@article{li_wang_zhou_liu_gichuki_hou_zhang_aryal_hu_wan_et al._2024, title={The Cissus quadrangularis genome reveals its adaptive features in an arid habitat}, volume={11}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhae038}, abstractNote={Abstract Cissus quadrangularis is a tetraploid species belonging to the Vitaceae family and is known for the Crassulacean acid metabolism (CAM) pathway in the succulent stem, while the leaves perform C3 photosynthesis. Here, we report a high-quality genome of C. quadrangularis comprising a total size of 679.2 Mb which was phased into two subgenomes. Genome annotation identified 51 857 protein-coding genes, while approximately 47.75% of the genome was composed of repetitive sequences. Gene expression ratios of two subgenomes demonstrated that the sub-A genome as the dominant subgenome played a vital role during the drought tolerance. Genome divergence analysis suggests that the tetraploidization event occurred around 8.9 million years ago. Transcriptome data revealed that pathways related to cutin, suberine, and wax metabolism were enriched in the stem during drought treatment, suggesting that these genes contributed to the drought adaption. Additionally, a subset of CAM-related genes displayed diurnal expression patterns in the succulent stems but not in leaves, indicating that stem-biased expression of existing genes contributed to the CAM evolution. Our findings provide insights into the mechanisms of drought adaptation and photosynthesis transition in plants.}, number={4}, journal={HORTICULTURE RESEARCH}, author={Li, Qingyun and Wang, Yi and Zhou, Huimin and Liu, Yuanshuang and Gichuki, Duncan Kiragu and Hou, Yujun and Zhang, Jisen and Aryal, Rishi and Hu, Guangwan and Wan, Tao and et al.}, year={2024}, month={Apr} }
 @article{chizk_clark_johns_nelson_ashrafi_aryal_worthington_2023, title={Genome-wide association identifies key loci controlling blackberry postharvest quality}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1182790}, abstractNote={IntroductionBlackberry (Rubus subgenus Rubus) is a soft-fruited specialty crop that often suffers economic losses due to degradation in the shipping process. During transportation, fresh-market blackberries commonly leak, decay, deform, or become discolored through a disorder known as red drupelet reversion (RDR). Over the past 50 years, breeding programs have achieved better fruit firmness and postharvest quality through traditional selection methods, but the underlying genetic variation is poorly understood.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Chizk, T. Mason and Clark, John R. R. and Johns, Carmen and Nelson, Lacy and Ashrafi, Hamid and Aryal, Rishi and Worthington, Margaret L. L.}, year={2023}, month={Jun} }
 @article{brůna_aryal_dudchenko_sargent_mead_buti_cavallini_hytönen_andrés_pham_et al._2022, title={A chromosome-length genome assembly and annotation of blackberry (<i>Rubus argutus</i>, cv. “Hillquist”)}, volume={11}, ISSN={2160-1836}, url={http://dx.doi.org/10.1093/g3journal/jkac289}, DOI={10.1093/g3journal/jkac289}, abstractNote={Abstract}, number={ue 2}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Brůna, Tomáš and Aryal, Rishi and Dudchenko, Olga and Sargent, Daniel James and Mead, Daniel and Buti, Matteo and Cavallini, Andrea and Hytönen, Timo and Andrés, Javier and Pham, Melanie and et al.}, editor={Pyhäjärvi, TEditor}, year={2022}, month={Nov} }
 @article{zareei_karami_aryal_saed-moucheshi_2022, title={Genotypic by phenotypic interaction affects the heritability and relationship among quantity and quality traits of strawberry (Fragaria x ananassa)}, ISSN={["1175-8783"]}, DOI={10.1080/01140671.2022.2039725}, abstractNote={ABSTRACT The success of plant breeding depends on diversity in plant genetic resources and their responses to changing environments. Accordingly, 20 strawberry genotypes with diverse genetic background were evaluated for their performance under different environments based on the estimation of their genetic variability and heritability. The results showed that environmental factors have great influences on changing the size of the measured traits. Also, a high heritability and genetic variation detected for yield and its components showed a strong potential for improvement among the strawberry genotypes and being considered as raw materials in breeding programs. Biplot and heatmap, in line with the clustering, showed to be key methods for finding the structural association among genotypes and traits. Cluster analysis showed that the genotypes originating from the same geographic area were not necessarily placed in the same clusters which could be due to the environmental variability and the different responses of the genotypes coming from altered genetic materials. The overall results regarding multivariate analyses showed that genotypes Kurdistan, Queen Elisa and No.14 could be considered as a cluster with high similarity for being crossed by other genotypes in the clusters such as groups of Pajaro and Chandler, or the group of Selva and Gaviota.}, journal={NEW ZEALAND JOURNAL OF CROP AND HORTICULTURAL SCIENCE}, author={Zareei, Elnaz and Karami, Farhad and Aryal, Rishi and Saed-Moucheshi, Armin}, year={2022}, month={Feb} }
