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Publisher: Elsevier   (Total: 3175 journals)

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Showing 1 - 200 of 3175 Journals sorted alphabetically
A Practical Logic of Cognitive Systems     Full-text available via subscription   (Followers: 8)
AASRI Procedia     Open Access   (Followers: 14)
Academic Pediatrics     Hybrid Journal   (Followers: 28, SJR: 1.402, h-index: 51)
Academic Radiology     Hybrid Journal   (Followers: 22, SJR: 1.008, h-index: 75)
Accident Analysis & Prevention     Partially Free   (Followers: 90, SJR: 1.109, h-index: 94)
Accounting Forum     Hybrid Journal   (Followers: 25, SJR: 0.612, h-index: 27)
Accounting, Organizations and Society     Hybrid Journal   (Followers: 33, SJR: 2.515, h-index: 90)
Achievements in the Life Sciences     Open Access   (Followers: 5)
Acta Anaesthesiologica Taiwanica     Open Access   (Followers: 6, SJR: 0.338, h-index: 19)
Acta Astronautica     Hybrid Journal   (Followers: 376, SJR: 0.726, h-index: 43)
Acta Automatica Sinica     Full-text available via subscription   (Followers: 2)
Acta Biomaterialia     Hybrid Journal   (Followers: 27, SJR: 2.02, h-index: 104)
Acta Colombiana de Cuidado Intensivo     Full-text available via subscription   (Followers: 2)
Acta de Investigación Psicológica     Open Access   (Followers: 3)
Acta Ecologica Sinica     Open Access   (Followers: 8, SJR: 0.172, h-index: 29)
Acta Haematologica Polonica     Free   (Followers: 1, SJR: 0.123, h-index: 8)
Acta Histochemica     Hybrid Journal   (Followers: 3, SJR: 0.604, h-index: 38)
Acta Materialia     Hybrid Journal   (Followers: 235, SJR: 3.683, h-index: 202)
Acta Mathematica Scientia     Full-text available via subscription   (Followers: 5, SJR: 0.615, h-index: 21)
Acta Mechanica Solida Sinica     Full-text available via subscription   (Followers: 9, SJR: 0.442, h-index: 21)
Acta Oecologica     Hybrid Journal   (Followers: 10, SJR: 0.915, h-index: 53)
Acta Otorrinolaringologica (English Edition)     Full-text available via subscription  
Acta Otorrinolaringológica Española     Full-text available via subscription   (Followers: 2, SJR: 0.311, h-index: 16)
Acta Pharmaceutica Sinica B     Open Access   (Followers: 1)
Acta Poética     Open Access   (Followers: 4)
Acta Psychologica     Hybrid Journal   (Followers: 25, SJR: 1.365, h-index: 73)
Acta Sociológica     Open Access  
Acta Tropica     Hybrid Journal   (Followers: 6, SJR: 1.059, h-index: 77)
Acta Urológica Portuguesa     Open Access  
Actas Dermo-Sifiliograficas     Full-text available via subscription   (Followers: 3)
Actas Dermo-Sifiliográficas (English Edition)     Full-text available via subscription   (Followers: 2)
Actas Urológicas Españolas     Full-text available via subscription   (Followers: 3, SJR: 0.383, h-index: 19)
Actas Urológicas Españolas (English Edition)     Full-text available via subscription   (Followers: 1)
Actualites Pharmaceutiques     Full-text available via subscription   (Followers: 5, SJR: 0.141, h-index: 3)
Actualites Pharmaceutiques Hospitalieres     Full-text available via subscription   (Followers: 3, SJR: 0.112, h-index: 2)
Acupuncture and Related Therapies     Hybrid Journal   (Followers: 6)
Acute Pain     Full-text available via subscription   (Followers: 14)
Ad Hoc Networks     Hybrid Journal   (Followers: 11, SJR: 0.967, h-index: 57)
Addictive Behaviors     Hybrid Journal   (Followers: 15, SJR: 1.514, h-index: 92)
Addictive Behaviors Reports     Open Access   (Followers: 7)
Additive Manufacturing     Hybrid Journal   (Followers: 9, SJR: 1.039, h-index: 5)
Additives for Polymers     Full-text available via subscription   (Followers: 22)
Advanced Cement Based Materials     Full-text available via subscription   (Followers: 3)
Advanced Drug Delivery Reviews     Hybrid Journal   (Followers: 128, SJR: 5.2, h-index: 222)
