Article
Agronomy
Chon-Sik Kang, Young-Jun Mo, Kyeong-Min Kim, Kyeong-Hoon Kim, Jae-Buhm Chun, Chul-Soo Park, Seong-Woo Cho
Summary: This study identified several QTLs affecting yield potential in wheat by using a recombinant inbred line population derived from Korean wheat cultivars. Multiple stable QTLs were detected in at least two environments, including those influencing spike length, tiller number, and length of center rachis. Taejoong contributed significantly to the spike length QTLs.
Article
Agronomy
Akio Ohyama, Hiroshi Matsunaga, Yasushi Kawasaki, Kenta Shirasawa, Satomi Negoro, Koji Miyatake, Hirotaka Yamaguchi, Tsukasa Nunome, Hiroyoshi Iwata, Hiroyuki Fukuoka, Takeshi Hayashi
Summary: Compared to a population derived from bi-parental crosses of pure lines, a customized experimental population derived from multi-parental crosses is advantageous for detecting multiple QTL alleles. A population of recombinant inbred lines (RILs) was established from crossing two commercial elite F-1 hybrid cultivars of tomato. Using two Bayesian mapping methods, significant QTLs for agricultural traits were detected in this population. A practical approach to genomic selection was presented based on the effects of the QTL alleles estimated in this study.
Article
Biochemical Research Methods
Narges Sahranavard, Eisa Jorjani, Hossein Sabouri, Sharifeh Mohahamad Alegh, Mahnaz Katouzi
Summary: The aim of this study was to identify the genomic regions controlling traits related to grains and leaves in wheat. Through genotyping and phenotyping, 10 quantitative trait loci were identified for grain and leaf traits. These findings help to understand the genetic mechanisms of wheat and support marker-assisted breeding programs.
PLANT MOLECULAR BIOLOGY REPORTER
(2023)
Article
Agronomy
Aina E. Prinzenberg, Hanneke Schoot, Richard G. F. Visser, Leo F. M. Marcelis, Ep Heuvelink, Henk J. Schouten
Summary: This study found that the severity of intumescence in tomato plants is highly dependent on genotype, with a high heritability. QTLs for intumescence were identified at chromosomal positions, and these QTLs are consistent among different populations. Environmental factors such as light spectrum have no significant influence on intumescence score, but there is a low negative correlation with multiple aspects of plant performance.
Article
Plant Sciences
Tika B. B. Adhikari, Muhammad Irfan Siddique, Frank J. J. Louws, Sung-Chur Sim, Dilip R. R. Panthee
Summary: The objective of this study was to map the QTLs associated with early blight (EB) resistance in tomatoes. A mapping population consisting of 174 lines derived from a resistant and a susceptible parent was evaluated for disease resistance. QTL analysis identified six QTLs associated with EB resistance on chromosomes 2, 8, and 11.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Lidia Blanco-Sanchez, Rosario Planello, Lola Llorente, Juan A. Diaz-Pendon, Victoria Ferrero, Rafael Fernandez-Munoz, Oscar Herrero, Eduardo de la Pena
Summary: The study found that type IV glandular trichomes have an impact on host selection and proliferation of the aphid Macrosiphum euphorbiae, with aphids avoiding and showing impaired multiplication on genotypes with trichomes. Exposure to type IV glandular trichomes resulted in the overexpression of detoxication markers, repression of energetic metabolism, and activation of the ecdysone pathway, indicating key adaptations and metabolic trade-offs in aphids exposed to glandular trichomes.
PEST MANAGEMENT SCIENCE
(2021)
Article
Plant Sciences
Qiang Chen, Bingqiang Liu, Lijuan Ai, Long Yan, Jing Lin, Xiaolei Shi, Hongtao Zhao, Yu Wei, Yan Feng, Chunji Liu, Chunyan Yang, Mengchen Zhang
Summary: This study identified loci controlling heterophylly in soybean by using two populations of recombinant inbred lines with different leaf shapes. Several QTL and candidate genes were detected, providing a foundation for further understanding the genetic mechanism of heterophylly and marker-assisted breeding.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Quan Hu, Yanwei Zhang, Ruirui Ma, Jie An, Wenxuan Huang, Yueying Wu, Jingjing Hou, Dajian Zhang, Feng Lin, Ran Xu, Qun Sun, Lianjun Sun
Summary: This study identified 145 QTLs controlling the appearance quality of soybean seeds through QTL mapping, and integrated into 16 QTL hotspots. It was found that seed size was mainly controlled by hotspot-4-1, while seed color and texture were affected by hotspot-15. Mapping of the principal components of seed appearance also supported these findings.
