First Report of Athelia rolfsii Causing Stem Rot on Sunflower (Helianthus annuus L.) in Sichuan, China

Sunflower (Helianthus annuus L.) is a major oilseed crop in the world, but recently it has become a popular ornamental flower in China (Kaya ET AL., 2012). Notably, stem rot was frequently observed on 30-day-old sunflower plants in Sichuan Province, P. R. China. In May 2021, 207 plants with stem rot and premature death were found among the investigated 1732 plants, with 11.95% incidence rate. Stem rot were mainly observed on the base stem of plants. Infected stems developed brown lesions that became slightly sunken and covered with white mycelial mats. With disease progress, the affected plants eventually wilted at early stage (Fig. 1A). For pathogen isolation, mycelia were harvested directly from diseased tissue and cultured on potato dextrose agar (PDA) at 25±2℃ in incubator without light. Eighteen fungal isolates with similar colony morphology were consistently isolated by purifying from different sampling areas. These isolates would form radial colonies with white aerial mycelia possessing branches and septa, and some could form clamp connection structure on PDA. Their average growth rate was 27.6 ± 0.09 mm per day (Fig. 1B & C). White granular sclerotia were abundantly produced on 6-day-old colonies. The sclerotia with a diameter of 1.18 ± 0.26 mm (n=348) gradually changed from white to light yellow and finally to brown with age (Fig. 1B). A representative isolate NCSF5.20-8 was identified accurately by multi-locus approach, and its genomic DNA was extracted for amplifying and sequencing the fragments of ITS, 18 S and TEF1-α according to previous description (Zhong et al., 2021). The nucleotide BLAST search of these sequences was nearly 100% identical to Athelia rolfsii (the teleomorph of Sclerotium rolfsii Sacc.) with accession number MN258360.1 (499/499 bp, 100%), AY665774.1 (1428/1428 bp, 100%), and JF267794.1 (489/490, 99%), respectively. The obtained sequences were deposited in GenBank with accession number OK635580.1, OM319631.1 and OK665849.1. Phylogenetic analysis based on simultaneously available ITS, 18S and TEF1-α sequences of Athelia genus indicated that NCSF5.20-8 could be clustered into the A. rolfsii clade with a support value of 100% (Fig. 2). Combining the above morphological characteristics and molecular identification, the isolate NCSF5.20-8 was finally confirmed as the identity of A. rolfsii (Mordue 1974; Zhong et al., 2021). In order to fulfil Koch's postulates and prove the pathogenicity of NCSF5.20-8 to sunflower, mycelial plugs were leaned on the base stem of healthy sunflower plants (cv. Guangwu muntain) with 45-day-old, while plants with same growth treated by PDA plug free of mycelium were used as control. All the inoculated plants were kept in a greenhouse at 25±2°C with 14 h photoperiod and 80% relative humidity. The experiments were conducted for triple biological repeats. Two days after inoculation, all the plants inoculated with NCSF5.20-8 had typical symptoms of stem rot, whereas, the control plants remained asymptomatic (Fig. 1D). Using above mentioned protocol, A. rolfsii was re-isolated only from the symptomatic stem of inoculated plants. To our knowledge, stem rot caused by A. rolfsii on sunflower has been reported in Italy and Turkey (Infantino et al., 1997; Cer & Morca, 2020), but it is the first report in China. For this pathogen has a wide host range with serious destructiveness (Punja, 1985), our research is beneficial to develop strategies to mitigate future losses of sunflower in China.

Biological and Transcriptomic Characterization of Pre-Haustorial Resistance to Sunflower Broomrape (Orobanche cumana W.) in Sunflowers (Helianthus annuus)

Infestations with sunflower broomrape (Orobanche cumana Wallr.), an obligatory root parasite, constitute a major limitation to sunflower production in many regions around the world. Breeding for resistance is the most effective approach to reduce sunflower broomrape infestation, yet resistance mechanisms are often broken by new races of the pathogen. Elucidating the mechanisms controlling resistance to broomrape at the molecular level is, thus, a desirable way to obtain long-lasting resistance. In this study, we investigated broomrape resistance in a confectionery sunflower cultivar with a robust and long-lasting resistance to sunflower broomrape. Visual screening and histological examination of sunflower roots revealed that penetration of the broomrape haustorium into the sunflower roots was blocked at the cortex, indicating a pre-haustorial mechanism of resistance. A comparative RNA sequencing between broomrape-resistant and -susceptible accessions allowed the identification of genes that were significantly differentially expressed upon broomrape infestation. Among these genes were β-1,3-endoglucanase, β-glucanase, and ethylene-responsive transcription factor 4 (ERF4). These genes were previously reported to be pathogenesis-related in other plant species. This transcriptomic investigation, together with the histological examinations, led us to conclude that the resistance mechanism involves the identification of the broomrape and the consequent formation of a physical barrier that prevents the establishment of the broomrape into the sunflower roots.