Advanced Engineering Informatics     Hybrid Journal   (Followers: 11, SJR: 1.265, h-index: 53)
Advanced Powder Technology     Hybrid Journal   (Followers: 16, SJR: 0.739, h-index: 33)
Advances in Accounting     Hybrid Journal   (Followers: 8, SJR: 0.299, h-index: 15)
Advances in Agronomy     Full-text available via subscription   (Followers: 12, SJR: 2.071, h-index: 82)
Advances in Anesthesia     Full-text available via subscription   (Followers: 27, SJR: 0.169, h-index: 4)
Advances in Antiviral Drug Design     Full-text available via subscription   (Followers: 2)
Advances in Applied Mathematics     Full-text available via subscription   (Followers: 10, SJR: 1.054, h-index: 35)
Advances in Applied Mechanics     Full-text available via subscription   (Followers: 10, SJR: 0.801, h-index: 26)
Advances in Applied Microbiology     Full-text available via subscription   (Followers: 22, SJR: 1.286, h-index: 49)
Advances In Atomic, Molecular, and Optical Physics     Full-text available via subscription   (Followers: 14, SJR: 3.31, h-index: 42)
Advances in Biological Regulation     Hybrid Journal   (Followers: 4, SJR: 2.277, h-index: 43)
Advances in Botanical Research     Full-text available via subscription   (Followers: 2, SJR: 0.619, h-index: 48)
Advances in Cancer Research     Full-text available via subscription   (Followers: 28, SJR: 2.215, h-index: 78)
Advances in Carbohydrate Chemistry and Biochemistry     Full-text available via subscription   (Followers: 7, SJR: 0.9, h-index: 30)
Advances in Catalysis     Full-text available via subscription   (Followers: 5, SJR: 2.139, h-index: 42)
Advances in Cell Aging and Gerontology     Full-text available via subscription   (Followers: 3)
Advances in Cellular and Molecular Biology of Membranes and Organelles     Full-text available via subscription   (Followers: 12)
Advances in Chemical Engineering     Full-text available via subscription   (Followers: 27, SJR: 0.183, h-index: 23)
Advances in Child Development and Behavior     Full-text available via subscription   (Followers: 10, SJR: 0.665, h-index: 29)
Advances in Chronic Kidney Disease     Full-text available via subscription   (Followers: 10, SJR: 1.268, h-index: 45)
Advances in Clinical Chemistry     Full-text available via subscription   (Followers: 28, SJR: 0.938, h-index: 33)
Advances in Colloid and Interface Science     Full-text available via subscription   (Followers: 19, SJR: 2.314, h-index: 130)
Advances in Computers     Full-text available via subscription   (Followers: 14, SJR: 0.223, h-index: 22)
Advances in Dermatology     Full-text available via subscription   (Followers: 14)
Advances in Developmental Biology     Full-text available via subscription   (Followers: 10)
Advances in Digestive Medicine     Open Access   (Followers: 8)
Advances in DNA Sequence-Specific Agents     Full-text available via subscription   (Followers: 5)
Advances in Drug Research     Full-text available via subscription   (Followers: 21)
Advances in Ecological Research     Full-text available via subscription   (Followers: 42, SJR: 3.25, h-index: 43)
Advances in Engineering Software     Hybrid Journal   (Followers: 27, SJR: 0.486, h-index: 10)
Advances in Experimental Biology     Full-text available via subscription   (Followers: 6)
Advances in Experimental Social Psychology     Full-text available via subscription   (Followers: 42, SJR: 5.465, h-index: 64)
Advances in Exploration Geophysics     Full-text available via subscription   (Followers: 1)
Advances in Fluorine Science     Full-text available via subscription   (Followers: 7)
Advances in Food and Nutrition Research     Full-text available via subscription   (Followers: 54, SJR: 0.674, h-index: 38)
Advances in Fuel Cells     Full-text available via subscription   (Followers: 15)
Advances in Genetics     Full-text available via subscription   (Followers: 14, SJR: 2.558, h-index: 54)
