About

Hudson Ashrafi is an Associate Professor in the Department of Horticultural Science at NC State University, located in Kilgore Hall. He holds a PhD in Genetics from Pennsylvania State University, an MS in Plant Breeding from Azad University in Tehran, Iran, and a BS in Agronomy and Plant Breeding from the University of Technology in Esfahan, Iran. His research interests encompass conventional plant breeding, molecular breeding through marker-assisted selection, genetic mapping, QTL analysis, bioinformatics, and statistical genomics. As an assistant professor specializing in blueberry breeding, he is dedicated to utilizing his expertise to develop higher quality blueberries.

Research topics

• Biology
• Genetics
• Botany
• Computational biology
• Ecology
• Biotechnology
• Evolutionary biology
• Horticulture
• Agroforestry

Selected publications

• Genetic control of prickles in tetraploid blackberry

  G3 Genes Genomes Genetics · 2025-03-20 · 6 citations

  articleOpen access

  Prickle-free blackberry (Rubus subgenus Rubus) canes are strongly preferred by growers due to food and worker safety concerns and damage to fruit from mechanical injury by prickles. This project was conducted to identify the genetic region responsible for prickle-free canes derived from the recessive "Merton Thornless" source in autotetraploid blackberry using a genome-wide association study, develop diagnostic Kompetitive Allele-Specific PCR markers for prickle-free canes, and determine the effects of allele dosage at the prickle-free locus on prickle density in 2 biparental populations. The prickle locus was located on chromosome Ra04 from 30.48 to 36.04 Mb in an extensive LD block, with the peak single-nucleotide polymorphism located at 33.64 Mb. Five potential candidate genes with functional annotations related to epidermal, trichome, or prickle development were identified within the prickle-free locus. One missense mutation in the third exon of the HOX3 homolog Ra_g19498, which resulted in a serine to leucine substitution at position 91 in the amino acid sequence, was discovered using whole-genome sequence data of 17 tetraploid blackberry genotypes. Three diagnostic Kompetitive Allele-Specific PCR markers were developed targeting the missense mutation in Ra_g19498 and the 2 single-nucleotide polymorphisms most strongly associated with the prickle-free trait in the genome-wide association study. These 3 markers each correctly predicted the phenotype of between 96 and 97% and of 626 diverse fresh-market blackberry genotypes from multiple breeding programs, respectively. Allele dosage at the prickle-free locus had a significant impact on prickle density, with duplex prickly genotypes having significantly higher prickle density than simplex genotypes in both biparental populations studied.

  PublisherOA PDFDOI

• Optimizing regeneration systems for highbush blueberries

  Acta Horticulturae · 2025-11-01

  articleSenior author
  PublisherDOI

• The effect of zinc–methionine supplementation on physiological responses, oxidative stress, and the relative expression of IL-6, IL-10, and HSP70 genes in Sanjabi sheep under heat stress conditions

  Iranian Journal of Biological Sciences فصلنامه دانش زیستی ایران · 2025-12-06

  articleOpen access1st authorCorresponding

  مقدمه: تنش گرمایی یکی از مهم‌ترین عوامل محدودکننده تولید در گوسفندان است که با ایجاد عدم تعادل در هموستازی فیزیولوژیکی، افزایش گونه‌های اکسیژن واکنش‌پذیر و اختلال در تنظیم ایمنی، سبب کاهش عملکرد و بروز التهاب سیستمیک می‌شود. در این مطالعه اثر مکمل روی–متیونین بر پاسخ‌های فیزیولوژیکی، شاخص‌های استرس اکسیداتیو و بیان ژن‌های IL-6، IL-10 و HSP70 در میش‌های نژاد سنجابی غیرآبستن تحت تنش گرمایی شدید بررسی شد. مواد و روش ها: این تحقیق بر روی ۲۵ رأس میش نژاد سنجابی در قالب طرح کاملاً تصادفی در گروههای مختلف تنش گرمایی و با تیمار مکمل روی-متیونین به مدت 40 روز انجام پذیرفت. سپس پارامترهای فیزیولوزیکی و بیان ژن در گروه ها مورد بررسی قرار گرفت. یافته ها: تنش گرمایی باعث افزایش معنی‌دار ضربان قلب، نرخ تنفس و دمای مقعد و کاهش فعالیت GPX، SOD و TAC همراه با افزایش سطح MDA شد (05/0P<). همچنین، بیان ژن IL-6 و HSP70 به ترتیب 83/2 و 52/2 برابر افزایش و بیان ژن IL-10 به 63/0 برابر کاهش یافت (05/0P<). افزودن مکمل روی–متیونین به‌ویژه در سطوح ۳۰ و ۴۵ میلی‌گرم، به طور معنی‌داری شاخص‌های فیزیولوژیکی و آنتی‌اکسیدانی را بهبود بخشید، سطح MDA را کاهش داد و بیان ژن‌های IL-6 و HSP70 را تعدیل و بیان ژن IL-10 را افزایش داد (05/0P<). نتیجه گیری: افزودن مکمل روی–متیونین به جیره می‌تواند راهکار تغذیه‌ای مؤثری برای کاهش استرس فیزیولوژیک، بهبود وضعیت اکسیداتیو و تعدیل پاسخ‌های التهابی در گوسفندان سنجابی تحت تنش گرمایی باشد. استفاده از سطح ۳۰ میلی‌گرم بر کیلوگرم جیره به دلیل بیشترین اثربخشی توصیه می‌شود.

  PublisherDOI

• Identification of late blight resistance QTLs in an interspecific RIL population of tomato via genotyping-by-sequencing

  Molecular Breeding · 2025-04-01 · 1 citations

  articleOpen access

  Abstract Late blight (LB), caused by Phytophthora infestans , is a destructive disease of the cultivated tomato, Solanum lycopersicum . Environmental concerns and pathogen resistance have propelled research towards developing host resistance. The current LB-resistant cultivars of tomato exhibit susceptibility under severe disease pressure, necessitating the identification, characterization, and incorporation of additional resistance genes into new tomato cultivars. Recently, we identified Solanum pimpinellifolium accession PI 270443 with strong resistance to LB and developed a RIL population from its cross with an LB-susceptible tomato breeding line. In the present study, we constructed a high-density genetic map of the RIL population, using 8,470 SNP markers set into 1,195 genomic bins, with a total genetic distance of 1232 cM and an average bin size of 1 cM. We identified 2 major adjoining LB-resistance QTLs on chromosome 10 and a few minor QTLs on chromosomes 1 and 12 of PI 270443. While one of the QTLs on chromosome 10 colocalized with the known LB-resistance gene Ph- 2 and a LB-resistance QTL previously identified in an F 2 population of the same cross, the present study allowed marker saturation of the region, fine mapping of the QTL, and identification of candidate resistance genes in the region. One of the 2 major QTLs on chromosome 10 and the 3 QTLs on chromosomes 1 and 12 were not previously reported in S. pimpinellifolium for LB resistance. These results will expedite transferring of LB resistance from PI 270443 into the tomato cultigen via MAS and discovering the underpinning LB-resistance genes in PI 270443.

  PublisherOA PDFDOI

• Systematics and Evolution of Vaccinium Sect. Cyanococcus (Ericaceae): Progress and Prospects

  Rhodora · 2024-03-11 · 7 citations

  article

  The true blueberries (Vaccinium sect. Cyanococcus; Ericaceae) comprise a clade of about nine to 24 species distributed mainly in eastern temperate North America, with one species reaching farther west. Despite extensive study, the systematics and evolution of the group are still poorly understood. Limited morphological variation, multiple ploidy levels of uncertain origin, and natural hybridization all contribute to the challenge. Questionable analytical methods, such as the use of phenetics and an overemphasis on crossing experiments, have further impeded progress. Here we review the history of research on the systematics and evolution of V. sect. Cyanococcus with the aim of clarifying and summarizing hypotheses of species origins and diversification, especially in relation to polyploidy. We also present recent progress from our own work and, on that basis, offer promising lines of investigation with morphological and molecular data. We anticipate that these avenues of research will ultimately clarify patterns of natural species diversity in V. sect. Cyanococcus with benefits for biodiversity studies, conservation, and crop breeding.

