Hudson Ashrafi

A Blueberry (<i> Vaccinium</i> L.) Crop Ontology to Enable Standardized Phenotyping for Blueberry Breeding and Research

HORTSCIENCE, 59(10), 1433–1442.

Application of RAPD and ISSR markers tools for commercial monovarietal Tunisian extra virgin olive oils (EVOO) authenticity and traceability

Abdelhamid, S., Omri, A., Araouki, A., Chehab, H., Garcia-Ruiz, R., & Ashrafi, H. (2024, August 7). EURO-MEDITERRANEAN JOURNAL FOR ENVIRONMENTAL INTEGRATION, Vol. 8.

Genome-wide association identifies key loci controlling blackberry postharvest quality

FRONTIERS IN PLANT SCIENCE, 14.

A chromosome-length genome assembly and annotation of blackberry (<i>Rubus argutus</i>, cv. “Hillquist”)

G3 Genes|Genomes|Genetics, 11(ue 2).

A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)

Crowl, A. A., Fritsch, P. W., Tiley, G. P., Lynch, N. P., Ranney, T. G., Ashrafi, H., & Manos, P. S. (2022, October 17). AMERICAN JOURNAL OF BOTANY, Vol. 10.

Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum)

Mengist, M. F., Bostan, H., De Paola, D., Teresi, S. J., Platts, A. E., Cremona, G., … Iorizzo, M. (2022, September 3). NEW PHYTOLOGIST, Vol. 9.

Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441

Sullenberger, M. T., Jia, M., Gao, S., Ashrafi, H., & Foolad, M. R. (2022, August 12). PLANT GENOME, Vol. 8.

Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids

SCIENTIA HORTICULTURAE, 297.

RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry

FRONTIERS IN GENETICS, 12.

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

HORTICULTURE RESEARCH, 9.

An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids

Hulse-Kemp, A. M., Bostan, H., Chen, S., Ashrafi, H., Stoffel, K., Sanseverino, W., … Van Deynze, A. (2021, June 10). PLANT GENOME, Vol. 6.

An optimized protocol for stepwise optimization of real-time RT-PCR analysis

HORTICULTURE RESEARCH, 8(1).

Detection of Fruit Meals Within Laboratory-Raised and Field-Trapped Adult Drosophila suzukii (Diptera: Drosophilidae) Guts

Frontiers in Ecology and Evolution, 9.

Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type

G3-GENES GENOMES GENETICS, 11(2).

Genotype, Environment, Year, and Harvest Effects on Fruit Quality Traits of Five Blueberry (Vaccinium corymbosum L.) Cultivars

AGRONOMY-BASEL, 11(9).

High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry

HORTICULTURE RESEARCH, 8(1).

Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)

BMC GENOMICS, 22(1).

A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding

G3-GENES GENOMES GENETICS, 10(10), 3729–3740.

Biomass yields, cytogenetics, fertility, and compositional analyses of novel bioenergy grass hybrids (Tripidium spp.)

GLOBAL CHANGE BIOLOGY BIOENERGY, 12(5), 361–373.

3D point cloud data to quantitatively characterize size and shape of shrub crops

HORTICULTURE RESEARCH, 6.

Simulated storage causes carbohydrate loss and rooting differences in two poinsettia cultivars

CANADIAN JOURNAL OF PLANT SCIENCE, 100(4), 459–462.

Breeding Trait Priorities of the Blueberry Industry in the United States and Canada

HortScience, 53(7), 1021–1028.

Developing the Genomic Resources for a Tetraploid Blueberry cv "O'Neal"

Aryal, R., Yow, A., & Ashrafi, H. (2018, August). Poster presented at the National Association of Plant Breeders 2018 Annual Meeting, Guelph Canada.

Differential Gene Expression during Blueberry Fruits Ripening

Aryal, R., & Ashrafi, H. (2018, July). Poster presented at the Plant Biology 2018, Montreal, Quebec, Canada.