Advances in Genome Biology     Full-text available via subscription   (Followers: 7)
Advances in Geophysics     Full-text available via subscription   (Followers: 6, SJR: 2.325, h-index: 20)
Advances in Heat Transfer     Full-text available via subscription   (Followers: 21, SJR: 0.906, h-index: 24)
Advances in Heterocyclic Chemistry     Full-text available via subscription   (Followers: 9, SJR: 0.497, h-index: 31)
Advances in Human Factors/Ergonomics     Full-text available via subscription   (Followers: 23)
Advances in Imaging and Electron Physics     Full-text available via subscription   (Followers: 1, SJR: 0.396, h-index: 27)
Advances in Immunology     Full-text available via subscription   (Followers: 36, SJR: 4.152, h-index: 85)
Advances in Inorganic Chemistry     Full-text available via subscription   (Followers: 8, SJR: 1.132, h-index: 42)
Advances in Insect Physiology     Full-text available via subscription   (Followers: 2, SJR: 1.274, h-index: 27)
Advances in Integrative Medicine     Hybrid Journal   (Followers: 6)
Advances in Intl. Accounting     Full-text available via subscription   (Followers: 3)
Advances in Life Course Research     Hybrid Journal   (Followers: 8, SJR: 0.764, h-index: 15)
Advances in Lipobiology     Full-text available via subscription   (Followers: 1)
Advances in Magnetic and Optical Resonance     Full-text available via subscription   (Followers: 9)
Advances in Marine Biology     Full-text available via subscription   (Followers: 14, SJR: 1.645, h-index: 45)
Advances in Mathematics     Full-text available via subscription   (Followers: 10, SJR: 3.261, h-index: 65)
Advances in Medical Sciences     Hybrid Journal   (Followers: 6, SJR: 0.489, h-index: 25)
Advances in Medicinal Chemistry     Full-text available via subscription   (Followers: 5)
Advances in Microbial Physiology     Full-text available via subscription   (Followers: 4, SJR: 1.44, h-index: 51)
Advances in Molecular and Cell Biology     Full-text available via subscription   (Followers: 21)
Advances in Molecular and Cellular Endocrinology     Full-text available via subscription   (Followers: 8)
Advances in Molecular Toxicology     Full-text available via subscription   (Followers: 7, SJR: 0.324, h-index: 8)
Advances in Nanoporous Materials     Full-text available via subscription   (Followers: 3)
Advances in Oncobiology     Full-text available via subscription   (Followers: 1)
Advances in Organ Biology     Full-text available via subscription   (Followers: 1)
Advances in Organometallic Chemistry     Full-text available via subscription   (Followers: 15, SJR: 2.885, h-index: 45)
Advances in Parallel Computing     Full-text available via subscription   (Followers: 6, SJR: 0.148, h-index: 11)
Advances in Parasitology     Full-text available via subscription   (Followers: 5, SJR: 2.37, h-index: 73)
Advances in Pediatrics     Full-text available via subscription   (Followers: 24, SJR: 0.4, h-index: 28)
Advances in Pharmaceutical Sciences     Full-text available via subscription   (Followers: 10)
Advances in Pharmacology     Full-text available via subscription   (Followers: 15, SJR: 1.718, h-index: 58)
Advances in Physical Organic Chemistry     Full-text available via subscription   (Followers: 8, SJR: 0.384, h-index: 26)
Advances in Phytomedicine     Full-text available via subscription  
Advances in Planar Lipid Bilayers and Liposomes     Full-text available via subscription   (Followers: 3, SJR: 0.248, h-index: 11)
Advances in Plant Biochemistry and Molecular Biology     Full-text available via subscription   (Followers: 7)
Advances in Plant Pathology     Full-text available via subscription   (Followers: 5)
Advances in Porous Media     Full-text available via subscription   (Followers: 5)
Advances in Protein Chemistry     Full-text available via subscription   (Followers: 17)
