Article
Plant Sciences
Tao Li, Mingyue Feng, Yuanming Chi, Xing Shi, Zilin Sun, Zhen Wu, Aomei Li, Wangpeng Shi
Summary: This study explored the resistance mechanism of Vigna unguiculata against Megalurothrips usitatus by conducting behavior assays and analyzing transcriptome and metabonomics. The results showed that pre-treatment with jasmonic acid or infestation with the pest insect alleviated the damage caused by the insect. Transcriptome and metabolite changes were observed, leading to the accumulation of flavonoids and alpha-linolenic acid-related metabolites. These findings provide valuable information for breeding insect-resistant varieties of cowpea using molecular technology.
Article
Horticulture
Christian S. Bowman, Bao Lam Huynh, Philip Roberts, Jansen R. P. Santos, Kaylee Paul, Timothy J. Close
Summary: Consumer preferences are crucial for the success of new cowpea cultivars, and pigment leaching during the cooking or canning process is an undesirable trait that has been targeted for improvement. This study used bulked segregant analysis to identify a major locus on Vu06 that determines the pigment-leaching trait in blackeye seed-type cowpea. However, further analysis suggests that the trait is polygenic and other seed coat or cooking-related traits may also contribute to pigment leaching. A comparison with black bean suggests potential similarities in the genetic control of this trait.
Article
Plant Sciences
Luciany Favoreto, Rafaela Bueno, Angelica Calandrelli, Patricia P. Franca, Mauricio C. Meyer, Andressa C. Z. Machado
Summary: This study found that the nematode Aphelenchoides besseyi can parasitize cowpea, causing leaf deformation and stem necrosis. This is the first report of parasitism of this nematode on cowpea in Brazil.
Article
Plant Sciences
Mirella Pupo Santos, Antonio Jesus Dorighetto Cogo, Francisco J. L. Aragao
Summary: Cowpea is an important source of vitamins, protein, and minerals in Africa, Latin America, and Asia. The use of drought tolerant genotypes is crucial for climate change and global food security. Morphometric and physiological analysis were conducted to compare cowpea genotypes. PCA identified the traits that contribute the most to drought tolerance. Certain genotypes showed better morphological and physiological characteristics under drought conditions.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
Jacob R. MacWilliams, Paul D. Nabity, Kerry E. Mauck, Isgouhi Kaloshian
Summary: This study investigates the interaction between cowpea plants and aphids and identifies the genes underlying cowpea resistance to aphids. The results show that the feeding behavior of aphids remodels the transcriptome of cowpea and that this remodeling depends on both the duration of feeding and host-plant resistance. The study also identifies candidate genes involved in aphid resistance, including both conventional resistance genes and novel genes.
Article
Plant Sciences
Zhifen Zhang, Yinping Guo, Kathleen Monfero Marasigan, Joann A. Conner, Peggy Ozias-Akins
Summary: "Expression of Cre recombinase by AtRps5a(pro) or AtDD45(pro) enabled precise transgene activation in hybrid cowpea and tobacco, but limitations were observed with AtUbq3(pro) restricting ZsGreen expression. Overcoming this limitation was achieved by driving ZsGreen expression with the AtUbq10 promoter, while using AtDD45(pro) to express Cre resulted in varying recombination frequencies between transgenic lines and crosses."
PLANT CELL REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Ramon E. Rivera-Vicens, Catalina A. Garcia-Escudero, Nicola Conci, Michael Eitel, Gert Woerheide
Summary: The use of RNA sequencing and de novo transcriptome assembly is crucial for ecological and evolutionary studies, especially for nonmodel organisms lacking genome information. A multi-assembler approach, followed by a reduction step, is often employed to improve the assembly quality. TransPi is a comprehensive pipeline for de novo transcriptome assembly that achieves higher completeness percentages and reduces duplication rates compared to single assembler approaches. It is easy to configure and can be seamlessly deployed using Conda, Docker, and Singularity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Plant Sciences
Sandhya Suranjika, Seema Pradhan, Soumya Shree Nayak, Ajay Parida
Summary: This study provides foundational resources for gene discovery in Vigna aconitifolia, a legume crop with high protein content in its seeds. By analyzing the transcriptome, the study reveals the genes and metabolic pathways involved in seed development and potentially responsible for the unique nutrient values of moth bean seeds. The findings can contribute to the understanding and improvement of moth bean and related species.