MOLECULAR BREEDING
(2021)
Article
Plant Sciences
Mi Zhang, Enbai Zhou, Meng Li, Shenglan Tian, Han Xiao
Summary: This study explores the role of the SUPERMAN gene in tomato fruit and flower development. The researchers identified and characterized a mutant with abnormal fruit and flowers, and found that this mutant had a nonsense mutation in a gene similar to SUPERMAN. The study provides insights into the conservation and diversification of SUP genes in different species, and suggests that the FMF gene could be a potential target for yield improvement in tomato through genetic engineering.
Article
Agronomy
Asena Akkose Baytar, Ceng Peynircioglu, Volkan Sezener, Anne Frary, Sami Doganlar
Summary: Cotton is a valuable fiber crop that is produced worldwide, and association mapping can help in cotton breeding. Despite low genetic variability, significant marker-trait associations were identified in the study.
Article
Plant Sciences
Karla Gasparini, Joaquim Gasparini, Rodrigo Therezan, Mateus Henrique Vicente, Tetsu Sakamoto, Antonio Figueira, Agustin Zsogon, Lazaro E. P. Peres
Summary: Research findings on the genetic changes in trichome development and density in tomato and its wild relatives provide insights for breeding insect-resistant varieties.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Agronomy
Chao Ma, Shengnan Ma, Qinglin Kang, Yue Wang, Yutian Sun, Zhaoming Qi, Jianan Zou, Chunyan Liu, Mingliang Yang, Dawei Xin, Qingshan Chen, Jinhui Wang
Summary: Soybean and rhizobium symbiosis is influenced by Nod factor signaling pathway, particularly the NodB gene. Using soybean recombinant inbred lines, genes related to nodule number and weight were identified.
Article
Plant Sciences
Rin Tsuzuki, Rosa Maria Cabrera Pintado, Jorge Andres Biondi Thorndike, Dina Lida Gutierrez Reynoso, Carlos Alberto Amasifuen Guerra, Juan Carlos Guerrero Abad, Liliana Maria Aragon Caballero, Medali Heidi Huarhua Zaquinaula, Cledy Ureta Sierra, Olenka Ines Alberca Cruz, Milca Gianira Elespuru Suna, Raul Humberto Blas Sevillano, Ines Carolina Torres Arias, Joel Flores Ticona, Fatima Caceres de Baldarrago, Enrique Rodoriguez Perez, Takuo Hozum, Hiroki Saito, Shunsuke Kotera, Yasunori Akagi, Motoichiro Kodama, Ken Komatsu, Tsutomu Arie
Summary: Tomato susceptibility or resistance to stem canker disease caused by Alternaria alternata f. sp. lycopersici is determined by the Asc1 gene, with certain commercial cultivars reported to have a mutation in this gene making them susceptible. Through evaluating 119 ancestral tomato accessions, it was found that some varieties with mutations in Asc1 were susceptible to the pathogenic AAL-toxin. These mutations seem to have been inherited throughout tomato domestication and breeding history.
Article
Plant Sciences
Sivan David, Elena Levin, Elazar Fallik, Sharon Alkalai-Tuvia, Majid R. Foolad, Amnon Lers
Summary: Storage at low temperatures is a common practice to prolong the postharvest life of fruits and vegetables. This study investigates the response of tomato fruit to postharvest chilling stress. Screening of a tomato population revealed significant variations in chilling tolerance, and weight loss, chlorophyll fluorescence parameters, and performance index were identified as efficient markers for evaluating chilling response in postharvest fruit.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Yahui Zhang, Yunqi Tang, Weicai Jin, Yu Liu, Guangyu Li, Wenhao Zhong, Jun Huang, Wenyi Wang
Summary: This study investigated the genetic basis of zeaxanthin content regulation in sweet corn and identified 8 QTLs, with a specific QTL on chromosome 7 being the main regulator of zeaxanthin content in sweet corn grains.
Article
Genetics & Heredity
Ashley G. Yow, Yucheng Zhang, Kamaldeep Bansal, Stephen M. Eacker, Shawn Sullivan, Ivan Liachko, Marc A. Cubeta, Jeffrey A. Rollins, Hamid Ashrafi
Summary: Mummy berry disease, caused by Monilinia vaccinii-corymbosi (Mvc), is a significant disease affecting blueberries in North America. A chromosome-scale reference genome for Mvc was created, revealing potential effectors for host infection and the MAT locus for mating type determination. Further research is needed to verify the roles of individual effectors and the role of the MAT locus in outcrossing.
