Article
Multidisciplinary Sciences
Xinzhu Sun, Songmiao Hu, Xin Wang, He Liu, Yun Wei Zhou, Qingjie Guan
Summary: The study revealed the sensitivity of Amorpha fruticosa L. seedlings to drought stress and the important role of Salicylic acid in response to drought. Transcriptomic analysis showed that under drought stress, the differentially expressed genes were mostly up-regulated. DEGs were functionally enriched in cell wall, signal transduction, and hormonal regulation pathways.
Article
Environmental Sciences
Junxia Mao, Xiaofang Huang, Hongyan Sun, Xin Jin, Wenjuan Guan, Jiahui Xie, Yiying Wang, Xubo Wang, Donghong Yin, Zhenlin Hao, Ying Tian, Jian Song, Jun Ding, Yaqing Chang
Summary: This study investigates the molecular response mechanism of scallops to a combination of high temperature and hypoxia stress. The research reveals that scallops exhibit different sensitivities to environmental stress, and high temperature and hypoxia have a synergistic effect on scallops. Immune and apoptosis-related pathways play important roles in scallops' response to environmental stress, and heat shock proteins play a key role in scallops' adaptation to altered environments.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Ruilian Lai, Xin Feng, Jin Chen, Yongyan Zhang, Xiaoxia Wei, Yiting Chen, Chunzhen Cheng, Rujian Wu
Summary: A de novo transcriptome analysis in C. album revealed distinct gene expression patterns under chilling and freezing temperatures, with plant hormone signal transduction playing a significant role in the freezing temperature response.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Mingcheng Wang, Shaofei Tong, Tao Ma, Zhenxiang Xi, Jianquan Liu
Summary: Sichuan pepper, commonly used in Asian cuisine, has medicinal properties. Study showed that genes related to drought tolerance and apomixis are crucial for improving drought tolerance in Zanthoxylum armatum. Additionally, genes involved in sanshool and wgx-50/gx-50 biosynthesis were identified through gene homology searching and co-expression patterns analysis.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Sagarika Mishra, Gyanasri Sahu, Birendra Prasad Shaw
Summary: The study identified 198 highly conserved, 21 legume-specific, 14 less-conserved, and 10 novel drought-responsive microRNAs (miRNAs) in an elite high-yielding drought-tolerant Indian cowpea cultivar. It was found that over-expressing miR408 could enhance drought and salinity tolerance in cowpea plants, leading to increased chlorophyll content, proline content, relative water content, and reduced cellular H2O2 levels. The study also revealed changes in stomatal aperture and trichome density in transgenic lines, indicating a potential role of miR408 in regulating drought tolerance in cowpea through lipid catabolic processes.
PLANT CELL REPORTS
(2022)
Article
Plant Sciences
Catalina Vidal, Giovanni Larama, Anibal Riveros, Claudio Meneses, Pablo Cornejo
Summary: The study conducted transcriptomic analysis on the metallophyte Imperata cylindrica grown in copper-polluted soils in Central Chile to investigate the response to Cu stress. Results showed that roots had more differentially expressed genes compared to shoots, with a focus on actin and cytoskeleton formation, as well as some genes associated with metal transporters and superoxide dismutase activity.
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
Agriculture, Dairy & Animal Science
Hoa Quynh Nguyen, Yuseob Kim, Yikweon Jang
Summary: Cicadas living in hotter urban heat islands exhibit higher thermal tolerance than those in cooler areas, with activated genes mainly related to heat shock, energy metabolism, and detoxification. These findings suggest that cicadas in high-UHIs can rapidly express genes related to heat stress responses to increase their thermal tolerance.
