.

Arbuscular mycorrhizal fungi alleviate the heavy metal toxicity on sunflower (Helianthus annuus L.) plants cultivated on a heavily contaminated field soil at a WEEE-recycling site

An 8-week pot experiment was conducted to investigate the growth and responses of sunflower (Helianthus annuus L.) to arbuscular mycorrhizal (AM) fungal inoculations on a heavily heavy metal (HM)-contaminated (H) soil and a lightly HM-enriched (L) soil, both of which were collected from a waste electrical and electronic equipment (WEEE)-recycling site. Compared with the L soil, the H soil induced significantly larger (P<0.05) concentrations of Cd, Cu, Pb, Cr, Zn and Ni in sunflower (except for root Cr and shoot Ni), which impaired the thylakoid lamellar folds in leaves. The biomasses and P concentrations of shoots and roots, as well as the total P acquisitions per pot were all significantly decreased (P<0.05). Both Funneliformis mosseae (Fm) and F. caledonium (Fc) inoculation significantly increased (P<0.05) root mycorrhizal colonization. For the L soil, AM fungal inoculations had no significant effects on the soil-plant system, except for a decrease of soil pH and increases of soil available P and DTPA-extractable Zn concentrations with the Fm-inoculated treatment. For the H soil, however, AM fungal inoculations significantly increased (P<0.05) the biomasses and P concentrations of shoots and roots, as well as the total P acquisitions per pot, and significantly reduced (P<0.05) the concentrations of HMs in shoots (except for Cu and Pb with Fm- and Fc- inoculated treatments, respectively) and alleviated the toxicity symptoms of HMs in thylakoid structure of leaves. AM fungal inoculations in the H soil also significantly increased (P<0.05) the shoot uptake of HMs (except for Cr), and tended to decrease the total concentrations of HMs in soils. This suggests the potential application of AM fungi for both reducing HM stress and promoting phytoextraction of HM-contaminated soils caused by WEEE recycling.

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation

Microbes are key determinants of plant health and productivity. Previous studies have characterized the rhizosphere microbiomes of numerous plant species, but little information is available on how rhizosphere microbial communities change over time under crop rotation systems. Here, we document microbial communities in the rhizosphere of sorghum and sunflower (at seedling, flowering and senescence stages) grown in crop rotation in four different soils under field conditions. A comprehensive 16S rRNA-based amplicon sequencing survey revealed that the differences in alpha-diversity between rhizosphere and bulk soils changed over time. Sorghum rhizosphere soil microbial diversity at flowering and senescence were more diverse than bulk soils, whereas the microbial diversity of sunflower rhizosphere soils at flowering were less diverse with respect to bulk soils. Sampling time was also important in explaining the variation in microbial community composition in soils grown with both crops. Temporal changes observed in the rhizosphere microbiome were both plant-driven and due to seasonal changes in the bulk soil biota. Several individual taxa were relatively more abundant in the rhizosphere and/or found to be important in maintaining rhizosphere microbial networks. Interestingly, some of these taxa showed similar patterns at different sampling times, suggesting that the same organisms may play the same functional/structural role at different plant growth stages and in different crops. Overall, we have identified prominent microbial taxa that might be used to develop microbiome-based strategies for improving the yield and productivity of sorghum and sunflower.

Myco-phytoremediation of arsenic- and lead-contaminated soils by Helianthus annuus and wood rot fungi, Trichoderma sp. isolated from decayed wood

In the present study, Helianthus annuus grown in arsenic- (As) and lead- (Pb) contaminated soil were treated with plant-growth promoting fungi Trichoderma sp. MG isolated from decayed wood and assessed for their phytoremediation efficiency. The isolate MG exhibited a high tolerance to As (650mg/L) and Pb (500mg/L), and could remove > 70% of metals in aqueous solution with an initial concentration of 100mg/L each. In addition, the isolate MG was screened for plant-growth-promoting factors such as siderophores, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA) synthesis, and phosphate solubilisation. Phytoremediation studies indicated that treatment of H. annuus with the isolate MG had the maximum metal-accumulation in shoots (As; 67%, Pb; 59%). Furthermore, a significant increase in the soil extracellular enzyme-activities was observed in myco-phytoremediated soils. The activities of phosphatase (35 U/g dry soil), dehydrogenase (41mg TPF/g soil), cellulase (37.2mg glucose/g/2h), urease (55.4mgN/g soil/2h), amylase (49.3mg glucose/g/2h) and invertase (45.3mg glucose/g/2h) significantly increased by 12%, 14%, 12%, 22%, 19% and 14% in As contaminated soil, respectively. Similarly, the activities of phosphatase (31.4U/g dry soil), dehydrogenase (39.3mg TPF/g soil), cellulase (37.1mg glucose/g/2h), urease (49.8mgN/g soil/2h), amylase (46.3mg glucose/g/2h), and invertase (42.1mg glucose/g/2h) significantly increased by 11%, 15%, 11%, 18%, 20% and 14% in Pb contaminated soil, respectively. Obtained results indicate that the isolate MG could be a potential strain for myco-phytoremediation of As and Pb contaminated soil.