Genetic and phenotypic analyses indicate that resistance to flooding stress is uncoupled from performance in cultivated sunflower

Given the rising risk of extreme weather caused by climate change, enhancement of abiotic stress resistance in crops is increasingly urgent. But will the development of stress-resistant cultivars come at the cost of yield under ideal conditions? We hypothesize that this need not be inevitable, because resistance alleles with minimal pleiotropic costs may evade artificial selection and be retained in crop germplasm. Genome-wide association (GWA) analyses for variation in plant performance and flooding response were conducted in cultivated sunflower, a globally important oilseed. We observed broad variation in flooding responses among genotypes. Flooding resistance was not strongly correlated with performance in control conditions, suggesting no inherent trade-offs. Consistent with this finding, we identified a subset of loci conferring flooding resistance, but lacking antagonistic effects on growth. Genetic diversity loss at candidate genes underlying these loci was significantly less than for other resistance genes during cultivated sunflower evolution. Despite bottlenecks associated with domestication and improvement, low-cost resistance alleles remain within the cultivated sunflower gene pool. Thus, development of cultivars that are both flooding-tolerant and highly productive should be straightforward. Results further indicate that estimates of pleiotropic costs from GWA analyses explain, in part, patterns of diversity loss in crop genomes.

Development and Validation of Markers for the Fertility Restorer Gene Rf1 in Sunflower

Hybrid breeding in sunflowers based on CMS PET1 requires development of restorer lines carrying, in most cases, the restorer gene Rf1. Markers for marker-assisted selection have been developed, but there is still need for closer, more versatile, and co-dominant markers linked to Rf1. Homology searches against the reference sunflower genome using sequences of cloned markers, as well as Bacterial Artificial Chromosome (BAC)-end sequences of clones hybridizing to them, allowed the identification of two genomic regions of 30 and 3.9 Mb, respectively, as possible physical locations of the restorer gene Rf1 on linkage group 13. Nine potential candidate genes, encoding six pentatricopeptide repeat proteins, one tetratricopeptide-like helical domain, a probable aldehyde dehydrogenase 22A1, and a probable poly(A) polymerase 3 (PAPS3), were identified in these two genomic regions. Amplicon targeted next generation sequencing of these nine candidate genes for Rf1 was performed in an association panel consisting of 27 maintainer and 32 restorer lines and revealed the presence of 210 Single Nucleotide Polymorphisms (SNPs) and 67 Insertions/Deletions (INDELs). Association studies showed significant associations of 10 SNPs with fertility restoration (p-value < 10⁻⁴), narrowing Rf1 down to three candidate genes. Three new markers, one co-dominant marker 67N04_P and two dominant markers, PPR621.5R for restorer, and PPR621.5M for maintainer lines were developed and verified in the association panel of 59 sunflower lines. The versatility of the three newly developed markers, as well as of three existing markers for the restorer gene Rf1 (HRG01 and HRG02, Cleaved Amplified Polymorphic Sequence (CAPS)-marker H13), was analyzed in a large association panel consisting of 557 accessions.

Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat

The kinetochore is a protein complex including kinetochore-specific proteins that plays a role in chromatid segregation during mitosis and meiosis. The complex associates with centromeric DNA sequences that are usually species-specific. In plant species, tandem repeats including satellite DNA sequences and retrotransposons have been reported as centromeric DNA sequences. In this study on sunflowers, a cDNA-encoding centromere-specific histone H3 (CENH3) was isolated from a cDNA pool from a seedling, and an antibody was raised against a peptide synthesized from the deduced cDNA. The antibody specifically recognized the sunflower CENH3 (HaCENH3) and showed centromeric signals by immunostaining and immunohistochemical staining analysis. The antibody was also applied in chromatin immunoprecipitation (ChIP)-Seq to isolate centromeric DNA sequences and two different types of repetitive DNA sequences were identified. One was a long interspersed nuclear element (LINE)-like sequence, which showed centromere-specific signals on almost all chromosomes in sunflowers. This is the first report of a centromeric LINE sequence, suggesting possible centromere targeting ability. Another type of identified repetitive DNA was a tandem repeat sequence with a 187-bp unit that was found only on a pair of chromosomes. The HaCENH3 content of the tandem repeats was estimated to be much higher than that of the LINE, which implies centromere evolution from LINE-based centromeres to more stable tandem-repeat-based centromeres. In addition, the epigenetic status of the sunflower centromeres was investigated by immunohistochemical staining and ChIP, and it was found that centromeres were heterochromatic.

