@article{redpath_aryal_lynch_spencer_hulse-kemp_ballington_green_bassil_hummer_ranney_et al._2022, title={Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids}, volume={297}, ISSN={["1879-1018"]}, DOI={10.1016/j.scienta.2022.110955}, abstractNote={Breeding strategies for improving blueberry (Vaccinium corymbosum and V. virgatum) cultivars often include introgressing regionally adapted species into the cultivated gene pools through interspecific hybridization. However, these approaches are complicated by variation in ploidy, triploid blocks and infertility, production of unreduced gametes, and aneuploidy. The objective of this study was to use flow cytometry, k-mer distribution analysis, and known pedigree information to evaluate genome sizes (2C nuclear and 1Cx monoploid), and ploidy of diverse accessions from Vaccinium sections and species. A total of 369 accessions, including a diversity panel (DP) of 251 inter- and intra-specific hybrid Vaccinium accessions, as well as 118 non-hybrid Vaccinium species across multiple sections, were sampled from the North Carolina State University blueberry breeding program and the National Clonal Germplasm Repository. The nuclear DNA content was analyzed via flow cytometry. The mean (range) DNA content of diploid, tetraploid, and hexaploid reference species were 1.20 pg (0.99 pg in V. crassifolium 'Well's Delight' to 1.41 pg in V. caesariense NC79–24), 2.37 pg (2.11 pg in V. corymbosum 'Concord' to 3.01 pg in V. corymbosum DE599), and 3.64 pg (3.24 in V. constablaei NC83–21–2 to 3.80 in V. virgatum 'Premier' and NC4790), respectively. Of the 369 unique accessions analyzed for ploidy, 259 were tetraploid, 46 were diploid, one was triploid, 51 were pentaploid or aneuploid with 2C values between tetraploid and hexaploid values, and 12 were hexaploid. Tetraploid hybrid pedigrees, which involved hexaploid crosses within three prior generations, had a 2C value range between 2.22 pg and 2.59 pg. Interspecific pentaploid and aneuploid progeny 2C DNA content ranged from 2.61 pg to 3.15 pg. We speculate some of these progeny to be near tetraploids with extra chromosomes from hexaploid progenitors. Further karyotyping of these individuals is necessary to ascertain aneuploidy anomalies. This research provides an expanded knowledge base of genome sizes, ploidy, and reproductive pathways for diverse species and hybrids to enhance future breeding, improvement, and the genomic study of blueberry.}, journal={SCIENTIA HORTICULTURAE}, author={Redpath, Lauren E. and Aryal, Rishi and Lynch, Nathan and Spencer, Jessica A. and Hulse-Kemp, Amanda M. and Ballington, James R. and Green, Jaimie and Bassil, Nahla and Hummer, Kim and Ranney, Thomas and et al.}, year={2022}, month={Apr} }
 @article{adhikari_aryal_redpath_broeck_ashrafi_philbrick_jacobs_sozzani_louws_2022, title={RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry}, volume={12}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2021.805771}, abstractNote={Two hemibiotrophic pathogens, Colletotrichum acutatum (Ca) and C. gloeosporioides (Cg), cause anthracnose fruit rot and anthracnose crown rot in strawberry (Fragaria × ananassa Duchesne), respectively. Both Ca and Cg can initially infect through a brief biotrophic phase, which is associated with the production of intracellular primary hyphae that can infect host cells without causing cell death and establishing hemibiotrophic infection (HBI) or quiescent (latent infections) in leaf tissues. The Ca and Cg HBI in nurseries and subsequent distribution of asymptomatic infected transplants to fruit production fields is the major source of anthracnose epidemics in North Carolina. In the absence of complete resistance, strawberry varieties with good fruit quality showing rate-reducing resistance have frequently been used as a source of resistance to Ca and Cg. However, the molecular mechanisms underlying the rate-reducing resistance or susceptibility to Ca and Cg are still unknown. We performed comparative transcriptome analyses to examine how rate-reducing resistant genotype NCS 10-147 and susceptible genotype ‘Chandler’ respond to Ca and Cg and identify molecular events between 0 and 48 h after the pathogen-inoculated and mock-inoculated leaf tissues. Although plant response to both Ca and Cg at the same timepoint was not similar, more genes in the resistant interaction were upregulated at 24 hpi with Ca compared with those at 48 hpi. In contrast, a few genes were upregulated in the resistant interaction at 48 hpi with Cg. Resistance response to both Ca and Cg was associated with upregulation of MLP-like protein 44, LRR receptor-like serine/threonine-protein kinase, and auxin signaling pathway, whereas susceptibility was linked to modulation of the phenylpropanoid pathway. Gene regulatory network inference analysis revealed candidate transcription factors (TFs) such as GATA5 and MYB-10, and their downstream targets were upregulated in resistant interactions. Our results provide valuable insights into transcriptional changes during resistant and susceptible interactions, which can further facilitate assessing candidate genes necessary for resistance to two hemibiotrophic Colletotrichum spp. in strawberry.}, journal={FRONTIERS IN GENETICS}, author={Adhikari, Tika B. and Aryal, Rishi and Redpath, Lauren E. and Broeck, Lisa and Ashrafi, Hamid and Philbrick, Ashley N. and Jacobs, Raymond L. and Sozzani, Rosangela and Louws, Frank J.}, year={2022}, month={Mar} }
 @article{redpath_gumpertz_ballington_bassil_ashrafi_2021, title={Genotype, Environment, Year, and Harvest Effects on Fruit Quality Traits of Five Blueberry (Vaccinium corymbosum L.) Cultivars}, volume={11}, ISSN={["2073-4395"]}, url={https://doi.org/10.3390/agronomy11091788}, DOI={10.3390/agronomy11091788}, abstractNote={Blueberries (Vaccinium spp.) comprise a broad range of perennial woody species. Introgression of native species into cultivated germplasm has adapted Vaccinium germplasm to a range of climates and growing conditions for cultivated blueberry. Genetic differences signify phenotypic variance that is observed among blueberry accessions. In addition, variability in geographic and climatic growing conditions between environments or within the same environment across different years may further affect fruit and plant phenotypic expression. As a result, a phenotype is a function of genetic background (G), environment (E), and their interaction (G × E). In addition, other temporally regulated factors such as year (Y) and harvest time (H) impact plant and fruit quality phenotypic variation. Our research aimed to assess the genotypic performance of five blueberry cultivars, including ‘Echota’, ‘O’Neal’, ‘Reveille’, ‘Summit’, and ‘Sunrise’. The selected cultivars were phenotyped for various fruit quality-related traits over two sequential harvests in two years and two locations. Our results indicated that genotype was a significant source of variation for most phenotypic characteristics. Further, the effect of Y × H and G × Y × H significantly affected the majority of studied phenotypic traits. Within the studied genotypes, ‘Reveille’ and ‘O’Neal’ phenotypic stability were consistent across locations and years; additionally, ‘Summit’ phenotypic characteristics were stable across years, environments, and harvests. Clonal plant replicates within a genotype, harvest, and environment, in addition to individual fruit measures, were the most significant sources of variability.}, number={9}, journal={AGRONOMY-BASEL}, author={Redpath, Lauren E. and Gumpertz, Marcia and Ballington, James R. and Bassil, Nahla and Ashrafi, Hamid}, year={2021}, month={Sep} }