Article
Entomology
Beatrice N. Dingha, Louis E. Jackai, Barbara A. Amoah, Clement Akotsen-Mensah
Summary: The study showed that cowpeas can increase resources for pollinators and improve pollinator abundance and diversity. Different cowpea varieties significantly influenced the number of pollinators, and various sampling methods affected the distribution of pollinators.
Article
Biochemistry & Molecular Biology
Byeong Hee Kang, Woon Ji Kim, Sreeparna Chowdhury, Chang Yeok Moon, Sehee Kang, Seong-Hoon Kim, Sung-Hwan Jo, Tae-Hwan Jun, Kyung Do Kim, Bo-Keun Ha
Summary: This study identified genes related to salt stress in cowpea by comparing germplasms with contrasting salt tolerance. The results provide useful information for the development of molecular markers in cowpea breeding programs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Shanying Zhang, Yu Zhang, Saihao Ren, Hongwei Lu, Jiaomei Li, Xiaoyu Liang, Lifeng Wang, Yuanbo Li, Meng Wang, Chenghui Zhang
Summary: Acetamiprid (ACE) and cyromazine (CYR) are frequently used pesticides in cowpea growing areas in Hainan. This study investigated their uptake, translocation, subcellular distribution, and metabolic pathway in cowpea. The results showed that both pesticides were mainly distributed in leaves, and their subcellular distribution was primarily in the cell soluble fraction. Metabolic reactions such as dealkylation, hydroxylation, and methylation were observed. The dietary risk assessment revealed that while ACE is safe, CYR poses an acute risk to infants and young children.
ENVIRONMENTAL POLLUTION
(2023)
Article
Plant Sciences
Wei Long, Xiaohua Yao, Kailiang Wang, Yu Sheng, Leyan Lv
Summary: In this study, the gene expression and global gene expression profiles during Camellia oleifera seed germination were analyzed using transcriptome sequencing. Differentially expressed genes were identified, indicating the role of cotyledons in seed germination and seedling growth. This study will contribute to the breeding and cultivation of C. oleifera.
Review
Biochemical Research Methods
Venket Raghavan, Louis Kraft, Fantin Mesny, Linda Rigerte
Summary: A transcriptome constructed from short-read RNA sequencing is a proxy catalog of protein-coding genes. De novo assembly and annotation of the transcriptome can be challenging due to the lack of standardized workflows and authoritative literature.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Muhammed Opoku Gyamfi, John Saviour Yaw Eleblu, Lawrencia Gyamfi Sarfoa, Isaac Kojo Asante, Frank Opoku-Agyemang, Eric Yirenkyi Danquah
Summary: Ethyl methane sulfonate (EMS) was used to induce genetic variability in cowpea, resulting in unique agro-morphological abnormalities such as leaf color, shape, growth habit, pod curvature, seed shape, and seed coat color. This research highlights the importance of EMS mutagenesis for breeding and developing new farmer preferred varieties.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Vincent Ezin, Thibaut A. W. Tossou, Ifagbemi Bienvenue Chabi, Adam Ahanchede
Summary: This study investigated the combining ability and genetic correlations for water deficit tolerance traits in cowpea. The results showed the presence of additive and non-additive gene action, with additive genes playing a predominant role. Several genotypes were identified as good general combiners for traits related to yield and water deficit tolerance. The study also identified specific combiners for water deficit tolerance traits. The heritability of traits such as days to pod maturity, pod length, number of pods per plant, and weight of hundred seeds was found to be high.
Article
Plant Sciences
Yongqin Wang, Weihong Dong, Malay C. Saha, Michael K. Udvardi, Yun Kang
Summary: Node culture method is an efficient way for propagating switchgrass vegetatively. Contamination from microorganisms can be reduced by adding biocides and fungicides. The in planta node culture method is labor- and cost-efficient, with a high success rate for producing rooted plants directly from aerial axillary buds on parent plants.
