First Report of Bacterial Wilt Disease Caused by Ralstonia solanacearum on Southern Highbush Blueberries (Vaccinium corymbosum interspecific hybrids) in Georgia U.S.A.

Members of the Ralstonia solanacearum (Rs) species complex have recently been reported to cause bacterial wilt on southern highbush (SHB) blueberries in Florida (Norman et al. 2018), a disease first reported on blueberry (northern highbush; Vaccinium corymbosum) in New Jersey (Patel et al. 2013). SHB blueberries are widely grown in the southern United States, and SHB cultivars represent the majority of the blueberry acreage in Georgia - the U.S. state with the largest blueberry acreage (NASS 2022). In Fall 2020, three-year old SHB plants (cv. 'Indigocrisp') showing leaf bronzing, wilting, and dieback were collected from two field sites in Clinch County, GA. At these locations, numerous plants were rapidly dying, with symptoms appearing to have spread down rows. Plant material tested positive using the ImmunoStrip® for Rs (Agdia, Inc., Elkhart, IN). From one location, the remaining sample was submitted to USDA-APHIS Select Agent Services who determined that Rs was present but a select agent (Rs Race 3, Biovar 2) was not. Following this, six adjacent, symptomatic SHB plants were collected from the same field location. These plants tested positive using the ImmunoStrip® for Rs, and red-pigmented mucoid colonies typical of Rs formed within 48 h at 28°C on triphenyltetrazolium chloroide (TZC) isolation medium (Kelman 1954). DNA was extracted from pure Rs cultures using the cetyltrimethylammonium bromide (CTAB) method (Doyle and Doyle 1987) and tested using polymerase chain reaction (PCR). Primers pairs AMB013/AMB014 (Fegan and Prior 2005) and ENDO-F/ENDO-R (Ji et al. 2007) were used to amplify 558 nt and 843 nt portions of the 16S rRNA region and Rs endoglucanase gene, respectively. Resulting amplicons were purified using an E.Z.N.A.® Cycle Pure Kit (Omega Bio-Tek, Norcross, GA), Sanger sequenced in both directions (Eurofins Genomics, Louisville, KY), and compared to publicly available Rs sequences in Genbank. The 16 rRNA sequence from all obtained isolates (accession ON938207) had 100% identity to Rs strain CFBP2957 (FP885897), while the endoglucase sequence (ON938206) had 100% identity to phylotype IIa, sequevar 5 Rs strain CIP-426 (MF461810) and phylotype IIa, sequevar 39 Rs strain 19-058 (MT314067), among others. To fulfill Koch's postulates, an isolate ('Ral21-1') was grown on TZC medium for 48 h at 28°C and suspended in 8.5 g/L NaCl at 1 x 108 CFU/ml. Five young, tissue cultured SHB plants (cv. 'Kestrel') in 25 cm pots were drenched with 50 ml of Rs suspension. For six weeks, plants were maintained in the greenhouse at 21-32°C. Typical bacterial wilt symptoms (leaf bronzing/scorching) developed in all inoculated plants, and infections were confirmed using Immunostrip®. Rs was reisolated and confirmed via PCR and sequencing as previously described. While Ralstonia has been known to cause disease on numerous crops in Georgia, this represents a first report of bacterial wilt in Georgia blueberries. Relative to rabbiteye blueberries (V. virgatum), recent reports suggest that SHB are much more susceptible to bacterial wilt (Conner et al. 2022). Accordingly, given the transition from rabbiteye to SHB within Georgia's blueberry production region over the past two decades and the ability of Rs to spread easily in water, soil, or via infected plant material, the presence of this disease within the state represents a significant threat to blueberry production. Additional characterization of Ralstonia isolates from Georgia may help assess the risk of future outbreaks.

Identification of genes differentially expressed during early interactions between the stem rot fungus (Sclerotium rolfsii) and peanut (Arachis hypogaea) cultivars with increasing disease resistance levels.

Sclerotium rolfsii, a destructive soil-borne fungal pathogen causes stem rot of the cultivated peanut, Arachis hypogaea. This study aimed to identify differentially expressed genes associated with peanut resistance and fungal virulence. Four peanut cultivars (A100-32, Georgia Green, GA-07W and York) with increasing resistance levels were inoculated with a virulent S. rolfsii strain to study the early plant-pathogen interaction. 454 sequencing was performed on RNAs from infected tissue collected at 4 days post inoculation, generating 225,793 high-quality reads. Normalized read counts and fold changes were calculated and statistical analysis used to identify differentially expressed genes. Several genes identified as differential in the RNA-seq experiment were selected based on functions of interest and real-time PCR employed to corroborate their differential expression. Expanding the analysis to include all four cultivars revealed a small but interesting set of genes showing colinearity between cultivar resistance and expression levels. This study identified a set of genes possibly related to pathogen response that may be useful marker assisted selection or transgenic disease control strategies. Additionally, a set of differentially expressed genes that have not been functionally characterized in peanut or other plants and warrant additional investigation were identified.

High-throughput discovery of mutations in tef semi-dwarfing genes by next-generation sequencing analysis.

Tef (Eragrostis tef) is a major cereal crop in Ethiopia. Lodging is the primary constraint to increasing productivity in this allotetraploid species, accounting for losses of ∼15-45% in yield each year. As a first step toward identifying semi-dwarf varieties that might have improved lodging resistance, an ∼6× fosmid library was constructed and used to identify both homeologues of the dw3 semi-dwarfing gene of Sorghum bicolor. An EMS mutagenized population, consisting of ∼21,210 tef plants, was planted and leaf materials were collected into 23 superpools. Two dwarfing candidate genes, homeologues of dw3 of sorghum and rht1 of wheat, were sequenced directly from each superpool with 454 technology, and 120 candidate mutations were identified. Out of 10 candidates tested, six independent mutations were validated by Sanger sequencing, including two predicted detrimental mutations in both dw3 homeologues with a potential to improve lodging resistance in tef through further breeding. This study demonstrates that high-throughput sequencing can identify potentially valuable mutations in under-studied plant species like tef and has provided mutant lines that can now be combined and tested in breeding programs for improved lodging resistance.

Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity.