Article
Multidisciplinary Sciences
Jianhua Chen, Hao Xu, Jian Zhang, Shengjun Dong, Quangang Liu, Ruoxi Wang
Summary: The key stage for male sterility in Prunus sibirica was identified as the microspore stage, with the pollen maturity stage being the post stage for anther abortion. Transcriptome analysis revealed various biological pathways related to male sterility, such as protein kinase activity, apoptosis process, and starch and sucrose metabolism. Abnormal metabolic processes like the release of cytochrome c in the male sterile flower buds and the imbalance of the antioxidant system were found to contribute to the occurrence of male sterility.
Article
Forestry
Angela S. Prudencio, Frank A. Hoeberichts, Federico Dicenta, Pedro Martinez-Gomez, Raquel Sanchez-Perez
Summary: Flower bud dormancy in temperate fruit tree species, such as almond, is a survival mechanism that requires chilling requirements for endodormancy and transcriptome reprogramming for ecodormancy. Candidate genes related to metabolism, signaling, cell wall remodeling, and pollen development were identified during endodormancy and ecodormancy phases in almond flower buds. This information can contribute to the development of dormancy molecular markers for breeding in a changing climate context.
Article
Plant Sciences
Yuki Monden, Hirona Tanaka, Ryota Funakoshi, Seiya Sunayama, Kiyotaka Yabe, Eri Kimoto, Kentaro Matsumiya, Takanori Yoshikawa
Summary: This study identified two rice lines with higher protein content by analyzing the insertion sites of mPing transposons and the transcriptome. The results provide insights into the mechanism behind increased protein content in rice and contribute to solving malnutrition and health problems by improving rice protein content.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Magdalena Szeliga, Beata Bakera, Magdalena Swiecicka, Miroslaw Tyrka, Monika Rakoczy-Trojanowska
Summary: Wheat flowers can be divided into two groups, one with closed flowers for flowering and pollination, and another with open flowers. The swelling of lodicules is involved in the flowering process and can be differentiated between the two groups. Understanding the mechanism of chasmogamy can help in selecting plants with desired outcrossing rates.
Article
Food Science & Technology
Ping Sun, Chengkun Yang, Wencan Zhu, Jiaqi Wu, Xianrui Lin, Yi Wang, Jianxi Zhu, Chenfei Chen, Kaibing Zhou, Minjie Qian, Jiansheng Shen
Summary: Anthocyanin accumulation in the flesh of peach exhibits a spatial pattern, but the mechanism is still unknown. In this study, flavonoid metabolites, plant hormones, and transcriptome analyses were performed to investigate the regulation of anthocyanin accumulation in peach flesh. The results revealed the up-regulation of anthocyanin biosynthetic genes, transportation genes, and regulatory genes, as well as the enrichment and distribution of various hormones in peach flesh.
Article
Plant Sciences
Yang Wu, Huimin Shi, Haifeng Yu, Yu Ma, Haibo Hu, Zhigang Han, Yonghu Zhang, Zilong Zhen, Liuxi Yi, Jianhua Hou
Summary: This study identified 14 candidate genes that may play a crucial role in sunflower drought response through a combination of genome-wide association studies and RNA-seq analysis. These genes, including abscisic acid related protein kinases and transcription factors, provide new insights into the response mechanisms of sunflowers against drought stress and serve as a valuable reference for further genetic breeding efforts.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Thira Faruangsaeng, Sermporn Thaweesapphitak, Chompak Khamwachirapitak, Thantrira Porntaveetus, Vorasuk Shotelersuk
Summary: The molecular control of tooth development differs between the maxilla and mandible, with PITX1 gene expression significantly higher in mandibular posterior teeth compared to maxillary posterior teeth. These differences should be considered in molecular studies of dental pulp stem cells and may contribute to more precise treatments in regenerative dentistry.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Michael Schwabe, Sven Griep, Henrike Schmidtberg, Rudy Plarre, Alexander Goesmann, Andreas Vilcinskas, Heiko Vogel, Karina Brinkrolf
Summary: The clothes moth Tineola bisselliella is capable of digesting keratin, and the analysis of its gut transcriptome reveals various enzymes involved in keratin digestion. Additionally, the unstable intestinal microbiome of T. bisselliella larvae may play a role in keratin digestion.
Article
Plant Sciences
Man Zhang, Qingqing Yang, Xi Yuan, Xiaolan Yan, Jia Wang, Tangren Cheng, Qixiang Zhang
Summary: Our study identified 1,445 candidate genes consistently linked with flowering time across multiple years through genome-wide association studies on 235 Prunus mume landraces. Transcriptome analysis revealed 617 genes differentially expressed during the flowering process, and co-expression network analysis identified 191 gene candidates with conserved transcriptional patterns during blooming across cultivars. Our findings will contribute to a greater understanding of flowering time control in woody perennials and facilitate molecular breeding of novel Prunus mume varieties.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Wenxiang Lu, Qin Zhou, Yi Chen
Summary: RNA sequencing is an innovative technology for studying transcriptomes, but clinical specimens face challenges due to sample degradation. This study replicated the process of RNA degradation and found that even slight levels of degradation can significant affect RNA expression.
Article
Agriculture, Multidisciplinary
Harun Karci
Summary: This study used the QTL-seq approach to identify genomic regions associated with double seeds in almonds. Three genomic fragments responsible for double seeds were identified, and two putative genes related to double seeds were detected. The findings provide useful information for marker-assisted selection in future almond breeding programs.
TURKISH JOURNAL OF AGRICULTURE AND FORESTRY
(2023)
Article
Agriculture, Dairy & Animal Science
Nidhi Sukhija, Anoop Anand Malik, Joel M. Devadasan, Aishwarya Dash, Kangabam Bidyalaxmi, D. Ravi Kumar, M. Kousalaya Devi, Anjali Choudhary, K. K. Kanaka, Rekha Sharma, Shashi Bhushan Tripathi, Saket Kumar Niranjan, Jayakumar Sivalingam, Archana Verma
Summary: This study identified selection signatures in Indian Gir and Tharparkar cattle using ddRAD-seq, and discovered genes related to production, reproduction, immunity, and adaptation. Pathway analysis revealed the roles of these genes in milk production, reproduction, and adaptation.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Henry E. Pratt, Gregory R. Andrews, Nishigandha Phalke, Michael J. Purcaro, Arjan van der Velde, Jill E. Moore, Zhiping Weng
Summary: The update to Factorbook significantly expands the coverage of cell types and TF, includes an expanded motif catalog and new tools for applying motif models within machine learning frameworks, and offers integrative analysis options including annotation of variants and disease traits. The database is available at www.factorbook.org and will continue to expand with the release of ENCODE Phase IV data.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Allergy
Lena Moebus, Elke Rodriguez, Inken Harder, Nicole Boraczynski, Silke Szymczak, Matthias Huebenthal, Dora Stoelzl, Sascha Gerdes, Andreas Kleinheinz, Susanne Abraham, Annice Heratizadeh, Christiane Handrick, Eva Haufe, Thomas Werfel, Jochen Schmitt, Stephan Weidinger
Summary: This study explored the blood transcriptomic features of moderate to severe atopic dermatitis (AD). The results showed that AD patients exhibited pronounced inflammatory expression signatures and could be stratified into eosinophilic and noneosinophilic endotypes. Additionally, treatment strategies for the eosinophil-high endotype may require more attention to the restoration of natural killer cell function.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Plant Sciences
J. Song, I Mavraganis, W. Shen, H. Yang, D. Cram, D. Xiang, N. Patterson, J. Zou
Summary: This study used RNA sequencing analysis to investigate the transcriptome of developing lentil seeds and compared it with that of pod shells and leaves. The study identified 2622 genes that were differentially expressed among the tissues examined. Genes preferentially expressed in seeds were associated with development, nitrogen/carbon metabolism, and lipid synthesis. The findings provide valuable insights for breeding strategies to improve lentil seed quality traits.