Article
Multidisciplinary Sciences
John T. Lovell, Alice H. MacQueen, Sujan Mamidi, Jason Bonnette, Jerry Jenkins, Joseph D. Napier, Avinash Sreedasyam, Adam Healey, Adam Session, Shengqiang Shu, Kerrie Barry, Stacy Bonos, LoriBeth Boston, Christopher Daum, Shweta Deshpande, Aren Ewing, Paul P. Grabowski, Taslima Haque, Melanie Harrison, Jiming Jiang, Dave Kudrna, Anna Lipzen, Thomas H. Pendergast, Chris Plott, Peng Qi, Christopher A. Saski, Eugene Shakirov, David Sims, Manoj Sharma, Rita Sharma, Ada Stewart, Vasanth R. Singan, Yuhong Tang, Sandra Thibivillier, Jenell Webber, Xiaoyu Weng, Melissa Williams, Guohong Albert Wu, Yuko Yoshinaga, Matthew Zane, Li Zhang, Jiyi Zhang, Kathrine D. Behrman, Arvid R. Boe, Philip A. Fay, Felix B. Fritschi, Julie D. Jastrow, John Lloyd-Reilley, Juan Manuel Martinez-Reyna, Roser Matamala, Robert B. Mitchell, Francis M. Rouquette, Pamela Ronald, Malay Saha, Christian M. Tobias, Michael Udvardi, Rod A. Wing, Yanqi Wu, Laura E. Bartley, Michael Casler, Katrien M. Devos, David B. Lowry, Daniel S. Rokhsar, Jane Grimwood, Thomas E. Juenger, Jeremy Schmutz
Summary: Climate change and environmental extremes threaten food and fuel security, as well as global crop productivity. Molecular and adaptive breeding strategies can help improve crop resilience, but require in-depth knowledge of productivity and adaptation genes. The study on the genome of switchgrass revealed extensive genomic evidence of climate adaptation and accelerated climate adaptation through gene flow during postglacial colonization. These findings not only provide insights into climate adaptation patterns, but also offer tools for breeders to increase switchgrass yield for sustainable bioenergy production.
Article
Plant Sciences
Wenchao Zhang, Yun Kang, Xiaofei Cheng, Jiangqi Wen, Hongying Zhang, Ivone Torres-Jerez, Nick Krom, Michael K. Udvardi, Wolf-Rudiger Scheible, Patrick Xuechun Zhao
Summary: HapMap projects provide valuable genetic resources for life science research, but the validation of individuals is necessary before conducting GWAS analyses, and there are currently no existing methods to distinguish multiple individuals in a HapMap population effectively.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Bikash Raul, Oindrila Bhattacharjee, Amit Ghosh, Priya Upadhyay, Kunal Tembhare, Ajeet Singh, Tarannum Shaheen, Asim Kumar Ghosh, Ivone Torres-Jerez, Nick Krom, Josh Clevenger, Michael Udvardi, Brian E. Scheffler, Peggy Ozias-Akins, Ravi Datta Sharma, Kaustav Bandyopadhyay, Vineet Gaur, Shailesh Kumar, Senjuti Sinharoy
Summary: The study reveals dynamic changes in plant gene expression during peanut nodule development using comprehensive analysis and transcriptomics. Compared to other model legumes, peanut demonstrates diversification in oxygen-scavenging mechanisms and molecular mechanisms of terminal bacteroid differentiation.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Plant Sciences
Sonali Roy, Marcus Griffiths, Ivone Torres-Jerez, Bailey Sanchez, Elizabeth Antonelli, Divya Jain, Nicholas Krom, Shulan Zhang, Larry M. York, Wolf-Ruediger Scheible, Michael Udvardi
Summary: This study describes a high throughput phenotyping platform for testing the effects of small signaling peptides (SSP) on root uptake of multiple nutrients in plants. The results show that SSP CEP1 can enhance nitrate uptake rate in Medicago truncatula plants deprived of nitrogen. Furthermore, specific structural variants of CEP1 peptides not only enhance nitrate uptake, but also phosphate and sulfate uptake in both Medicago truncatula and Arabidopsis thaliana. Transcriptome analysis reveals that CEP1 peptides can induce the expression of several genes, including nutrient transporters and signaling pathway genes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Jaiana Malabarba, Zhijuan Chen, David Windels, Jerome Verdier
Summary: Desiccation tolerance is crucial for seed survival and seedling germination in favorable conditions. This study investigates the epigenetic control of desiccation tolerance acquisition during seed maturation in the model legume Medicago truncatula under control and heat stress conditions. Two histone marks, H3K27me3 and H3ac, were examined for their roles in gene transcription and chromatin accessibility. The findings provide insights into the epigenetic regulation of seed maturation and desiccation tolerance in response to heat stress.
Article
Agronomy
Yun Kang, Amaia Seminario, Michael Udvardi, Paolo Annicchiarico
Summary: This study aimed to explore the relationship between leaf morphophysiological traits and adaptive response in alfalfa, and it provided support for breeding strategies. The results showed that cultivars specifically adapted to drought-prone environments exhibited better drought tolerance and smaller leaves compared to those specifically adapted to moisture-favourable environments. In addition, the study identified some inexpensive morphophysiological traits that could be used for early selection targeting drought-prone environments.