Advances in Protein Chemistry and Structural Biology     Full-text available via subscription   (Followers: 18, SJR: 1.5, h-index: 62)
Advances in Psychology     Full-text available via subscription   (Followers: 59)
Advances in Quantum Chemistry     Full-text available via subscription   (Followers: 6, SJR: 0.478, h-index: 32)
Advances in Radiation Oncology     Open Access  
Advances in Small Animal Medicine and Surgery     Hybrid Journal   (Followers: 3, SJR: 0.1, h-index: 2)
Advances in Space Biology and Medicine     Full-text available via subscription   (Followers: 5)
Advances in Space Research     Full-text available via subscription   (Followers: 375, SJR: 0.606, h-index: 65)
Advances in Structural Biology     Full-text available via subscription   (Followers: 5)
Advances in Surgery     Full-text available via subscription   (Followers: 9, SJR: 0.823, h-index: 27)
Advances in the Study of Behavior     Full-text available via subscription   (Followers: 29, SJR: 1.321, h-index: 56)
Advances in Veterinary Medicine     Full-text available via subscription   (Followers: 17)
Advances in Veterinary Science and Comparative Medicine     Full-text available via subscription   (Followers: 13)
Advances in Virus Research     Full-text available via subscription   (Followers: 5, SJR: 1.878, h-index: 68)
Advances in Water Resources     Hybrid Journal   (Followers: 46, SJR: 2.408, h-index: 94)
Aeolian Research     Hybrid Journal   (Followers: 6, SJR: 0.973, h-index: 22)
Aerospace Science and Technology     Hybrid Journal   (Followers: 333, SJR: 0.816, h-index: 49)
AEU - Intl. J. of Electronics and Communications     Hybrid Journal   (Followers: 8, SJR: 0.318, h-index: 36)
African J. of Emergency Medicine     Open Access   (Followers: 6, SJR: 0.344, h-index: 6)
Ageing Research Reviews     Hybrid Journal   (Followers: 9, SJR: 3.289, h-index: 78)
Aggression and Violent Behavior     Hybrid Journal   (Followers: 429, SJR: 1.385, h-index: 72)
Agri Gene     Hybrid Journal  
Agricultural and Forest Meteorology     Hybrid Journal   (Followers: 15, SJR: 2.18, h-index: 116)
Agricultural Systems     Hybrid Journal   (Followers: 31, SJR: 1.275, h-index: 74)
Agricultural Water Management     Hybrid Journal   (Followers: 43, SJR: 1.546, h-index: 79)
Agriculture and Agricultural Science Procedia     Open Access   (Followers: 1)
Agriculture and Natural Resources     Open Access   (Followers: 2)
Agriculture, Ecosystems & Environment     Hybrid Journal   (Followers: 56, SJR: 1.879, h-index: 120)
Ain Shams Engineering J.     Open Access   (Followers: 5, SJR: 0.434, h-index: 14)
Air Medical J.     Hybrid Journal   (Followers: 5, SJR: 0.234, h-index: 18)
AKCE Intl. J. of Graphs and Combinatorics     Open Access   (SJR: 0.285, h-index: 3)
Alcohol     Hybrid Journal   (Followers: 11, SJR: 0.922, h-index: 66)
Alcoholism and Drug Addiction     Open Access   (Followers: 9)
Alergologia Polska : Polish J. of Allergology     Full-text available via subscription   (Followers: 1)
Alexandria Engineering J.     Open Access   (Followers: 1, SJR: 0.436, h-index: 12)
Alexandria J. of Medicine     Open Access   (Followers: 1)
Algal Research     Partially Free   (Followers: 9, SJR: 2.05, h-index: 20)
Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (Followers: 2)
Allergologia et Immunopathologia     Full-text available via subscription   (Followers: 1, SJR: 0.46, h-index: 29)
Allergology Intl.     Open Access   (Followers: 5, SJR: 0.776, h-index: 35)
Alpha Omegan     Full-text available via subscription   (SJR: 0.121, h-index: 9)
ALTER - European J. of Disability Research / Revue Européenne de Recherche sur le Handicap     Full-text available via subscription   (Followers: 9, SJR: 0.158, h-index: 9)
Alzheimer's & Dementia     Hybrid Journal   (Followers: 48, SJR: 4.289, h-index: 64)
Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring     Open Access   (Followers: 4)
