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Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and fungal communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and fungal communities. We also assessed fungal communities in the sunflower seeds to investigate the degree to which root and rhizosphere communities were influenced by vertical transmission of the microbiome through seeds. Neither root nor rhizosphere bacterial communities were affected by the extent of sunflower domestication, but domestication did affect the composition of rhizosphere fungal communities. In particular, more modern sunflower strains had lower relative abundances of putative fungal pathogens. Seed-associated fungal communities strongly differed across strains, but several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants. Our results indicate that plant-associated fungal communities are more strongly influenced by host genetic factors and plant breeding than bacterial communities, a finding that could influence strategies for optimizing microbial communities to improve crop yields.

Rhizobacteria are well recognized for their beneficial multifunctions as key promoters of plant development, suppressing pathogens, and improving soil health. In this study, experiments focused on characterizing the plant growth promotion (PGP) and extracellular hydrolase production traits of rhizobacteria, and their impact on Jerusalem artichoke growth. A total of 50 isolates proved capable of either direct PGP or hydrolase-producing traits. Two promising strains ( Enterobacter cloacae S81 and Pseudomonas azotoformans C2-114) showed potential on phosphate and potassium solubilization, IAA production, and 1-aminocyclopropane-1-carboxylic acid deaminase activity and hydrolase production. A hydrolase-producing strain ( Bacillus subtilis S42) was able to generate cellulase, protease, amylase, β-glucosidase, and phosphatase. These three selected strains also gave positive results for indirect PGP traits such as siderophore, ammonia, oxalate oxidase, polyamine, exopolysaccharide, biofilm, motility, and tolerance to salinity and drought stress. Colonization was observed using a scanning electron microscope and rhizobacteria appeared at the root surface. Interestingly, inoculation with consortia strains (S42, S81, and C2-114) significantly increased all plant parameters, including height, biomass, root (length, surface, diameter, and volume), and tuber fresh weight. Therefore, we recommend that potential consortia of PGP and hydrolase-producing rhizobacteria be employed as a biofertilizer to improve soil and boost crop productivity.

Sunflower is one of the four major oil crops in the world. ‘Zaoaidatou’ (ZADT), the main variety of oil sunflower in the northwest of China, has a short growth cycle, high yield, and high resistance to abiotic stress. However, the ability to tolerate adervesity is limited. Therefore, in this study, we used the retention line of backbone parent ZADT as material to establish its tissue culture and genetic transformation system for new variety cultivating to enhance resistance and yields by molecular breeding. The combination of 0.05 mg/L IAA and 2 mg/L KT in MS was more suitable for direct induction of adventitious buds with cotyledon nodes and the addition of 0.9 mg/L IBA to MS was for adventitious rooting. On this basis, an efficient Agrobacterium tumefaciens -mediated genetic transformation system for ZADT was developed by the screening of kanamycin and optimization of transformation conditions. The rate of positive seedlings reached 8.0%, as determined by polymerase chain reaction (PCR), under the condition of 45 mg/L kanamycin, bacterial density of OD 600 0.8, infection time of 30 min, and co-cultivation of three days. These efficient regeneration and genetic transformation platforms are very useful for accelerating the molecular breeding process on sunflower.

Sunflower rust, caused by the fungus Puccinia helianthi, poses a significant threat to global sunflower production. However, the fundamental mechanisms of P. helianthi infection and development remain poorly understood. This study aims to elucidate the infection process of P. helianthi in sunflower leaves through histological and cytological observations. P. helianthi is an autoecious fungus that undergoes five spore stages: teliospores, basidiospores, pycniospores, aeciospores, and urediospores. Our findings revealed that basidiospores germinated by producing a germ tube at 24 hours post-inoculation (hpi). This germ tube entered the leaf through the stomata or directly penetrated the epidermal cells without forming an appressorium, resulting in the formation of monokaryotic intercellular hyphae. The hyphae grew along the cell wall, which thickened when the hyphae came in touch with the mesophyll cells. The monokaryotic haustorium formed within the host cells at 48 hpi. Chlorotic dots began to appear on the upper surface of the leaves five to six days after the basidiospores were inoculated. After 14 days post-inoculation (dpi), flask-shaped orange pycnia developed. By approximately 18 d, honeydew started appearing on the pycnia. Aecia began to develop six or seven days after fertilization; they were cylinder-shaped and adorned with coglike ornaments. Aeciospores and urediospores germinated by producing a germ tube at 4 hpi, which subsequently developed a dome-shaped appressorium that penetrated the sunflower leaves through the stomata at 6 hpi. Intercellular hyphae produced septa apically and further differentiated into haustorial mother cells, which invaded the host cell and formed multinucleate haustoria at 24 hpi, with all the cytoplasm from the haustorial mother cells flowing into the haustorium. Aeciospores with warty surfaces invaded the host and produced oval-shaped urediospores at 14 dpi, which exhibited dense, thorny protrusions on their surfaces. By regulating the temperature, the urediospore-infected leaves were induced to produce teliospores after 20 days, which consisted of two cells with smooth surfaces.

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.