JOURNAL OF AGRONOMY AND CROP SCIENCE
(2023)
Article
Cell Biology
Kashif Mahmood, Ivone Torres-Jerez, Nick Krom, Wei Liu, Michael K. Udvardi
Summary: This study used RNA-sequencing to investigate the molecular basis of age-dependent and dark-induced leaf senescence in Medicago truncatula, a forage crop. The results revealed the differentially expressed genes and identified the key biological processes associated with leaf senescence. The study also identified a set of transcription factors that promoted senescence in tobacco leaves when expressed. These findings provide valuable insights into the mechanisms of leaf senescence in forage crops and suggest potential targets for controlling senescence in these crops.
Article
Biology
Zhao Hao, Yuan Wang, Na Ding, Malay C. Saha, Wolf-Rudiger Scheible, Kelly Craven, Michael Udvardi, Peter S. Nico, Mary K. Firestone, Eoin L. Brodie
Summary: In this study, it was found that switchgrass adapts well to marginal soils with low phosphorus content. The research also discovered that phosphorus limitation affects the chemical composition and quality of switchgrass, and different soil conditions impact nutrient allocation strategies, which in turn affects biomass yields in the subsequent year. The use of a machine learning model effectively addresses these challenges and provides important information about switchgrass growth conditions and feedstock quality.
COMMUNICATIONS BIOLOGY
(2022)
Article
Plant Sciences
Mailen Ortega-Cuadros, Tiago Lodi De Souza, Romain Berruyer, Sophie Aligon, Sandra Pelletier, Jean-Pierre Renou, Tatiana Arias, Claire Campion, Thomas Guillemette, Jerome Verdier, Philippe Grappin
Summary: The transmission of seed-borne pathogens during seed germination is a major cause of crop diseases. However, the immune responses of germinating seeds to biotic invaders are poorly understood. This study used the Arabidopsis thaliana/Alternaria brassicicola patho-system to investigate the transcriptional responses of germinating seeds and young seedlings to infection by the necrotrophic fungus. The results revealed non-canonical immune responses in early germinating seeds compared to early seedling establishment stages.
Article
Multidisciplinary Sciences
Mailen Ortega-Cuadros, Laurine Chir, Sophie Aligon, Tatiana Arias, Jerome Verdier, Philippe Grappin
Summary: This study utilized RNA-seq experiments to identify the transcripts of Arabidopsis thaliana seeds and Alternaria brassicicola and described the molecular mechanisms involved in seed interaction with the necrotrophic fungus. The results showed differentially expressed genes during seed germination and seedling establishment stages, and the dynamic transcript changes in the fungal pathogen during this process.
Editorial Material
Biochemistry & Molecular Biology
Nancy A. Eckardt, Sean Cutler, Thomas E. Juenger, Amy Marshall-Colon, Michael Udvardi, Paul E. Verslues
Article
Multidisciplinary Sciences
Sebastien Carrere, Baptiste Mayjonade, David Lalanne, Sylvain Gaillard, Jerome Verdier, Nicolas W. G. Chen
Summary: Flageolet bean, originating from France, has a high-quality genome sequence that can be used for further genomic and genetic studies on common bean and legumes in general. This is the first whole-genome sequence of a common bean accession from Europe.
Article
Plant Sciences
Elise Bizouerne, Joseph Ly Vu, Benoit Ly Vu, Isidore Diouf, Frederique Bitton, Mathilde Causse, Jerome Verdier, Julia Buitink, Olivier Leprince
Summary: This study investigated the impact of heat stress during fruit ripening on tomato seed lifespan during storage. The results showed that heat stress reduced the longevity and germination homogeneity of seeds, but there was genetic variability in the seed response to heat stress. Several QTLs associated with seed quality traits were identified, and candidate genes were proposed based on previous transcriptome and gene network data.
Article
Agronomy
Gamal ElMasry, Nasser Mandour, Yahya Ejeez, Didier Demilly, Salim Al-Rejaie, Jerome Verdier, Etienne Belin, David Rousseau
Summary: This study developed a computer-integrated multichannel spectral imaging system to non-destructively monitor the germination capacity and changes in moisture, protein, and sugars in individual cowpea seeds at different developmental stages. Partial least squares regression and linear discriminant analysis models accurately predicted the changes in moisture, protein, and sugar contents. The proposed system proved to be an effective tool for rapid screening and non-destructive estimation of the chemical composition and germination capacity of cowpea seeds.