G3-GENES GENOMES GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Nathan Maren, Fangzhou Zhao, Rishi Aryal, Darren Touchell, Wusheng Liu, Thomas Ranney, Hamid Ashrafi
Summary: Reproduction in grasses involves complex gene regulatory networks and developmental processes. This research identified differentially expressed transcripts associated with floral induction, inflorescence development, and seed development in T. ravennae, providing insights into the molecular regulation of reproductive development and laying a foundation for future studies in genome annotation, functional genomics, gene family evolutionary studies, comparative genomics, and precision breeding.
Article
Plant Sciences
Amanda M. Hulse-Kemp, Hamed Bostan, Shiyu Chen, Hamid Ashrafi, Kevin Stoffel, Walter Sanseverino, Linzhou Li, Shifeng Cheng, Michael C. Schatz, Tyler Garvin, Lindsey J. du Toit, Elizabeth Tseng, Jason Chin, Massimo Iorizzo, Allen Van Deynze
Summary: The study assembled and annotated the genome of spinach, developing a chromosome-level genetically anchored assembly. The long-read assembly predicted significantly more genes compared to the short-read assembly. Spinacia was confirmed to be a paleohexaploid with biased resistant gene motifs typical of monocots. Diversity analysis indicated ample variation in genes for hypothesis-driven genomic-assisted breeding.
Article
Plant Sciences
Molla F. Mengist, Hamed Bostan, Elisheba Young, Kristine L. Kay, Nicholas Gillitt, James Ballington, Colin D. Kay, Mario G. Ferruzzi, Hamid Ashrafi, Mary Ann Lila, Massimo Iorizzo
Summary: This study focused on the genetic basis of fruit quality traits in blueberry, constructing a high-density linkage map and identifying 18 loci associated with fruit quality traits over a three-year period. The study also found associations between fruit quality traits and metabolites, providing valuable insights into the genetic factors affecting blueberry fruit quality.
HORTICULTURE RESEARCH
(2021)
Article
Plant Sciences
Fangzhou Zhao, Nathan A. Maren, Pawel Z. Kosentka, Ying-Yu Liao, Hongyan Lu, James R. Duduit, Debao Huang, Hamid Ashrafi, Tuanjie Zhao, Alejandra Huerta, Thomas G. Ranney, Wusheng Liu
Summary: Optimizing primer design and qPCR parameters are crucial for improving primer efficiency and data analysis accuracy.
HORTICULTURE RESEARCH
(2021)
Article
Agronomy
Lauren E. Redpath, Marcia Gumpertz, James R. Ballington, Nahla Bassil, Hamid Ashrafi
Summary: Blueberries comprise a diverse group of perennial species that have adapted to different climates and growing conditions through the introgression of native species. Phenotypic variance among blueberry accessions is influenced by genetic differences and variability in geographic and climatic conditions. The phenotype of blueberries is determined by a combination of genetic background, environment, and their interaction, as well as other factors such as year and harvest time. Certain blueberry cultivars show stable phenotypic characteristics across locations and years, with clonal plant replicates and individual fruit measures being significant sources of variability.
Article
Ecology
Laura J. Kraft, Tim L. Sit, Lauren M. Diepenbrock, Hamid Ashrafi, Rishi Aryal, Gina E. Fernandez, Hannah J. Burrack
Summary: The study focused on the feeding habits of adult Brachycera, particularly the polyphagous small fruit pest Drosophila suzukii. Molecular methods were developed to analyze adult D. suzukii gut contents, revealing differences in detection time between blueberry and blackberry meals, as well as variability between male and female gut contents. Field trials indicated that adult flies may not heavily rely on fruit food resources, as there were no significant differences in the presence of fruit DNA among collection points along transects in both locations.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Horticulture
Lauren E. Redpath, Rishi Aryal, Nathan Lynch, Jessica A. Spencer, Amanda M. Hulse-Kemp, James R. Ballington, Jaimie Green, Nahla Bassil, Kim Hummer, Thomas Ranney, Hamid Ashrafi
Summary: This study used flow cytometry, k-mer distribution analysis, and known pedigree information to evaluate genome sizes, ploidy, and reproductive pathways of Vaccinium species. The findings showed that tetraploidy was the most common ploidy level, but pentaploidy and aneuploidy were also present. This research provides important data for the study of blueberry genomics, breeding, and improvement.