Alzheimer's & Dementia: Translational Research & Clinical Interventions     Open Access   (Followers: 4)
Ambulatory Pediatrics     Hybrid Journal   (Followers: 6)
American Heart J.     Hybrid Journal   (Followers: 50, SJR: 3.157, h-index: 153)
American J. of Cardiology     Hybrid Journal   (Followers: 50, SJR: 2.063, h-index: 186)
American J. of Emergency Medicine     Hybrid Journal   (Followers: 42, SJR: 0.574, h-index: 65)
American J. of Geriatric Pharmacotherapy     Full-text available via subscription   (Followers: 10, SJR: 1.091, h-index: 45)
American J. of Geriatric Psychiatry     Hybrid Journal   (Followers: 14, SJR: 1.653, h-index: 93)
American J. of Human Genetics     Hybrid Journal   (Followers: 31, SJR: 8.769, h-index: 256)
American J. of Infection Control     Hybrid Journal   (Followers: 26, SJR: 1.259, h-index: 81)
American J. of Kidney Diseases     Hybrid Journal   (Followers: 32, SJR: 2.313, h-index: 172)
American J. of Medicine     Hybrid Journal   (Followers: 42, SJR: 2.023, h-index: 189)
American J. of Medicine Supplements     Full-text available via subscription   (Followers: 3)
American J. of Obstetrics and Gynecology     Hybrid Journal   (Followers: 189, SJR: 2.255, h-index: 171)
American J. of Ophthalmology     Hybrid Journal   (Followers: 62, SJR: 2.803, h-index: 148)
American J. of Ophthalmology Case Reports     Open Access   (Followers: 6)
American J. of Orthodontics and Dentofacial Orthopedics     Full-text available via subscription   (Followers: 6, SJR: 1.249, h-index: 88)
American J. of Otolaryngology     Hybrid Journal   (Followers: 25, SJR: 0.59, h-index: 45)
American J. of Pathology     Hybrid Journal   (Followers: 27, SJR: 2.653, h-index: 228)
American J. of Preventive Medicine     Hybrid Journal   (Followers: 27, SJR: 2.764, h-index: 154)
American J. of Surgery     Hybrid Journal   (Followers: 37, SJR: 1.286, h-index: 125)
American J. of the Medical Sciences     Hybrid Journal   (Followers: 12, SJR: 0.653, h-index: 70)
Ampersand : An Intl. J. of General and Applied Linguistics     Open Access   (Followers: 6)
Anaerobe     Hybrid Journal   (Followers: 4, SJR: 1.066, h-index: 51)
Anaesthesia & Intensive Care Medicine     Full-text available via subscription   (Followers: 61, SJR: 0.124, h-index: 9)
Anaesthesia Critical Care & Pain Medicine     Full-text available via subscription   (Followers: 14)
Anales de Cirugia Vascular     Full-text available via subscription  
Anales de Pediatría     Full-text available via subscription   (Followers: 2, SJR: 0.209, h-index: 27)
Anales de Pediatría (English Edition)     Full-text available via subscription  
Anales de Pediatría Continuada     Full-text available via subscription   (SJR: 0.104, h-index: 3)
Analytic Methods in Accident Research     Hybrid Journal   (Followers: 4, SJR: 2.577, h-index: 7)
Analytica Chimica Acta     Hybrid Journal   (Followers: 39, SJR: 1.548, h-index: 152)
Analytical Biochemistry     Hybrid Journal   (Followers: 165, SJR: 0.725, h-index: 154)
Analytical Chemistry Research     Open Access   (Followers: 10, SJR: 0.18, h-index: 2)
Analytical Spectroscopy Library     Full-text available via subscription   (Followers: 11)
Anesthésie & Réanimation     Full-text available via subscription   (Followers: 1)
Anesthesiology Clinics     Full-text available via subscription   (Followers: 22, SJR: 0.421, h-index: 40)
Angiología     Full-text available via subscription   (SJR: 0.124, h-index: 9)
Angiologia e Cirurgia Vascular     Open Access   (Followers: 1)

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Journal Cover Agri Gene
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   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Online) 2352-2151
   Published by Elsevier Homepage  [3175 journals]
  • Bioinformatics profiling and expressional studies of microRNAs in root,
           stem and leaf of the bioenergy plant switchgrass (Panicum virgatum L.)