Article
Genetics & Heredity
Dhawale Ramesh Narayanrao, R. S. Tomar, Padhiyar Sm, Kheni Jasminkumar, Gulwe Ashish, Nitin Mahendra Chauhan, Suresh Chandra Singh, Vijay Upadhye, Mohammed Kuddus, Laxmikant Kamble, Sunil Tulshiram Hajare
Summary: This study aimed to identify potential genes and metabolites associated with drought resistance in the little millet Panicum sumatrense. The results revealed the differential expression of key genes in the drought-resistant genotype and highlighted the role of polyamines in drought stress tolerance.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Biotechnology & Applied Microbiology
Chao Yuan, Shaowei Zhang, Ruolin Hu, Dayong Wei, Qinglin Tang, Yongqin Wang, Shibing Tian, Yi Niu, Zhimin Wang
Summary: RNA sequencing was used to analyze the transcriptomic profiles of eggplants with different fertility levels, revealing genes and pathways associated with anther dehiscence. This study provides a comprehensive understanding of the molecular mechanisms of anther dehiscence in eggplant.
Article
Multidisciplinary Sciences
Alireza Akbari, Ahmad Ismaili, Nazanin Amirbakhtiar, Masoumeh Pouresmael, Zahra-Sadat Shobbar
Summary: This study used RNA sequencing to investigate the gene expression differences between two cold tolerant and sensitive chickpea genotypes. The results showed that the sensitive genotype had significant down-regulation of genes related to photosynthesis under cold stress, while the tolerant genotype exhibited several protective and signaling genes. These findings are important for improving cold tolerance in chickpea through molecular breeding or genetic engineering.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Luis F. Maceda-Lopez, Elsa B. Gongora-Castillo, Enrique Ibarra-Laclette, Dalia C. Moran-Velazquez, Amaranta Giron Ramirez, Matthieu Bourdon, Jose L. Villalpando-Aguilar, Gabriela Toomer, John Z. Tang, Parastoo Azadi, Jorge M. Santamaria, Itzel Lopez-Rosas, Mercedes G. Lopez, June Simpson, Fulgencio Alatorre-Cobos
Summary: Through transcriptome data mining, we investigated the cellulose biosynthesis pathway and metabolism mechanism in the Agave species. Our findings shed light on the molecular basis of cell wall biogenesis in Agave, particularly in relation to secondary cell wall formation.
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
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Lirong Wang, Meng Du, Bo Wang, Huirong Duan, Benyin Zhang, Dong Wang, Yi Li, Jiuli Wang
Summary: Nitraria tangutorum exhibits excellent salt tolerance through complex regulatory mechanisms modulated by multiple genes, including catabolism of organic compounds, antioxidant defense, signaling pathways regulation, ion homeostasis maintenance, and cell expansion.
SCIENTIFIC REPORTS
(2022)
Review
Plant Sciences
Khurram Bashir, Zarnab Ahmad, Takanori Kobayashi, Motoaki Seki, Naoko K. Nishizawa
Summary: Improving crop production in response to changing environmental conditions is a challenge for plant breeders and biotechnologists. Micronutrients like iron, zinc, manganese, and copper are essential for plant growth and reproduction, but must be carefully regulated to avoid toxicity. Understanding subcellular metal distribution and availability mechanisms is crucial for developing crops better suited to changing environmental conditions.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Anicet Agossa Batcho, Muhammad Bilal Sarwar, Bushra Rashid, Sameera Hassan, Tayyab Husnain
Summary: This study focused on improving local cotton's tolerance against heat and other abiotic stresses through genetic transformation with the AsHSP70 gene. Results showed enhanced heat tolerance at molecular, physiological, and biochemical levels in transgenic plants, including increased AsHSP70 expression and improved membrane stability. Single copy of the transgene was detected in T-1 progeny, indicating potential for selecting pure heat-tolerant lines for cotton breeding programs under heat stress.
THEORETICAL AND EXPERIMENTAL PLANT PHYSIOLOGY
(2021)
Article
Genetics & Heredity
Mattia Fois, Andrea Bellucci, Marta Malinowska, Morten Greve, Anja Karine Ruud, Torben Asp
Summary: A population of 239 Lolium perenne genotypes was analyzed to identify marker-trait associations for crown rust and brown rust resistance. The high-density SNP dataset allowed for accurate evaluation of LD decay, and candidate genes for the traits were detected.