  PublisherDOI

• Genetic Control of Prickles in Tetraploid Blackberry

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-02

  preprintOpen access

  Abstract Prickle-free blackberry ( Rubus subgenus Rubus ) canes are strongly preferred by growers due to food and worker safety concerns and damage to fruit from mechanical injury by prickles. This project was conducted to identify the genetic region responsible for prickle-free canes derived from the recessive ’Merton Thornless’ source in autotetraploid blackberry using a genome-wide association study, develop diagnostic KASP markers for prickle-free canes, and determine the effects of allele dosage at the prickle-free locus on prickle density in two biparental populations. The prickle locus was located on chromosome Ra04 from 30.48 to 36.04 Mb in an extensive LD block, with the peak SNP located at 33.64 Mb. Two diagnostic KASP markers were developed that correctly predicted the phenotype of 97% and 96% of 626 diverse fresh-market blackberry genotypes from multiple breeding programs, respectively. Allele dosage at the prickle-free locus had a significant impact on prickle density, with duplex prickly genotypes having significantly higher prickle density than simplex genotypes in both biparental populations studied. Five potential candidate genes with functional annotations related to epidermal, trichome, and/or prickle development were identified within the prickle-free locus, but no nonsynonymous polymorphism within these genes were identified. Article Summary Blackberry cultivars with prickle-free canes are strongly preferred by growers and shipper marketers. The objectives of this study were to map the prickle-free locus in tetraploid fresh- market blackberries using a genome-wide association approach and develop diagnostic molecular markers that breeders can use to plan crosses and screen seedlings for prickle-free canes. The prickle-free locus was mapped to a 5.6 Mb region on chromosome Ra04. Two molecular markers developed in this region correctly predicted the phenotype of 96% or more of the breeding selections and cultivars in a large validation panel composed of germplasm from three breeding programs.

  PublisherOA PDFDOI

• Open-Source High-Throughput Phenotyping for Blueberry Yield and Maturity Prediction Across Environments: Neural Network Model and Labeled Dataset for Breeders

  Horticulturae · 2024-12-13 · 7 citations

  articleOpen access

  Time to maturity and yield are important traits for highbush blueberry (Vaccinium corymbosum) breeding. Proper determination of the time to maturity of blueberry varieties and breeding lines informs the harvest window, ensuring that the fruits are harvested at optimum maturity and quality. On the other hand, high-yielding crops bring in high profits per acre of planting. Harvesting and quantifying the yield for each blueberry breeding accession are labor-intensive and impractical. Instead, visual ratings as an estimation of yield are often used as a faster way to quantify the yield, which is categorical and subjective. In this study, we developed and shared a high-throughput phenotyping method using neural networks to predict blueberry time to maturity and to provide a proxy for yield, overcoming the labor constraints of obtaining high-frequency data. We aim to facilitate further research in computer vision and precision agriculture by publishing the labeled image dataset and the trained model. In this research, true-color images of blueberry bushes were collected, annotated, and used to train a deep neural network object detection model [You Only Look Once (YOLOv11)] to detect mature and immature berries. Different versions of YOLOv11 were used, including nano, small, and medium, which had similar performance, while the medium version had slightly higher metrics. The YOLOv11m model shows strong performance for the mature berry class, with a precision of 0.90 and an F1 score of 0.90. The precision and recall for detecting immature berries were 0.81 and 0.79. The model was tested on 10 blueberry bushes by hand harvesting and weighing blueberries. The results showed that the model detects approximately 25% of the berries on the bushes, and the correlation coefficients between model-detected and hand-harvested traits were 0.66, 0.86, and 0.72 for mature fruit count, immature fruit count, and mature ratio, respectively. The model applied to 91 blueberry advance selections and categorized them into groups with diverse levels of maturity and productivity using principal component analysis (PCA). These results inform the harvest window and yield of these breeding lines with precision and objectivity through berry classification and quantification. This model will be helpful for blueberry breeders, enabling more efficient selection, and for growers, helping them accurately estimate optimal harvest windows. This open-source tool can potentially enhance research capabilities and agricultural productivity.

