Combined Omics Approaches Reveal Distinct Mechanisms of Resistance and/or Susceptibility in Sugar Beet Double Haploid Genotypes at Early Stages of Beet Curly Top Virus Infection

Sugar beet is highly susceptible to Beet curly top virus (BCTV) which significantly reduces yield and sugar production in the semi-arid growing regions worldwide. Sources of genetic resistance to BCTV is highly limited and primarily dependent upon seed treatment with neonicotinoids, the use of which is gradually being restricted. Through double haploid production and genetic selection, we have developed BCTV resistant breeding lines. Using BCTV resistant (R) [KDH13; Line 13, and KDH4-9; Line 4] and susceptible (S) [KDH19-17; Line 19] lines, beet leafhopper meditated natural infection, mRNA/sRNA sequencing, and metabolite analyses we demonstrate potential mechanisms of resistance against the virus. At early infection stages (2- and 6-days post inoculation), examples of differentially expressed genes highly up-regulated in the ‘R’ lines (vs. ‘S’) include EL10Ac5g10437 (inhibitor of trypsin and hageman factor), EL10Ac6g14635 (jasmonate induced protein), EL10Ac3g06016 (ribosome related), EL10Ac2g03119 (unknown) etc. Pathway enrichment analysis showed differentially expressed genes predominantly involved with peroxisome, amino acids metabolism, fatty acid degradation, amino/nucleotide sugar metabolism etc. Metabolite analysis revealed significantly higher amounts of isoflavonoid O-glycosides, flavonoid 8-C glycosides, triterpenoid, iridoid-O-glycosides in the leaves of the ‘R’ lines (vs. ‘S’). The data presented here suggest a combination of transcriptional regulation and production of antiviral metabolites might contribute to BCTV resistance. In addition, genome divergence among BCTV strains differentially affects the production of small non-coding RNAs (sncRNAs) and small peptides which may potentially affect pathogenicity and disease symptom development

Cell wall degrading enzymes originating from rhizoctonia solani increase sugar beet root damage in the presence of leuconostoc mesenteroides

Sugar beet crown and root rot caused by Rhizoctonia solani is a major yield constraint. Root rot is highly increased when R. solani and Leuconostoc mesenteroides co-infect roots. We hypothesized that the absence of plant cell wall degrading enzymes in L. mesenteroides and their supply by R. solani during close contact, causes increased damage. In planta root inoculation with or without cell wall degrading enzymes showed greater rot when L. mesenteroides was combined with cellulase (49 mm rot), polygalacturonase (48 mm), and pectin lyase (35 mm) versus these enzymes (0–11 mm), R. solani (13 mm), and L. mesenteroides (22 mm) individually. Carbohydrate analysis revealed increase in simpler carbohydrates namely glucose + galactose, and fructose in the infected roots versus mock control, possibly due to the degradation of complex cell wall carbohydrates. Expression of R. solani cellulase, polygalacturonase, and pectin lyase genes during root infection corroborated well with the enzyme data. Global mRNAseq analysis identified candidate genes and highly co-expressed gene clusters (in all 3 organisms) that might be critical in host plant defense and pathogenesis. Future targeting of R. solani cell wall degrading enzymes could be an effective strategy to mitigate root damage during interaction with L. mesenteroides

Leaf bacteriome in sugar beet show differential response against beet curly top virus during resistant and susceptible interactions

Beet curly top virus (BCTV) is an important sugar beet yield limiting disease in semi-arid production areas. Genetic resistance to BCTV is limited; therefore, identification of additional resistance associated factors is highly desired. Using 16S rRNA sequencing and BCTV resistant (R) genotypes (KDH13, KDH4-9) along with a susceptible (S) genotype (KDH19-17), we investigated leaf bacteriome changes during BCTV post inoculation (pi). At day 6 (~6 week-old plants), Cyanobacteria were predominant (~90%), whereas at week 4 (~10 week-old plants) Firmicutes (11-66%), Bacteroidetes (17-26%), and Verrucomicrobia (12-29%) were predominant and genotype dependent. Both Bacteroidetes and Verrucomicrobia, increased post infection only in the R lines. Brevibacillus increased at 6 dpi, and Akkermansia and Bacteroides at 4 wkpi in the R lines. Linear discriminant analysis Effect Size identified potential biomarkers in the R lines vs. S line. Functional profiling revealed bacterial enrichment associated with TCA cycle, polyisoprenoid, and L-methione biosynthesis pathways only in KDH4-9 at 6 dpi. At 4 wkpi, bacteria associated with tryptophan and palmitate biosynthesis in the R lines and uridine monophosphate, phosphatidyl glycerol, and phospholipid biosynthesis in the S line, were enriched. Future characterization of bacterial genera with antiviral properties will help establish their use as biocontrol agents/biomarkers against BCTV