Differential Gene Expression during Flower and Fruit Development of the Blueberry Cv. "O'Neal"

Aryal, R., Bostan, H., Yow, A. G., Tseng, E., Iorizzo, M., & Ashrafi, H. (Januaary 13-17, 2018Januaary 13-17, 2018). Poster presented at the Plant and Animal Genome XXVI Conference, San Diego CA.

Differential Gene Expression of Southern Highbush Blueberry cv. ‘O’Neal’ Floral Buds in Response to Freeze Treatment and Recovery Periods

Redpath, L. E., Yow, A. G., Aryal, R., Hulse-Kemp, A. M., Franks, R. G., Whetten, R., & Ashrafi, H. (2018, July). Poster presented at the American Society for Horticultural Science, Washington D.C.

Differential Gene Expression of ‘O’Neal’ Blueberry Floral Buds in Response to Freeze Treatment and Recovery Periods

Redpath, L. E., & Ashrafi, H. (2018, April). Presented at the Genomic Science and Biomathematics Symposium, NC State University, Raleigh NC.

Evaluation of Mechanically Harvested Southern Highbush Blueberries (Vaccinium corymbosum) Advanced Selections for Fresh Market

Redpath, L. E., Bland, T. W., Ballington, J. R., Jiang, Y., Li, C., & Ashrafi, H. (2018, July). Presented at the American Society for Horticultural Science, Washington D.C.

Fruit Quality Related Trait Evaluation in a Segregating F1 Population of Blueberry from a Cross Between "Reveille" and "Arlen" Cultivars

Young, E., Redpath, L., Iorizzo, M., & Ashrafi, H. (2018, August). Poster presented at the National Association of Plant Breeders 2018 Annual Meeting, Guelph, Canada.

Identification and Mapping of Late Blight Resistance Quantitative Trait Loci in Tomato Accession PI 163245

The Plant Genome, 0(0), 0.

RNA-Seq Analysis of Floral Bud Response to Freeze Treatments in Southern Highbush Blueberry CV "O’Neal"

Redpath, L. E., Yow, A. G., Aryal, R., Hulse-Kemp, A. M., Franks, R. G., Whetten, R., & Ashrafi, H. (2018, August). Poster presented at the National Plant Breeders Association, Guelph Ontario, Canada August.

Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection

PLANT GENOME, 12(1).

Single Nucleotide Polymorphic (SNP) Marker Discovery in a Diverse Panel of Blueberry (Vaccinium sp.) Species

Young., E., Ballington, J. R., & Ashrafi, H. (2018, July). Presented at the American Society of Horticulture Sciences, Washington, D.C.

Differential Gene Expression Analysis of Blueberry Cultivar “Arlen” in Response to Mummy Berry (Monilinia vaccinii-corymbosi) Disease Infection

Yow, A. G., Burchhardt, K., Rollins, J. A., Cubeta, M. A., & Ashrafi, H. (2017, September). Presented at the Plant Molecular Biology Consortium Retreat, Asheville, NC.

Disease Resistance to Multiple Fungal and Oomycete Pathogens Evaluated Using a Recombinant Inbred Line Population in Pepper

PHYTOPATHOLOGY, 107(12), 1522–1531.

Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry

Yow, A. G., Burchhardt, K., Cubeta, M. A., & Ashrafi, H. (2017, March). Poster presented at the NCSU Graduate Student Research Symposium, Raleigh, NC.

Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry

Yow, A. G., Burchhardt, K., Cubeta, M. A., & Ashrafi, H. (2017, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXV), San Diego, CA.

Regions Underlying Population Structure and the Genomics of Organ Size Determination in

The Plant Genome, 10(3), 0.

A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding

HORTICULTURE RESEARCH, 3(1).

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

NATURE GENETICS, 48(6), 657-+.

DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

PLOS GENETICS, 12(5).

Identification of Differentially Expressed Genes for Mummy Berry (Monilinia vaccinii-corymbosi) Resistance in Blueberry

Yow, A. G., Burchhardt, K., Cubeta, M. A., & Ashrafi, H. (2016, August). Poster presented at the Conference for the American Society for Horticultural Science (ASHS), Atlanta, GA.