Article
Biotechnology & Applied Microbiology
Istvan Nagy, Elisabeth Veeckman, Chang Liu, Michiel Van Bel, Klaas Vandepoele, Christian Sig Jensen, Tom Ruttink, Torben Asp
Summary: In this study, a chromosome-scale genome sequence assembly of perennial ryegrass was reported, which will serve as valuable resources for evolutionary and comparative genomics as well as breeding applications.
Article
Plant Sciences
Khurram Bashir, Daisuke Todaka, Sultana Rasheed, Akihiro Matsui, Zarnab Ahmad, Kaori Sako, Yoshinori Utsumi, Anh Thu Vu, Maho Tanaka, Satoshi Takahashi, Junko Ishida, Yuuri Tsuboi, Shunsuke Watanabe, Yuri Kanno, Eigo Ando, Kwang-Chul Shin, Makoto Seito, Hinata Motegi, Muneo Sato, Rui Li, Saya Kikuchi, Miki Fujita, Miyako Kusano, Makoto Kobayashi, Yoshiki Habu, Atsushi J. Nagano, Kanako Kawaura, Jun Kikuchi, Kazuki Saito, Masami Yokota Hirai, Mitsunori Seo, Kazuo Shinozaki, Toshinori Kinoshita, Motoaki Seki
Summary: This study demonstrates that exogenous application of ethanol can significantly enhance drought tolerance in Arabidopsis thaliana, rice, and wheat. Ethanol treatment leads to the upregulation of genes related to sugar and phenylpropanoid metabolism, as well as the accumulation of sugars and drought-tolerance-related amino acids. Ethanol treatment induces stomatal closure and decreases transpiration rate, resulting in enhanced drought tolerance. ABA signaling and acetic acid biosynthesis are involved in ethanol-mediated drought tolerance.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Plant Sciences
Elesandro Bornhofen, Dario Fe, Ingo Lenk, Morten Greve, Thomas Didion, Christian Sig Jensen, Torben Asp, Luc Janss
Summary: The present study investigated the relevance of incorporating the longitudinal dimension of within-season multiple measurements of forage perennial ryegrass traits in a reaction-norm model setup. Genetic parameters and accuracy of genomic estimated breeding value predictions were investigated using genomic random regression models. The study found that the additive genetic correlations were higher in later harvests and that modeling the temporal dimension improved the accuracy of breeding value predictions for nutritive quality traits.
Article
Plant Sciences
Marta Malinowska, Anja Karine Ruud, Just Jensen, Simon Fiil Svane, Abraham George Smith, Andrea Bellucci, Ingo Lenk, Istvan Nagy, Mattia Fois, Thomas Didion, Kristian Thorup-Kristensen, Christian Sig Jensen, Torben Asp
Summary: This study used various data integration analysis methods to explore the regulatory mechanisms of polygenic effects in perennial ryegrass, providing a new statistical paradigm for the study of complex traits.
Article
Agronomy
Maria de la O. Leyva-Perez, Lea Vexler, Stephen Byrne, Corentin R. Clot, Fergus Meade, Denis Griffin, Tom Ruttink, Jie Kang, Dan Milbourne
Summary: We have developed a novel low-cost genome-scanning marker platform called PotatoMASH. By using multiplex amplicon sequencing, PotatoMASH efficiently analyzes 339 multi-allelic regions in the potato genome and has been successfully applied to over 700 potato lines. PotatoMASH is able to diagnose pest-resistance markers, detect quantitative trait loci, and track genetic variation.