Article
Horticulture
J. A. Salazar, P. Martinez-Gomez, D. Ruiz
Summary: The study evaluated postharvest behavior and shelf-life of different apricot varieties, identifying several varieties with long shelf-life up to 35 days, which can improve exportation and prolong storage time.
EUROPEAN JOURNAL OF HORTICULTURAL SCIENCE
(2022)
Article
Plant Sciences
Marjan Jafari, Behrouz Shiran, Gholamreza Rabiei, Rudabeh Ravash, Badraldin Ebrahim Sayed Tabatabaei, Pedro J. Martinez-Garcia, Pedro Martinez-Gomez
Summary: This study elucidates the genetic control of seed size in almonds using the xenia phenomenon. Differential gene expression analysis reveals DEGs associated with hormone signaling, metabolite synthesis, and cell communication. Several genes and proteins, including PduBEN1, PduSUS2, play a significant role in determining kernel size.
PLANT GROWTH REGULATION
(2022)
Article
Biochemistry & Molecular Biology
Beatriz E. Garcia-Gomez, Juan A. Salazar, Jose A. Egea, Manuel Rubio, Pedro Martinez-Gomez, David Ruiz
Summary: This study monitored the ripening progression of apricot fruit in nine cultivars with different fruit color and ripening date through gene expression analysis. Certain genes were identified as key predictors for fruit color, anthocyanins content, and carotenoids content, providing potential RNA markers for monitoring the ripening stage and estimating pigment compounds in apricot fruit.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Bernardo Rodamilans, Juan C. Oliveros, David San Leon, Pedro J. Martinez-Garcia, Pedro Martinez-Gomez, Juan A. Garcia, Manuel Rubio
Summary: The study found that 'Garrigues' almond trees could transfer resistance to peach trees through grafting, reducing symptoms and viral load in PPV-infected plants. Additionally, it was discovered that 'Garrigues' almond plants were infected by different plant viruses that could be collaborating in the observed effect by inducing a strong antiviral response through RNA silencing in grafted peaches.
Article
Biochemical Research Methods
Monica Canton, Silvia Farinati, Cristian Forestan, Justin Joseph, Claudio Bonghi, Serena Varotto
Summary: This study established specific protocols for chromatin extraction and immunoprecipitation in reproductive tissues of peach and investigated the role of two chromatin marks in modulating specific gene expression. The findings provide useful methods for evaluating the involvement of histone modifications in the regulation of gene expression during bud dormancy and fruit ripening.
Article
Plant Sciences
Monica Canton, Cristian Forestan, Gianpiero Marconi, Esther Carrera, Claudio Bonghi, Serena Varotto
Summary: In temperate zones, fruit trees adjust their annual growth cycle to seasonal changes. Chilling accumulation allows peach flower bud development to be completed, accompanied by changes in transcription, epigenetic modifications, and chromatin structure.
Article
Horticulture
Manuel Rubio, Pedro Martinez-Gomez, Federico Dicenta
Summary: Spain is a key producer of fresh apricots. The traditional cultivars are susceptible to viral diseases that affect fruit quality and production. By using foreign resistance sources, new apricot cultivars resistant to Plum pox virus (PPV) and Apple chlorotic leaf spot virus (ACLSV) have been developed.