Regulatory roles of small non-coding RNAs in sugar beet resistance against beet curly top virus

Beet curly top virus (BCTV) mediated yield loss in sugar beets is a major problem worldwide. The circular single-stranded DNA virus is transmitted by the beet leafhopper. Genetic sources of BCTV resistance in sugar beet are limited and commercial cultivars rely on chemical treatments versus durable genetic resistance. Phenotypic selection and double haploid production have resulted in sugar beet germplasm (KDH13-13 and KDH4-9-4) that are highly resistant to BCTV. The molecular mechanism of resistance to the virus is unknown, especially the role of small noncoding RNAs (sncRNAs) during early plant-viral interaction. Using the resistant lines along with a susceptible line (KDH19-17; 19), we demonstrate the role of sugar beet miRNAs in BCTV resistance during early infection stages when symptoms are not yet visible. The differentially expressed miRNAs altered the expression of their corresponding target genes such as pyruvate dehydrogenase (EL10Ac1g02046), carboxylesterase (EL10Ac1g01087), serine/threonine protein phosphatase (EL10Ac1g01374), and LRR receptor-like (EL10Ac7g17778), that were highly expressed in the resistant lines versus susceptible lines. Pathway enrichment analysis of the miRNA target genes showed an enrichment of genes involved in glycolysis/gluconeogenesis, galactose metabolism, starch, and sucrose metabolism to name a few. Carbohydrate analysis revealed altered glucose, galactose, fructose, and sucrose concentration in the infected leaves of resistant versus susceptible lines. We also demonstrate differential regulation of BCTV derived sncRNAs in the resistant versus susceptible lines that target sugar beet genes such as LRR (EL10Ac1g01206), 7-deoxyloganetic acid glucosyltransferase (EL10Ac5g12605), and transmembrane emp24 domain containing (EL10Ac6g14074) and altered their expression. In response to viral infection, we found that plant derived miRNAs targeted BCTV capsid protein/replication related genes and showed differences in expression among resistant and susceptible lines. The data presented here demonstrate the contribution of miRNA mediated regulation of metabolic pathways and cross-kingdom RNAi in sugar beet BCTV resistance

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

A contiguous assembly of the inbred ‘EL10’ sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation

Video-Game Play Induces Plasticity in the Visual System of Adults with Amblyopia

A pilot study suggests that playing video games may enhance a range of spatial vision functions in adults with amblyopia

The future for Mediterranean wetlands: 50 key issues and 50 important conservation research questions

Wetlands are critically important for biodiversity and human wellbeing, but face a range of challenges. This is especially true in the Mediterranean region, where wetlands support endemic and threatened species and remain integral to human societies, but have been severely degraded in recent decades. Here, in order to raise awareness of future challenges and opportunities for Mediterranean wetlands, and to inform proactive research and management, we identified (a) 50 key issues that might affect Mediterranean wetlands between 2020 and 2050, and (b) 50 important research questions that, if answered, would have the greatest impact on the conservation of Mediterranean wetlands between 2020 and 2050. We gathered ideas through an online survey and review of recent literature. A diverse assessment panel prioritised ideas through an iterative, anonymised, Delphi-like process of scoring, voting and discussion. The prioritised issues included some that are already well known but likely to have a large impact on Mediterranean wetlands in the next 30 years (e.g. the accumulation of dams and reservoirs, plastic pollution and weak governance), and some that are currently overlooked in the context of Mediterranean wetlands (e.g. increasing desalination capacity and development of antimicrobial resistance). Questions largely focused on how best to carry out conservation interventions, or understanding the impacts of threats to inform conservation decision-making. This analysis will support research, policy and practice related to environmental conservation and sustainable development in the Mediterranean, and provides a model for similar analyses elsewhere in the world