Sclerotinia sclerotiorum as a necrotrophic fungus causes the devastating diseases in many important oilseed crops worldwide. The preferred strategy for controlling S . sclerotiorum is to develop resistant varieties, but the molecular mechanisms underlying S . sclerotiorum resistance remain poorly defined in sunflower ( Helianthus annuus ). Here, a comparative transcriptomic analysis was performed in leaves of two contrasting sunflower genotypes, disease susceptible (DS) B728 and disease resistant (DR) C6 after S . sclerotiorum inoculation. At 24 h post-inoculation, the DR genotype exhibited no visible growth of the hyphae as well as greater activity of superoxide dismutase activity (SOD), peroxidase (POD), catalase (CAT), glutathione-S-transferase (GST), ascorbate peroxidase (APX) and monodehydroascorbate reductase (MDAR) than DS genotype. A total of 10151 and 7439 differentially expressed genes (DEGs) were detected in DS and DR genotypes, respectively. Most of DEGs were enriched in cell wall organisation, protein kinase activity, hormone, transcription factor activities, redox homeostasis, immune response, and secondary metabolism. Differential expression of genes involved in expansins, pectate lyase activities, ethylene biosynthesis and signaling and antioxidant activity after S . sclerotiorum infection could potentially be responsible for the differential resistance among two genotypes. In summary, these finding provide additional insights into the potential molecular mechanisms of S . sclerotiorum ’s defense response and facilitate the breeding of Sclerotinia -resistant sunflower varieties.

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.

The interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0–20 cm soil layer vertically and 0–30 cm horizontally from the plant centre. Root concentrations of K + , Na + , Mg 2+ and particularly Ca 2+ were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0–5 cm and 5–10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities.

Background Sunflower Verticillium wilt (SVW) is a vascular disease caused by root infection with Verticillium dahliae (V. dahlia) . It is a serious threat to the yield and quality of sunflower. However, chemical and agronomic measures for controlling this disease are not effective. The selection of more resistant genotypes is a desirable strategy to reduce contamination. A deeper knowledge of the molecular mechanisms and genetic basis underlying sunflower Verticillium wilt is necessary to accelerate breeding progress. Results An RNA-Seq approach was used to perform global transcriptome profiling on the roots of resistant (S18) and susceptible (P77) sunflower genotypes infected with V. dahlia . Different pairwise transcriptome comparisons were examined over a time course (6, 12 and 24 h, and 2, 3, 5 and 10 d post inoculation). In RD, SD and D datasets, 1231 genes were associated with SVW resistance in a genotype-common transcriptional pattern. Moreover, 759 and 511 genes were directly related to SVW resistance in the resistant and susceptible genotypes, respectively, in a genotype-specific transcriptional pattern. Most of the genes were demonstrated to participate in plant defense responses; these genes included peroxidase (POD), glutathione peroxidase, aquaporin PIP, chitinase, L-ascorbate oxidase, and LRR receptors. For the up-regulated genotype-specific differentially expressed genes (DEGs) in the resistant genotype, higher average fold-changes were observed in the resistant genotype compared to those in the susceptible genotype. An inverse effect was observed in the down-regulated genotype-specific DEGs in the resistant genotype. KEGG analyses showed that 98, 112 and 52 genes were classified into plant hormone signal transduction, plant-pathogen interaction and flavonoid biosynthesis categories, respectively. Many of these genes, such as CNGC, RBOH, FLS2, JAZ, MYC2 NPR1 and TGA, regulate crucial points in defense-related pathway and may contribute to V. dahliae resistance in sunflower. Conclusions The transcriptome profiling results provided a clearer understanding of the transcripts associated with the crosstalk between sunflower and V. dahliae . The results identified several differentially expressed unigenes involved in the hyper sensitive response (HR) and the salicylic acid (SA)/jasmonic acid (JA)-mediated signal transduction pathway for resistance against V. dahliae . These results are useful for screening resistant sunflower genotypes.

The degradable film can solve the problem that the traditional plastic film is difficult to recycle and heavy pollution for a long time. The effects of degraded film mulching on microbial diversity are significant. However, the responses of relevant microbial communities to degraded film mulching in different ecological niches (e.g., bulk soil, rhizosphere and endosphere) of sunflower roots are poorly understood. This study analyzed the effects of plastics film mulching on bacterial and fungal α-diversities (Shannon index), community assembly process, key dominant species of sunflower different ecological niches in roots. The results showed that degradable film mulching significantly increased the α-diversity (Shannon index) of bulk soil and rhizosphere soil bacteria and decreased the α-diversity of fungi (Shannon index), and the mulching treatment promoted the gradual shift of the rhizosphere microbial community assembly process to a deterministic process. Degradation film mulching increased the connectivity and complexity of bacterial networks and decreased the complexity of fungal networks. Plastic film mulching improves soil nutrients, temperature and moisture, enhances the positive correlation among microorganisms. At the same time, core species such as Amycolatopsis , Rhizobiaceae , and Sphingomonas that recruit beneficial microorganisms and accelerate the degradation of plastic film are significantly enriched. Degradable film covering promoted soil nutrient cycling, increased urease, alkaline phosphatase, sucrase, and thus increased sunflower yield. A comprehensive analysis of random forest and structural equations showed that the main driving microbial factors of yield were bulk soil bacterial diversity and endosphere fungal diversity. This study provides new ideas for the analysis of soil microbial mutual feedback mechanisms between degraded film mulch and rhizosphere ecosystems.