Location: Southern Horticultural Research Unit
2020 Annual Report
Accomplishments
1. Determination of nuclear DNA content, ploidy, and Fluorescence In Situ Hybridization (FISH) location of ribosomal DNA (rDNA) in Hibiscus hamabo. Genome size is a distinguishing character of living organisms and estimates of genome size have been useful in systematic and evolutionary studies as well as in planning sequencing work. ARS researchers in Poplarville, Mississippi, in collaboration with scientists of USDA-Forest Service, determined genome size, ploidy, and rDNA location in Hibiscus hamabo. H. hamabo is salt-tolerant, so it is considered one of the best afforestation plants used in reclamation areas and shelterbelt tree species along the coasts as well as urban landscaping. H. hamabo is a good plant material to study the response mechanisms of salt-stressed woody plants. A practical application of these results was the hybridization of H. hamabo with an ornamentally superior species, H. paramutabilis, which has the same chromosome number as H. hamabo. Seedlings of these crosses are being evaluated.
2. Comparative analysis of rhizosphere microbiomes of southern highbush, Darrow’s, and rabbiteye blueberry. Plants are inhabited by millions of microorganisms that coexist in complex ecological communities, and profoundly affects the plant’s productivity and capacity to cope with abiotic stress. An ARS researcher in Poplarville, Mississippi, in collaboration with university collaborators, employed molecular approaches to characterize and compare microbial communities inhabiting the roots of three Vaccinium species, Darrow’s blueberry, rabbiteye, and southern highbush. Results from this study revealed that the Vaccinium species share a common core rhizobiome, but at the same time differ significantly in the diversity, relative abundance, richness, and evenness of multiple groups of prokaryotic and eukaryotic microorganisms. Further, they differ in the abundance of beneficial rhizobacteria and ericoid mycorrhizal fungi, which play a vital role in their adaptation to soils with low pH and slow turnover of organic matter. Results of the study will contribute to the selection of cultivars that maximally benefit from the mycorrhizal associations and exhibit better adaptability to prevalent field conditions.
3. Draft whole genome sequencing of Xylella fastidiosa strains OK3, VB11, and NOB1. Pierce’s disease, caused by the bacterium X. fastidiosa, is an economically important grapevine disease that endangers the grape industry worldwide. Analysis of whole genome sequences of X. fastidiosa strains from bunch and muscadine grapes is important to better understand the pathogenic potential and to breed new resistant cultivars. ARS researchers in Poplarville, Mississippi, in collaboration with universities scientists generated high-quality draft whole-genome assemblies of X. fastidiosa subsp. fastidiosa strains OK3, VB11, and NOB1 isolated from symptomatic bunch and muscadine grape plants grown in southern Mississippi. Findings from this study will benefit grape growers by providing knowledge required to screen germplasm for resistance and to develop novel methods of disease control.
4. Genomic insight into the developmental history of southern highbush blueberry populations. Southern highbush blueberry (SHB) is a cultivar group that has been intensively bred by multiple interspecific crosses between northern highbush blueberry (NHB) and low-chill Vaccinium species to expand the geographic limits of highbush blueberry production. Despite years of research, little is known about the genetic diversity and population structure of SHB. An ARS researcher in Poplarville, Mississippi, working with collaborators from Japan, used DNA sequencing technique to genotype a diverse set of SHB, NHB, and rabbiteye accessions. Sequence data indicated that rabbiteye accessions were genetically distinct from SHB and NHB cultivars, whereas NHB and SHB were genetically indistinguishable. The population structure results appeared to reflect the differences in the allele selection strategies breeders used for developing germplasm adapted to local climates. The genotype data implied there are no or very few genomic segments that were commonly introgressed from low-chill Vaccinium species to the SHB genome. These findings will enable genetic variability to be associated with specific phenotype and enhance germplasm selection based on DNA sequences.
Review Publications
Li, J., Mavrodi, O., Hou, J., Blackman, C., Babiker, E.M., Mavrodi, D. 2020. Comparative analysis of rhizosphere microbiomes of southern highbush blueberry (Vaccinium corymbosum L.), Darrow’s blueberry (V. darrowii Camp.), and rabbiteye blueberry (V. virgatum Aiton). Frontiers in Microbiology. 11:370. https://www.frontiersin.org/articles/10.3389/fmicb.2020.00370/full.
Mavrodi, O.V., Mavrodi, D.V., Stafine, E.T., Adamczyk Jr, J.J., Babiker, E.M. 2020. Draft genome sequences of Xylella fastidiosa subsp. fastidiosa strains OK3, VB11, and NOB1 isolated from bunch and muscadine grapes grown in southern Mississippi. Microbiology Resource Announcements. 9(25):1-2. https://doi.org/10.1128/MRA.00562-20.