 @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{kraft_sit_diepenbrock_ashrafi_aryal_fernandez_burrack_2021, title={Detection of Fruit Meals Within Laboratory-Raised and Field-Trapped Adult Drosophila suzukii (Diptera: Drosophilidae) Guts}, volume={9}, ISSN={2296-701X}, url={http://dx.doi.org/10.3389/fevo.2021.719645}, DOI={10.3389/fevo.2021.719645}, abstractNote={The feeding habits of adult Brachycera are understudied and may provide important context for understanding invasive pest biology, as with the polyphagous small fruit pest Drosophila suzukii. We developed molecular methods to study adult D. suzukii gut content in order to understand its feeding habits. We designed and verified two primer pairs specific for either blueberries or blackberries and used a qPCR melt curve analysis to determine whether we can detect the presence or absence of berry feeding by adult flies. In a laboratory assay, the blueberry fly meal DNA can be detected for longer periods than the blackberry meal DNA. Generally, female gut contents are less variable than male gut contents. We also tested recently emerged flies that were not fed as adults but developed as larvae in either blueberries or blackberries. Some adult flies from each fruit had detectable fruit DNA in their gut, which could be due to pupal meconium feeding after emergence. Next, we aimed to test the primers in the field to develop techniques to track fruit feeding by D. suzukii in its natural field environment. First, to identify the most appropriate collection method, we determined how long we could detect fruit DNA, using previously developed primers within D. suzukii gut preserved in four types of trap fluid in the laboratory. The likelihood of detecting blackberry DNA differed by day, trap fluid, and between sexes. For the blueberry primer, the possibility of detecting blueberry DNA differed by trap fluid only. Based on those results, we used RV antifreeze with a Scentry SWD lure in field trials at two research station locations, one containing blackberries and one with blueberries. We established transects away from each fruit planting and collected up to 120 total flies at each point along transects. There were no significant differences in the number of flies containing berry DNA among collection points along the transect in both locations. These results suggest that adult flies move between crop and non-crop habitats and may not be highly dependent on fruit food resources.}, journal={Frontiers in Ecology and Evolution}, publisher={Frontiers Media SA}, author={Kraft, Laura J. and Sit, Tim L. and Diepenbrock, Lauren M. and Ashrafi, Hamid and Aryal, Rishi and Fernandez, Gina E. and Burrack, Hannah J.}, year={2021}, month={Aug} }
 @article{zareei_karami_gholami_ershadi_avestan_aryal_gohari_farooq_2021, title={Physiological and biochemical responses of strawberry crown and leaf tissues to freezing stress}, volume={21}, ISSN={["1471-2229"]}, DOI={10.1186/s12870-021-03300-2}, abstractNote={Abstract}, number={1}, journal={BMC PLANT BIOLOGY}, author={Zareei, Elnaz and Karami, Farhad and Gholami, Mansour and Ershadi, Ahmad and Avestan, Saber and Aryal, Rishi and Gohari, Gholamreza and Farooq, Muhammad}, year={2021}, month={Nov} }
 @article{maren_zhao_aryal_touchell_liu_ranney_ashrafi_2021, title={Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)}, volume={22}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-021-07641-y}, abstractNote={Abstract}, number={1}, journal={BMC GENOMICS}, author={Maren, Nathan and Zhao, Fangzhou and Aryal, Rishi and Touchell, Darren and Liu, Wusheng and Ranney, Thomas and Ashrafi, Hamid}, year={2021}, month={Jun} }
 @article{zurn_driskill_jung_main_yin_clark_cheng_ashrafi_aryal_clark_et al._2020, title={A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding}, volume={10}, ISSN={["2160-1836"]}, DOI={10.1534/g3.120.401449}, abstractNote={Abstract}, number={10}, journal={G3-GENES GENOMES GENETICS}, author={Zurn, Jason D. and Driskill, Mandie and Jung, Sook and Main, Dorrie and Yin, Melinda H. and Clark, Melissa C. and Cheng, Lailiang and Ashrafi, Hamid and Aryal, Rishi and Clark, John R. and et al.}, year={2020}, month={Oct}, pages={3729–3740} }
 @article{zareei_javadi_aryal_2018, title={Biochemical composition and antioxidant activity affected by spraying potassium sulfate in black grape (Vitis vinifera L. cv. Rasha)}, volume={98}, ISSN={["1097-0010"]}, DOI={10.1002/jsfa.9107}, abstractNote={Abstract}, number={15}, journal={JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE}, author={Zareei, Elnaz and Javadi, Taimoor and Aryal, Rishi}, year={2018}, month={Dec}, pages={5632–5638} }