           under drought stress
    • Authors: Muhammad Younas Khan Barozai; Zhujia Ye; Sasikiran Reddy Sangireddy; Suping Zhou
      Abstract: Publication date: Available online 22 February 2018
      Source:Agri Gene
      Author(s): Muhammad Younas Khan Barozai, Zhujia Ye, Sasikiran Reddy Sangireddy, Suping Zhou
      Switchgrass (Panicum virgatum L.) is a perennial fodder grass and well known as a model renewable bioenergy crop. The plant's high production of biomass for biofuel supply is due to its fast-growing and wide adaptation properties. Very little studies and data are available about microRNAs (miRNAs) in this important biofuel crop. This situation demands to focus and identify new miRNAs and also to study their expressional analysis. In current research, a combination of computational and expressional approaches is applied to profile and characterize miRNAs in switchgrass and analyze some of them under drought stress. A total of 158 new miRNAs belonging to 83 families are identified and characterized from switchgrass expressed sequence tags (ESTs) and genomic survey sequences (GSS). In addition, five pre-miRNA clusters as well as four sense and antisense pre-miRNAs are also predicted from these newly identified miRNAs. Furthermore, 39 miRNAs were randomly selected and subjected to quantitative real-time RT-PCR expressional studies in root, leaf and stem of switchgrass under drought stress. A set of 13, 20 and 25 miRNAs are found as drought responding miRNAs in root, stem and leaf respectively. A total of 894 putative targets are also predicted for 158 switchgrass' miRNAs. These targets play roles in metabolism, transcription factor, signaling pathways, growth & development, stress-related, transport protein and other vital processes. Such findings in switchgrass improved the baseline data of miRNAs and their targets. This data can be utilized to fine-tune this important bioenergy crop under biotic and abiotic stresses. Furthermore, it can also be used for the improvement of biofuel properties of the plant.

      PubDate: 2018-02-27T05:12:50Z
      DOI: 10.1016/j.aggene.2018.02.001
  • In silico identification of microRNAs and their targets associated with
           coconut embryogenic calli
    • Authors: A.A. Sabana; Ginny Antony; C.U. Rahul; M.K. Rajesh
      Abstract: Publication date: Available online 10 January 2018
      Source:Agri Gene
      Author(s): A.A. Sabana, Ginny Antony, C.U. Rahul, M.K. Rajesh
      Coconut palms are propagated mainly through nuts, which does not meet the requirement of quality planting materials for large scale planting. In vitro propagation to enhance production of high yielding, disease-free planting material in coconut has remained a distant reality because of its in vitro recalcitrance. MicroRNAs (miRNAs) have been implicated in the regulation of a plethora of cellular, physiological and developmental processes which include developmental regulation, hormone response and adaptation to stresses. In this study, computational methods were utilized to identify conserved miRNA from transcriptome data of coconut embryogenic calli. A total of 117,790 unigenes from coconut embryogenic calli were compared against monocot mature miRNA sequences. A total of 27 mature miRNA sequences, belonging to 15 miRNA families, viz. miR156, miR164, miR166, miR167, miR169, miR171, miR172, miR394, miR397, miR408, miR444, miR535, miR827, miR1134 and miR2118, were identified. Many of these have well defined and crucial roles in developmental pathways and hormone signalling in other plant species. Each of the identified miRNA had its own predicted targets. This is the first in silico study describing miRNAs and their role in the regulation of in vitro embryogenesis in coconut. The results obtained in this study would provide a base for future studies to address molecular mechanisms that govern in vitro recalcitrance in coconut and the role of miRNAs in the process.

      PubDate: 2018-01-26T21:08:39Z
      DOI: 10.1016/j.aggene.2018.01.002
  • Transgenic expression of a maize geranyl geranyl transferase gene sequence
           in maize callus increases resistance to ear rot pathogens
    • Authors: Patrick F. Dowd; Bruce W. Zilkowski; Eric T. Johnson; Mark A. Berhow; Ephantus J. Muturi
      Abstract: Publication date: Available online 3 January 2018
      Source:Agri Gene
      Author(s): Patrick F. Dowd, Bruce W. Zilkowski, Eric T. Johnson, Mark A. Berhow, Ephantus J. Muturi
      Determining the genes responsible for pest resistance in maize can allow breeders to develop varieties with lower losses and less contamination with undesirable toxins. A gene sequence coding for a geranyl geranyl transferase-like protein located in a fungal ear rot resistance quantitative trait locus was cloned from an inbred with reported resistance to Fusarium proliferatum and Fusarium verticillioides ear rot. Transgenic expression of the gene in maize callus reduced colonization by these two Fusarium species and also Fusarium graminearum relative to a β-glucuronidase (GUS) transformant control. Some transformants were also more insect resistant. The more fungal resistant transformant lines produced higher levels of headspace ethanol which were significantly associated with antifungal activity, especially for F. verticillioides. Maize pyruvate decarboxylase appears to have a moiety capable of interacting with the geranyl geranyl transferase, suggesting ethanol production is enhanced due to more efficient transfer of pyruvate through the mitochondrial membrane. Other undetermined mechanisms may also be enhancing resistance of the transformants to the Fusarium fungus, however. This is the first report of the involvement of a geranyl geranyl transferase-like sequence in fungal resistance in plants, and represents a novel mechanism for producing higher yielding and better quality maize.