  PublisherDOI

• Modeling and simulation of a Novel Actuator for Medium-Voltage Vacuum Circuit Breakers Based on PMSM Servo Drive

  2024-12-24

  article

  This study proposes to utilize a permanent magnet synchronous motor drive as the operating mechanism in medium-voltage vacuum circuit breakers. Electric motors are easy-to-control actuator, which makes them suitable candidate for implementing the opening and closing processes in the vacuum circuit breakers. The behavior of the proposed electric motor-based actuator is studied and simulated for a 36 kV vacuum circuit breaker in MATLAB/Simulink. A slider-crank mechanism is placed between the electric motor shaft and movable contact to convert rotary motion to linear movement. Moreover, the mathematical analysis of the mechanical mechanism is presented. The simulation result confirms that the proposed actuator can fulfil stable operations needs of a 36 kV vacuum circuit breaker.

  PublisherDOI

• Development of a targeted genotyping platform for reproducible results within tetraploid and hexaploid blueberry

  Frontiers in Horticulture · 2024-01-15 · 18 citations

  articleOpen access

  Blueberry ( Vaccinium spp.) is one of the most economically important berry crops worldwide. Validation of genetic mapping studies is often hindered by asynchronous marker technology. The development of a standardized genotyping platform that targets a specific set of polymorphic loci can be a practical solution to unify the scientific and breeding community toward blueberry improvement. The objective of this study was to develop and evaluate a targeted genotyping platform for cultivated blueberries that is affordable, reproducible, and sufficiently high density to warrant large-scale adoption for genomic studies. The Flex-Seq platform was developed in a two-step procedure that resulted in 22,000 loci that yielded 194,365 single nucleotide polymorphisms when assessed in a diversity set of 192 samples including cultivated and other related wild Vaccinium species. Locus recovery averaged 89.4% in the cultivated polyploid blueberry (northern highbush [NHB], southern highbush [SHB], and rabbiteye [RE]) and on average 88.8% were polymorphic. While recovery of these loci was lower in the other Vaccinium species assayed, recovery remained high and ranged between 60.8% and 70.4% depending on the taxonomic distance to the cultivated blueberry targeted in this platform. NHB had the highest mean number of variants per locus at 9.7, followed by RE with 9.1, SHB with 8.5, and a range between 7.7 and 8.5 in other species. As expected, the total number of unique-in-state haplotypes exceeded the total number of variants in the domesticated blueberries. Phylogenetic analysis using a subset of the SNPs and haplotypes mostly conformed to known relationships. The platform also offers flexibility about the number of loci, depth of sequencing for accurate dosage calling, loci and haplotype reconstruction from increased fragment length. This genotyping platform will accelerate the development and improvement of blueberry cultivars through genomic-assisted breeding tools.

  PublisherOA PDFDOI

• Anecdote of homozygosity in black raspberry (<i>Rubus occidentalis</i>)

  Acta Horticulturae · 2024-02-01

  articleSenior author
  PublisherDOI

Frequent coauthors

• Allen Van Deynze

  University of California, Davis

  40 shared

• Theresa Hill

  26 shared

• Amanda M. Hulse‐Kemp

  Agricultural Research Service

  18 shared

• Majid R. Foolad

  Pennsylvania State University

  17 shared

• Nahla Bassil

  National Clonal Germplasm Repository

  14 shared

• Massimo Iorizzo

  13 shared

• Rishi Aryal

  North Carolina State University

  13 shared

• E Aiden

  Broad Institute

  12 shared

Education

• PhD Genetics, Plant Sciences

  Pennsylvania State University Penn State World Campus

  2008