Quantifying temporal isolation: a modelling approach assessing the effect of flowering time differences on crop-to-weed pollen flow in sunflower

Flowering time divergence can be a crucial component of reproductive isolation between sympatric populations, but few studies have quantified its actual contribution to the reduction of gene flow. In this study, we aimed at estimating pollen-mediated gene flow between cultivated sunflower and a weedy conspecific sunflower population growing in the same field and at quantifying, how it is affected by the weeds' flowering time. For that purpose, we extended an existing mating model by including a temporal distance (i.e. flowering time difference between potential parents) effect on mating probabilities. Using phenological and genotypic data gathered on the crop and on a sample of the weedy population and its offspring, we estimated an average hybridization rate of approximately 10%. This rate varied strongly from 30% on average for weeds flowering at the crop flowering peak to 0% when the crop finished flowering and was affected by the local density of weeds. Our result also suggested the occurrence of other factors limiting crop-to-weed gene flow. This level of gene flow and its dependence on flowering time might influence the evolutionary fate of weedy sunflower populations sympatric to their crop relative.

Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus

Biotic and abiotic stresses affect plant development and production through alternation of the gene expression pattern. Gene expression itself is under the control of different regulators such as miRNAs and transcription factors (TFs). MiRNAs are known to play important roles in regulation of stress responses via interacting with their target mRNAs. Here, for the first time, seven conserved miRNAs, associated with drought, heat, salt and cadmium stresses were characterized in sunflower. The expression profiles of miRNAs and their targets were comparatively analyzed between leaves and roots of plants grown under the mentioned stress conditions. Gene ontology analysis of target genes revealed that they are involved in several important pathways such as auxin and ethylene signaling, RNA mediated silencing and DNA methylation processes. Gene regulatory network highlighted the existence of cross-talks between these stress-responsive miRNAs and the other stress responsive genes in sunflower. Based on network analysis, we suggest that some of these miRNAs in sunflower such as miR172 and miR403 may play critical roles in epigenetic responses to stress. It seems that depending on the stress type, theses miRNAs target several pathways and cellular processes to help sunflower to cope with drought, heat, salt and cadmium stress conditions in a tissue-associated manner.

Translatome profiling in dormant and nondormant sunflower (Helianthus annuus) seeds highlights post-transcriptional regulation of germination

Seed dormancy, which blocks germination in apparently favourable conditions, is a key regulatory control point of plant population establishment. As germination requires de novo translation, its regulation by dormancy is likely to be related to the association of individual transcripts to polysomes. Here, the polysome-associated mRNAs, that is, the translatome, were fractionated and characterized with microarrays in dormant and nondormant sunflower (Helianthus annuus) embryos during their imbibition at 10°C, a temperature preventing germination of dormant embryos. Profiling of mRNAs in polysomal complexes revealed that the translatome differs between germinating and nongerminating embryos. Association of transcripts with polysomes reached a maximum after 15 h of imbibition; at this time-point 194 polysome-associated transcripts were specifically found in nondormant embryos and 47 in dormant embryos only. The proteins corresponding to the polysomal mRNAs in nondormant embryos appeared to be very pertinent for germination and were involved mainly in transport, regulation of transcription or cell wall modifications. This work demonstrates that seed germination results from a timely regulated and selective recruitment of mRNAs to polysomes, thus opening novel fields of investigation for the understanding of this developmental process.

Early plant growth: identifying the end point of the seedling phase

•  Despite the importance of seedling establishment in plant biology, there is no consensus on what constitutes a 'seedling'. Here we examined aspects of early plant development that could be used to mark the transition from the seedling to the postseedling phase. •  Using a hypogeal species (pea, Pisum sativum) and an epigeal species (sunflower, Helianthus annuus), we investigated whether the utilization of cotyledon-stored mineral nutrients coincides with any changes in relative growth rate (RGR). We also examined how the timing of cotyledon removal at different points during early development affected subsequent growth. •  For both species, the timing of RGR_max , the exhaustion of cotyledon reserves, and the attainment of independence from cotyledons all roughly coincided (though exhaustion of seed reserves was not observed in the epigeal species because the cotyledons absorbed external nutrients). •  We conclude that because the point of attainment of RGR_max is a distinctly identifiable event, it is a more reliable marker for defining the end of the seedling stage than either the exhaustion of mineral reserves, or the cessation of dependence on cotyledon reserves.