Major CNV Detection by Read-Depth Analysis Using Capture-Based GBS in Cotton

Santiago, L. M. D., Hulse-Kemp, A. M., Resende, M., Neves, L. G., Ashrafi, H., Gill, C. A., & Stelly, D. M. (2016, January). Poster presented at the International Conference of Plant and Animal Genome Research (PAG XXIV), San Diego, CA.

New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

Frontiers in Plant Science, 7.

QTL Underlying Androgenic Haploid Production in Pepper (Capsicum annuum)

Hill, T., Afnan, K., Ray, T., Chaverri, A., Ashrafi, H., Deynze, A. V., & Bradford, K. (2016, January). Poster presented at the International Conference of Plant and Animal Genome Research (PAG XXIV), San Diego, CA.

Toward Deciphering of Mechanisms Underlying White Drupelet and Reversion Disorders of Blackberry

Fernandez, G., Carter, J. R., Yow, A. G., & Ashrafi, H. (2016, January). Poster presented at the International Conference of Plant and Animal Genome Research (PAG XXIV), San Diego, CA.

Using RNA-Seq for the Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry

Yow, A. G., Burchhardt, K., Cubeta, M. A., & Ashrafi, H. (2016, September). Presented at the Plant Molecular Biology Consortium Retreat, Wrightsville Beach, NC.

A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery

The Plant Genome, 8(2), 0.

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping

G3&Amp;#58; Genes|Genomes|Genetics, 5(6), 1095–1105.

Characterization of early blight resistance in a recombinant inbred line population of tomato: I. Heritability and trait correlations

Advanced Studies in Biology, 7, 131–148.

Characterization of early blight resistance in a recombinant inbred line population of tomato: II. Identification of QTLs and their co-localization with candidate resistance genes

Advanced Studies in Biology, 7, 149–168.

Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L)

G3 Gene| Genomes| Genetics, 5, 1187–1209.

Full-Length Transcriptome Sequencing Using PacBio Sequencing in Blueberry

Yow, A. G., Guo, W., & Ashrafi, H. (2015, November). Poster presented at the NCSU CALS Stewards of the Future Conference, Raleigh, NC.

Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species

G3-GENES GENOMES GENETICS, 5(11), 2341–2355.

Using spinach to compare technologies for whole genome assemblies

Presented at the Plant and Animal Genome XXIII Conference.

Cosegregates with QTL for Resistance to in Pepper ()

The Plant Genome, 7(2), 0.

Deciphering Resistance to Phytophthora capsici in Pepper

Deynze, A. V., Hill, T., Ashrafi, H., Kozik, A., Chin-Wo, S. R., & Rehrig, W. Z. (2014, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXI), San Diego, CA.

Detached-Leaflet Evaluation of Tomato Germplasm for Late Blight Resistance and Its Correspondence to Field and Greenhouse Screenings

Plant Disease, 99(5), 718–722.

Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts

BMC Genomics, 15(1), 945.

Genome sequence of the hot pepper provides insights into the evolution of pungency in <i>Capsicum</i> species

Nature Genetics, 46(3), 270–278.

Increasing Gossypium hirsutum Intraspecific SNPs via Genomic Sequencing

Deynze, A. V., Stelly, D., Ashrafi, H., Hulse, A. M., & Jones, D. C. (2014, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXI), San Diego, CA.

SNP marker discovery for tomato breeding using Genotyping-by-Sequencing (GBS)

Ashrafi, H., Ohlson, E. W., Sullenberger, M. T., Stoffel, K., Masoudi, M., Deynze, A. V., & Foolad, M. (2014, September). Presented at the Tomato Breeders Round Table, NC State University, Fletcher, NC.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

G3&Amp;#58; Genes|Genomes|Genetics, 3(4), 617–631.

Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip

PLoS ONE, 8(2), e56200.

Genome-wide SNP Development and Validation for Intraspecific SNPs in Upland Cotton

Hulse, A. M., Hoegenauer, K. A., Ashrafi, H., Wang, F., Stelly, D., Deynze, A. V., … Jones, D. C. (2013, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXI), San Diego, CA.

Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

G3&Amp;#58; Genes|Genomes|Genetics, 3(10), 1809–1818.

QTL Mapping of Fruit Rot Resistance to the Plant Pathogen Phytophthora capsici in a Recombinant Inbred Line Capsicum annuum Population

Phytopathology, 104(5), 479–483.

Resolving Tight Linkages Around Renlon by MAS for High-resolution Recombination in Chromosome-11

Zheng, X., Wang, F., Hoegenauer, K. A., Quintana, J., Ashrafi, H., Stelly, D., … Nichols, R. L. (2013, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XXI), San Diego, CA.

Structural Genomics

Deynze, A. V., Hill, T., & Ashrafi, H. (2013, January). Genetics, Genomics, and Breeding of Tomato, pp. 327–344.

Collaborative Development of SNPs for Cotton Research, Introgression, MAS and Breeding. Genome-Wide Gossypium SNP Development and Validation

Wang, F., Hulse, A. M., Hoegenauer, K., Stelly, D. M., Ashrafi, H., Deynze, A. V., & Yu, J. Z. (2012, January). Presented at the Cotton Improvement Conference, Beltwide Cotton Conferences. http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview

Comparison and evaluation of cotton SNPs developed by transcriptome, genome reduction on restriction site conservation and RAD-based sequencing

Ashrafi, H. (2012, October). Presented at the International Cotton Genome Initiative (ICGI) Research Conference, Raleigh, North Carolina, USA.

Comparisons of high-density EST-based maps in pepper species

Hill, T., Ashrafi, H., Reyes-Chin-Wo, S., Romero, M. S., Kozik, A., & Deynze, A. V. (2012, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XX), San Diego, CA.

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

BMC Genomics, 13(1), 571.

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

BMC Genomics, 13(1), 185.

Genome-Wide Gossypium SNP Development and Validation

Wang, F., Hulse, A. M., Hoegenauer, K., Stelly, D. M., Ashrafi, H., Deynze, A. V., & Yu, J. (2012, January). Presented at the Cotton Improvement Conference, Beltwide Cotton Conferences. http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview

Genome-wide SNP development and validation for allotetraploid Gossypium

Hulse, A. M., Wang, F., Hoegenauer, K., Stelly, D. M., Ashrafi, H., Deynze, A. V., … Jones, D. C. (2012, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XX), San Diego, CA.

Genome-wide SNP discovery from de novo assemblies of pepper (Capsicum annuum) transcriptomes

Ashrafi, H., Yao, J., Stoffel, K., Reyes-Chin-Wo, S., Hill, T., Kozik, A., & Van Deynze, A. (2012, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XX), San Diego, CA.

Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population

Genome, 56(1), 61–74.

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Nature, 492(7429), 423–427.

Selective genotyping to identify late blight resistance genes in an accession of the tomato wild species Solanum pimpinellifolium

Euphytica, 187(1), 63–75.

Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development

Science, 336(6089), 1711–1715.

An Integrated approach to breeding resistance to Phytophthora capsici In Pepper

Deynze, A. V., Hill, T. A., Yarnes, S., Rehrig, W. Z., Chin-Wo, S. R., Ashrafi, H., … Prince, J. (2011, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XIX), San Diego, CA.

Comparisons of high-density EST-based maps in pepper species

Hill, T., Ashrafi, H., Chin-Wo, S. R.-, Romero, M. S., Deynze, A. V., & Kozik, A. (Aug. 6-10, 2011Aug. 6-10, 2011). Presented at the Plant Biology, American Society of Plant Biologists, Minneapolis, MN.

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity

BMC Genomics, 12(1).

Development and Application of Genomic Tools in Pepper

Deynze, A. V., Hill, T., Prince, J., Yarnes, S., Chunthawodtiporn, J., Rehrig, W., … Kozik, A. (2011, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XIX), San Diego, CA.

Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population

Molecular Breeding, 30(1), 549–567.

The Genetic Map and Genome Sequencing of Lettuce

Deynze, A. V., Hill, T., Prince, J., Yarnes, S., Chunthawodtiporn, J., Rehrig, W., … Kozik, A. (2011, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XIX), San Diego, CA.