Article
Plant Sciences
Pernille Bjarup Hansen, Anja Karine Ruud, Gustavo de los Campos, Marta Malinowska, Istvan Nagy, Simon Fiil Svane, Kristian Thorup-Kristensen, Jens Due Jensen, Lene Krusell, Torben Asp
Summary: In this study, multi-omics models were evaluated to predict complex traits in barley. By integrating genomic, transcriptomic, and DNA methylation data, a higher proportion of phenotypic variance was explained compared to using genomic models alone. The addition of transcriptomic and DNA methylation information improved the accuracy of predictions and provided insights into the influence of the environment and non-additive genetic effects on complex traits in barley.
Article
Biochemistry & Molecular Biology
Marius Rohner, Chloe Manzanares, Steven Yates, Daniel Thorogood, Dario Copetti, Thomas Luebberstedt, Torben Asp, Bruno Studer
Summary: Self-incompatibility (SI) is a genetic mechanism in plants that prevents inbreeding after self-pollination. Researchers have identified two genes, ZDUF247-I and ZDUF247-II, as well as the gene sZ, which determine pollen and stigma components in perennial ryegrass. The genes for SI in ryegrass show similar composition and structure to those in the S-locus, supporting the hypothesis of a duplicated origin of the two-locus SI system in grasses. Comparative genomic analyses revealed that the absence of functional copies of SI determinants leads to self-compatibility. This study provides insights into the origin and evolution of the unique gametophytic SI system in grasses, which is economically important.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Elesandro Bornhofen, Dario Fe, Istvan Nagy, Ingo Lenk, Morten Greve, Thomas Didion, Christian S. Jensen, Torben Asp, Luc Janss
Summary: Research indicates substantial changes in gene co-expression and metabolite-metabolite network topologies as a result of genetic perturbation by hybridizing L. perenne with another species within the genus. However, conserved hub genes and hub metabolomic features were detected between pedigree classes and showed significant correlation with agronomic traits. Understanding the mechanisms of forage production and biomass nutritive quality is crucial for maximizing high-quality dry matter output per unit of land.
Review
Plant Sciences
C. Paina, P. L. Gregersen
Summary: Wheat is a crucial crop and has been selectively bred for improved performance since ancient times. Grain protein content (GPC), which is controlled by multiple genomic loci and influenced by the environment, is an important trait in breeding programs. This review summarizes recent genetic research on wheat GPC and grain protein deviation (GPD), as well as the performance of genomic prediction models for these traits. The study identifies 364 significant loci related to GPC and GPD on the hexaploid wheat genome, with a focus on two regions on chromosomes 3A and 5A. Overlapping independent QTL from different studies suggest stable genomic regions with potential for improving grain quality.
Article
Genetics & Heredity
Sadia Manzoor, Imran Riaz Malik, Shah Jahan, Muhammad Bilal Sarwar, Asma Bashir, Sulaiman Shams, Abrar Hussain
Summary: Hepatitis is a common liver disease with serious health consequences worldwide. This study quantified the expression of miRNAs, such as miRNA-182, 122, 21, 150, 199, and 222, in different stages of hepatitis C virus (HCV) infection. The results showed significant differences in biochemical parameters and viral load between diseased and control groups. Specific miRNAs were found to be overexpressed or down-regulated in different stages of HCV infection, and their expression levels changed after successful treatment. These miRNAs could potentially serve as biomarkers for diagnosing HCV stages.
Article
Biochemistry & Molecular Biology
Christina R. Ingvardsen, Julio A. Massange-Sanchez, Finn Borum, Winnie S. Fuchtbauer, Merethe Bagge, Soren Knudsen, Per L. Gregersen
Summary: The introduction of mlo-based resistance in wheat is a significant advancement in crop breeding for durable disease resistance. By screening mutant plants, we obtained triple homozygous mlo mutant lines that showed highly effective resistance against powdery mildew attacks. These mutations all contributed to resistance, but had varying effects on the occurrence of symptoms.
Correction
Plant Sciences
Flavia Pilar Forte, Marta Malinowska, Istvan Nagy, Jan Schmid, Paul Dijkwel, David E. Hume, Richard D. Johnson, Wayne R. Simpson, Torben Asp
FRONTIERS IN PLANT SCIENCE
(2023)