Impact of lead tolerant plant growth promoting rhizobacteria on growth, physiology, antioxidant activities, yield and lead content in sunflower in lead contaminated soil

Present study was conducted to evaluate the effect of lead tolerant plant growth promoting rhizobacteria (LTPGPR) on growth, physiology, yield, antioxidant activities and lead uptake in sunflower in soil contaminated with lead under pot conditions. Three pre-characterized LTPGP strains (S2 (Pseudomonas gessardii strain BLP141), S5 (Pseudomonas fluorescens A506) and S10 (Pseudomonas fluorescens strain LMG 2189)) were used to inoculate sunflower growing in soil contaminated with different levels (300, 600 and 900 mg kg^-1) of lead by using lead nitrate salt as source of lead. Treatments were arranged according to completely randomized design with factorial arrangements. At harvesting, data regarding growth attributes (root shoot length, root shoot fresh and dry weights), yield per plant, physiological attributes (Chlorophyll 'a', 'b' and carotenoids content), antioxidant activities (Ascorbate peroxidase, catalase, superoxide dismutase and glutathione reductase), proline and malanodialdehyde content, and lead content in root, shoot and achenes of sunflower were recorded. Data were analysed by standard statistical procedures. Results showed that lead contamination reduced the plants growth, physiology and yield at all levels of lead stress. But application of LTPGPR in soil contaminated with lead improved plant growth, physiology, yield, and antioxidant activities, proline, and reduced the malanodialdehyde content (that is reduced by the application of different strains in lead contamination) of sunflower as compared to plants grown in soil without inoculation. Inoculation also promoted the uptake of lead in root, shoots and reduced the uptake of lead in achenes of plants as compared to plants in lead contamination without inoculation.

Internalization of a sunflower mannose-binding lectin into phytopathogenic fungal cells induces cytotoxicity

Lectins are carbohydrate-affinity proteins with the ability to recognize and reversibly bind specific glycoconjugates. We have previously isolated a bioactive sunflower mannose-binding lectin belonging to the jacalin-related family called Helja. Despite of the significant number of plant lectins described in the literature, only a small group exhibits antifungal activity and the mechanism by which they kill fungi is still not understood. The aim of this work was to explore Helja activity on plant pathogenic fungi, and provide insights into its mechanism of action. Through cellular and biochemical experimental approaches, here we show that Helja exerts an antifungal effect on Sclerotinia sclerotiorum, a sunflower pathogen. The lectin interacts with the fungal spore surface, permeabilizes its plasma membrane, can be internalized into the cell and induces oxidative stress, finally leading to the cell death. On the other hand, Helja is inactive towards Fusarium solani, a non-pathogen of sunflower, showing the selective action of the lectin. The mechanistic basis for the antifungal activity of an extracellular jacalin lectin is presented, suggesting its initial interaction with fungal cell wall carbohydrates and further internalization. The implication of our findings for plant defense is discussed.

Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots

Arbuscular mycorrhizal (AM) fungi are essential elements of soil fertility, plant nutrition and productivity, facilitating soil mineral nutrient uptake. Helianthus annuus is a non-model, widely cultivated species. Here we used an RNA-seq approach for evaluating gene expression variation at early and late stages of mycorrhizal establishment in sunflower roots colonized by the arbuscular fungus Rhizoglomus irregulare. mRNA was isolated from roots of plantlets at 4 and 16 days after inoculation with the fungus. cDNA libraries were built and sequenced with Illumina technology. Differential expression analysis was performed between control and inoculated plants. Overall 726 differentially expressed genes (DEGs) between inoculated and control plants were retrieved. The number of up-regulated DEGs greatly exceeded the number of down-regulated DEGs and this difference increased in later stages of colonization. Several DEGs were specifically involved in known mycorrhizal processes, such as membrane transport, cell wall shaping, and other. We also found previously unidentified mycorrhizal-induced transcripts. The most important DEGs were carefully described in order to hypothesize their roles in AM symbiosis. Our data add a valuable contribution for deciphering biological processes related to beneficial fungi and plant symbiosis, adding an Asteraceae, non-model species for future comparative functional genomics studies.