SCIENTIA HORTICULTURAE
(2022)
Article
Genetics & Heredity
Tika B. Adhikari, Rishi Aryal, Lauren E. Redpath, Lisa Van den Broeck, Hamid Ashrafi, Ashley N. Philbrick, Raymond L. Jacobs, Rosangela Sozzani, Frank J. Louws
Summary: The study revealed that the spread of anthracnose is mainly due to asymptomatic infected transplants in nurseries. Strawberry varieties with rate-reducing resistance exhibit different gene expression patterns when combating the two pathogens, while susceptibility is associated with the phenylpropanoid pathway modulation.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Molla F. Mengist, Hamed Bostan, Domenico De Paola, Scott J. Teresi, Adrian E. Platts, Gaetana Cremona, Xinpeng Qi, Ted Mackey, Nahla Bassil, Hamid Ashrafi, Lara Giongo, Rubina Jibran, David Chagne, Luca Bianco, Mary A. Lila, Lisa J. Rowland, Marina Iovene, Patrick P. Edger, Massimo Iorizzo
Summary: Understanding the recombination behavior in polyploidy species is crucial for genetic discoveries. This study focused on blueberry, a tetraploid species, and investigated its genetic behavior using cytogenetics and high-density genetic maps. The study revealed the presence of an autotetraploid behavior and a translocation affecting chromosome pairing and recombination. No other structural genomic divergences were detected, providing valuable resources for future genetic and comparative genomic studies.
Article
Plant Sciences
Matthew T. Sullenberger, Mengyuan Jia, Sihui Gao, Hamid Ashrafi, Majid R. Foolad
Summary: By identifying and mapping the QTLs for late blight resistance in a wild tomato species, the resistance can be transferred to new tomato cultivars.
Article
Plant Sciences
Andrew A. Crowl, Peter W. Fritsch, George P. Tiley, Nathan P. Lynch, Thomas G. Ranney, Hamid Ashrafi, Paul S. Manos
Summary: This study presents the first phylogenomic hypothesis of the true blueberries of North America, providing insights into their evolutionary relationships and setting the stage for future research on taxonomy revision, verification of a homoploid hybrid taxon, and the study of polyploid lineages within the context of a diploid phylogeny.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Genetics & Heredity
Tomas Bruna, Rishi Aryal, Olga Dudchenko, Daniel James Sargent, Daniel Mead, Matteo Buti, Andrea Cavallini, Timo Hytonen, Javier Andres, Melanie Pham, David Weisz, Flavia Mascagni, Gabriele Usai, Lucia Natali, Nahla Bassil, Gina E. Fernandez, Alexandre Lomsadze, Mitchell Armour, Bode Olukolu, Thomas Poorten, Caitlin Britton, Jahn Davik, Hamid Ashrafi, Erez Lieberman Aiden, Mark Borodovsky, Margaret Worthington
Summary: In this study, a chromosome-length assembly and annotation of the diploid blackberry germplasm accession Hillquist were presented. The assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
T. Mason Chizk, John R. R. Clark, Carmen Johns, Lacy Nelson, Hamid Ashrafi, Rishi Aryal, Margaret L. L. Worthington
Summary: Blackberry breeding programs have improved fruit firmness and postharvest quality, but the underlying genetic variation is poorly understood. This study conducted a genome-wide association analysis of blackberry genotypes and identified genetic variants associated with fruit firmness and red drupelet reversion (RDR). The study found that multiple small-effect quantitative trait loci (QTLs) control these postharvest traits, and provides a framework for future genomic selection models to improve postharvest quality.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Patrick P. Edger, Massimo Iorizzo, Nahla Bassil, Juliana Benevenuto, Luis Felipe Ferrao, Lara Giongo, Kim Hummer, Lovely Mae F. Lawas, Courtney P. Leisner, Changying Li, Patricio R. Munoz, Hamid Ashrafi, Amaya Atucha, Ebrahiem M. Babiker, Elizabeth Canales, David Chagne, Lisa DeVetter, Mark Ehlenfeldt, Richard Espley, Karina Gallardo, Catrin S. Gunther, Michael Hardigan, Amanda M. Hulse-Kemp, MacKenzie Jacobs, Mary Ann Lila, Claire Luby, Dorrie Main, Molla F. Mengist, Gregory L. Owens, Penelope Perkins-Veazie, James Polashock, Marti Pottorff, Lisa J. Rowland, Charles A. Sims, Guo-qing Song, Jessica Spencer, Nicholi Vorsa, Alan E. Yocca, Juan Zalapa
Summary: The Vaccinium genus, which includes blueberries and cranberries, is culturally and economically important. This review article summarizes the research progress in taxonomy, genetics, genomics, and breeding of these berry crops and identifies future research areas and questions for crop improvement efforts.
HORTICULTURE RESEARCH
(2022)