Ultra High Density EST-Based Maps Reveal Genome Differences Between C. frutescence And C. annuum

Hill, T., Ashrafi, H., Kozik, A., & Deynze, A. V. (2010, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVIII), San Diego, CA.

A new genetic linkage map of tomato based on a Solanum lycopersicum × S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes

Genome, 52(11), 935–956.

Construction of an Ultra High Density Genetic Map of Lettuce using an Affymetrix GeneChip

Kozik, A., Leeuwen, H., Truco, M. J., Stoffel, K., McHale, L., Ashrafi, H., … Michelmore, R. W. (2009, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVII), San Diego, CA.

Development and Utilization of a High Density 6.6 Million Feature Affymetrix GeneChip for Marker Discovery and Genotyping in Lettuce

Leeuwen, H., Stoffel, K., Truco, M. J., Ashrafi, H., Cui, X., Kozik, A., … Deynze, A. V. (2009, January). Poster presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVII), San Diego, CA.

High-Density Mapping of the Lettuce Genome with SFP Markers in over 15,000 Unigenes

Leeuwen, H., Stoffel, K., Kozik, A., Cui, X., Ashrafi, H., McHale, L., … Michelmore, R. W. (2009, January). Presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVII), San Diego, CA.

The Application of a Whole Genome Pepper Array to Identify SFPs in a Diversity Panel

Ashrafi, H., Hill, T., Yao, J., Leeuwen, H., Michelmore, R., Kozik, A., & Deynze, A. V. (2009, January). Invited presentation in Solanaceae workshop presented at the International Conference on the Status of Plant and Animal Genome Research (PAG XVII), San Diego, CA.

The Application of a Whole Genome Pepper Array to Solanaceae Crops

Hill, T., Ashrafi, H., Yao, J., Jong, W. D., Francis, D., Kozik, A., & Deynze, A. V. (2009, October). Presented at the Cologne, Germany.

A Solanum lycopersicum × Solanum pimpinellifolium Linkage Map of Tomato Displaying Genomic Locations of R-Genes, RGAs, and Candidate Resistance/Defense-Response ESTs

International Journal of Plant Genomics, 2008, 1–18.

Genetics, Genomics and Breeding of Late Blight and Early Blight Resistance in Tomato

Critical Reviews in Plant Sciences, 27(2), 75–107.

HPLC and spectrophotometer analyses of fruit carotenoids In a Lycopersicon esculentum X L. pimpinellifolium RIL population reveals several new QTLs for lycopene content

Ashrafi, H., Kinkade, M. R., & Foolad, M. R. (2007, January). Presented at the The International Conference on the Status of Plant and Animal Genome Research, PAG XV, San Diego, CA.

Identification and molecular mapping of a new dominant gene (Ph5) conferring broad-spectrum resistance against tomato late blight

Merk, H. L., Ashrafi, H., Kinkade, M. P., & Foolad, M. R. (2007, January). Presented at the The International Conference on the Status of Plant and Animal Genome Research, PAG XV, San Diego, CA.

A molecular linkage map of tomato based on RFLP markers and candidate disease-resistance/defense-response genes in an F7 RIL population

Ashrafi, H., Lin, G. Y., & Foolad, M. R. (2006, March). Poster presented at the Graduate Research Exposition, College of Ag. Sciences, The Pennsylvania State University, University Park, PA.

Identification of QTLs for tomato early blight resistance in a RIL population of a cross between Lycopersicon esculentum and L. pimpinellifolium

Ashrafi, H., Lin, G. Y., & Foolad, M. R. (2006, April). Poster presented at the Pennsylvania State University Genetics Symposium, University Park, PA.

Identification of new sources of late blight resistance in tomato and mapping of a new resistance gene

Foolad, M. R., Merk, H. L., Ashrafi, H., & Kinkade, M. P. (Nov. 9-10, 2006). Proc. 21st Annual Tomato Disease Workshop. Fletcher, NC: NC State University.