SCIENTIA HORTICULTURAE
(2023)
Editorial Material
Horticulture
Federico Dicenta, Teresa Cremades, Jesus Lopez-Alcolea, Manuel Rubio, Pedro Jose Martinez-Garcia, Raquel Sanchez-Perez, Pedro Martinez-Gomez, Jose Egea
Review
Plant Sciences
Sama Rahimi Devin, Angela S. Prudencio, Sayyed Mohammad Ehsan Mahdavi, Manuel Rubio, Pedro J. Martinez-Garcia, Pedro Martinez-Gomez
Summary: We discuss the recent horticultural, biochemical, and molecular strategies adopted to improve the response of temperate fruit crops to water stress, as well as the feasibility of cultivating fruit trees in dry areas and protection methods. We provide a detailed analysis of the main factors involved in planting fruit trees in dry areas, such as plant material selection, regulated deficit irrigation strategies, rainwater harvesting, and anti-water stress materials. Additionally, we review the molecular mechanisms associated with the contribution of the microbiome to improving plant responses to drought.
Review
Biochemistry & Molecular Biology
Marina Martin-Valmaseda, Sama Rahimi Devin, German Ortuno-Hernandez, Cristian Perez-Caselles, Sayyed Mohammad Ehsan Mahdavi, Geza Bujdoso, Juan Alfonso Salazar, Pedro Martinez-Gomez, Nuria Alburquerque
Summary: CRISPR is a technology that selectively modifies the DNA of living organisms, adapted from naturally occurring genome-editing systems found in bacteria. Researchers reviewed the methods of introducing CRISPR/Cas-mediated genome editing into fruit tree species, and its impacts on tree development, yield, fruit quality, and tolerance to stresses. The gene-editing technology could enable the development of improved fruit crops, targeting different genetic segments or introducing traits without altering others. However, limitations such as limited regeneration and transformation protocols, genotype dependence, and the segregation of transgenic parts in the CRISPR system hinder its potential for fruit trees. The latest news on legislation and regulations regarding CRISPR/Cas-modified plants is also discussed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Proceedings Paper
Agricultural Engineering
J. Lopez-Alcolea, J. Mas-Gomez, M. Rubio, J. Guillamon Guillamon, P. J. Martinez-Garcia, P. Martinez-Gomez, F. Dicenta, R. Carrillo, R. Sanchez-Perez, D. Ruiz
Summary: In warm areas, peach culture faces adaptation problems due to climate change, resulting in issues such as uneven flowering and flower bud drop. A new formulation called 'Bloom-Tech (R) Spray' has been developed as a chemical treatment to compensate for the unfulfilled chill requirements. The study found that using this formulation resulted in a greater number of flower buds, more synchronized flowering, and increased yield compared to other products.
X INTERNATIONAL PEACH SYMPOSIUM
(2022)
Proceedings Paper
Agricultural Engineering
B. Rodamilans, J. C. Oliveros, D. San Leon, P. J. Martinez-Garcia, P. Martinez-Gomez, J. A. Garcia, M. Rubio
Summary: The study found that PPV-resistant 'Garrigues' almond could transfer its resistance to peach trees through grafting, resulting in a strong RNA silencing antiviral response in grafted peaches. Furthermore, it was discovered that 'Garrigues' almond plants carried different plant viruses that may collaborate by cross-protection in the observed effect.
X INTERNATIONAL PEACH SYMPOSIUM
(2022)
Proceedings Paper
Agricultural Engineering
M. Rubio, P. J. Martinez-Garcia, F. Dicenta, P. Martinez-Gomez
Summary: Research has shown the possibility of inducing resistance to Plum pox virus in peaches through almond grafting, utilizing almond cultivars as an interstock to prevent sharka infection. Ten peach cultivars were tested, all successfully protected from virus infection.
X INTERNATIONAL PEACH SYMPOSIUM
(2022)
Proceedings Paper
Agricultural Engineering
M. Rubio, P. J. Martinez-Garcia, P. Martinez-Gomez
Summary: This study investigated DNA methylation in peach rootstocks using Illumina sequencing technology, identifying differential methylated genic and promoter regions in response to intra and interspecific grafting. These epigenetic modifications, including DNA methylation, potentially contribute to gene expression regulation. Further RNA-Seq experiments will help correlate DNA methylated regions with differentially expressed genes.
X INTERNATIONAL PEACH SYMPOSIUM
(2022)