Main and epistatic QTL analyses for Sclerotinia Head Rot resistance in sunflower

Sclerotinia Head Rot (SHR), a disease caused by Sclerotinia sclerotiorum, is one of the most limiting factors in sunflower production. In this study, we identified genomic loci associated with resistance to SHR to support the development of assisted breeding strategies. We genotyped 114 Recombinant Inbred Lines (RILs) along with their parental lines (PAC2 -partially resistant-and RHA266 -susceptible-) by using a 384 single nucleotide polymorphism (SNP) Illumina Oligo Pool Assay to saturate a sunflower genetic map. Subsequently, we tested these lines for SHR resistance using assisted inoculations with S. sclerotiorum ascospores. We also conducted a randomized complete-block assays with three replicates to visually score disease incidence (DI), disease severity (DS), disease intensity (DInt) and incubation period (IP) through four field trials (2010-2014). We finally assessed main effect quantitative trait loci (M-QTLs) and epistatic QTLs (E-QTLs) by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively. As a result of this study, the improved map incorporates 61 new SNPs over candidate genes. We detected a broad range of narrow sense heritability (h2) values (1.86-59.9%) as well as 36 M-QTLs and 13 E-QTLs along 14 linkage groups (LGs). On LG1, LG10, and LG15, we repeatedly detected QTLs across field trials; which emphasizes their putative effectiveness against SHR. In all selected variables, most of the identified QTLs showed high determination coefficients, associated with moderate to high heritability values. Using markers shared with previous Sclerotinia resistance studies, we compared the QTL locations in LG1, LG2, LG8, LG10, LG11, LG15 and LG16. This study constitutes the largest report of QTLs for SHR resistance in sunflower. Further studies focusing on the regions in LG1, LG10, and LG15 harboring the detected QTLs are necessary to identify causal alleles and contribute to unraveling the complex genetic basis governing the resistance.

Exchanging missives and missiles: the roles of extracellular vesicles in plant-pathogen interactions

This article comments on: Regente M, Pinedo M, San Clemente H, Balliau T, Jamet E, de la Canal L. 2017. Plant extracellular vesicles are incorporated by a fungal pathogen and inhibit its growth. Journal of Experimental Botany 68, 5485–5495.

Plant extracellular vesicles are incorporated by a fungal pathogen and inhibit its growth

Extracellular vesicles (EV) are membrane particles released by cells into their environment and are considered to be key players in intercellular communication. EV are produced by all domains of life but limited knowledge about EV in plants is available, although their implication in plant defense has been suggested. We have characterized sunflower EV and tested whether they could interact with fungal cells. EV were isolated from extracellular fluids of seedlings and characterized by transmission electron microscopy and proteomic analysis. These nanovesicles appeared to be enriched in cell wall remodeling enzymes and defense proteins. Membrane-labeled EV were prepared and their uptake by the phytopathogenic fungus Sclerotinia sclerotiorum was verified. Functional tests further evaluated the ability of EV to affect fungal growth. Spores treated with plant EV showed growth inhibition, morphological changes, and cell death. Conclusive evidence on the existence of plant EV is presented and we demonstrate their ability to interact with and kill fungal cells. Our results introduce the concept of cell-to-cell communication through EV in plants.

Root endophytic fungus Piriformospora indica affected growth, cadmium partitioning and chlorophyll fluorescence of sunflower under cadmium toxicity

Cadmium (Cd) pollution in the soil threatens the quality of environmental health, and deleteriously affects physiological activities of crops. Symbiosis of endophytic fungi with various plants is a promising manner to improving numerous plant characteristics and remediating heavy metal-polluted soils. In this pot experiment, the influence of root endophyte fungus Piriformospora indica on growth, physiological parameters and organs Cd accumulation in sunflower cv. Zaria plants under the toxic levels of Cd (0, 40, 80 and 120mg/kg soil) were studied. Increasing Cd concentration in the soil reduced growth parameters, chlorophyll (Chl) a and Chl b contents, and Fv/Fm and ETR (electron transport rate) values, but increased root, stem and leaf Cd accumulation, and proline content. The presence of P. indica significantly enhanced growth, Chl a, Chl b and proline contents, and Fv/Fm and ETR values. Compared to non-inoculated ones, P. indica-inoculated plants had higher Cd accumulation in root, whereas lower Cd accumulation in stem and leaf. The present study strongly supports the established ability of P. indica to alleviate Cd toxicity by improving the physiological status in sunflower. Furthermore, this endophyte fungus can be useful for Cd phyto-stabilization in sunflower roots in contaminated soils.

Phenotyping Sunflower Genetic Resources for Sclerotinia Head Rot Response: Assessing Variability for Disease Resistance Breeding

Sclerotinia head rot (SHR) is one of the most serious constraints to sunflower (Helianthus annuus L. var. macrocarpus) production worldwide. Here, we evaluated the response to SHR in a sunflower inbred panel from a large INTA germplasm collection, consisting of 137 inbred lines (ILs). Field trials were performed over five consecutive seasons using a twice-replicated randomized complete-block design. Disease incidence, disease severity, incubation period, and area under disease progress curve for disease incidence and severity were determined after controlled inoculation with the pathogen. Statistical analysis using mixed-effect models detected significant differences among ILs for all variables (P < 0.001). In addition, principal component analysis (PCA) and distance-based methods were used to classify the ILs according to their response to SHR, with ILs ALB2/5261 and 5383 emerging as the most resistant. Broad-sense heritability estimates ranged from 20.64% for disease severity to 10.58% for incubation period. The ample phenotypic variability of our collection, along with the moderate heritability estimates, highlight the importance of molecular breeding approaches to gain new insights into the genetic basis of sunflower resistance to SHR. The exhaustive phenotypic characterization presented here provides a reliable set of variables to comprehensively evaluate the disease and identifies two new sources of resistance to SHR.