      PubDate: 2018-01-05T04:00:32Z
      DOI: 10.1016/j.aggene.2018.01.001
  • Season of collection and sperm head shape impacts expression of CARHSP and
           FTL from motile-rich boar sperm
    • Authors: L.A. Rempel; M.M. Krautkramer; T.M. Loether; J.J. Parrish; J.R. Miles
      Pages: 1 - 6
      Abstract: Publication date: March 2018
      Source:Agri Gene, Volume 7
      Author(s): L.A. Rempel, M.M. Krautkramer, T.M. Loether, J.J. Parrish, J.R. Miles
      The objective of the current study was to evaluate transcript activity of motile-rich sperm collected from June (spring) or August (summer), stored as cooled-extended (ExT) or cryopreserved (FrZ), and selected for least or most sperm head shape change, using Fourier harmonic analysis techniques, between June and August. Even with the lack of an extended heat stress, motile-rich sperm transcripts were influenced by season and putatively by sperm head shape change. Transcripts that had previously been associated with seasonality of sperm collection and methylation pathway transcripts were evaluated among semen samples. Calcium-regulated heat-stable protein 1-like transcript from motile-rich sperm tended (P=0.0829) to be greater in samples collected in June in comparison to August samples. Ferritin light polypeptide transcript tended (P=0.0838) to be greater from motile-rich sperm with least head shape change from June collection in contrast to sperm collected in August. Both transcripts have a functional role in cytoprotection and may serve to improve boar semen activity and quality during thermal stress or seasonal changes.

      PubDate: 2017-10-25T03:53:33Z
      DOI: 10.1016/j.aggene.2017.10.002
      Issue No: Vol. 7 (2017)
  • Genes, transcription factors and enzymes involved in lipid metabolism in
           fin fish
    • Authors: Christian Larbi Ayisi; Cheng Yamei; Jin-Liang Zhao
      Pages: 7 - 14
      Abstract: Publication date: March 2018
      Source:Agri Gene, Volume 7
      Author(s): Christian Larbi Ayisi, Cheng Yamei, Jin-Liang Zhao
      Lipid metabolism in fish which is a complex phenomenon has been studied in the past few years as its gradually gaining interest from researchers. Lipids serve essential roles in both physiological and life cycle of fish. In this study, we review the functions of some genes and enzymes that are related to the metabolism of lipids in fish. We also review how these enzymes and genes are affected by different lipid sources since alternative lipids are being sought for. From the study, genes such as PPARs, ACC, SCD, FASN, CPT, ACYL and a host of others regulate the lipid metabolic pathways.

      PubDate: 2017-10-25T03:53:33Z
      DOI: 10.1016/j.aggene.2017.09.006
      Issue No: Vol. 7 (2017)
  • Overexpression of mango alcohol dehydrogenase (MiADH1) mimics hypoxia in
           transgenic tomato and alters fruit flavor components
    • Authors: Rajesh Kumar Singh; Smriti Srivastava; Hemangi G. Chidley; Pravendra Nath; Vidhu A. Sane
      Pages: 23 - 33
      Abstract: Publication date: March 2018
      Source:Agri Gene, Volume 7
      Author(s): Rajesh Kumar Singh, Smriti Srivastava, Hemangi G. Chidley, Pravendra Nath, Vidhu A. Sane
      Plant alcohols and aldehydes are produced by the action of alcohol dehydrogenases (ADH) and play an important role during fruit ripening and aroma production. Alcohols are not only produced in different tissues at different stages of plant development but are also products of the fermentative pathway which gets activated by different stresses, including hypoxia. The ADH gene is a well-established marker for hypoxic response as well as plant aroma. In a previous report we have identified and characterized three ADHs (MiADH1, 2, 3) from Dashehari mango. MiADH1 was found to be fruit specific and was upregulated by ethylene and ABA, suggesting a role in fruit aroma volatile production. In order to functionally characterize MiADH1, transgenic tomato plants were developed under the control of the constitutive (CaMV35S) promoter. Transgenic tomato fruit expressing MiADH1 gene showed a change in the levels of several alcohols and aldehydes related to flavor in comparison to the control. The change in aroma and volatiles compounds was more prominent during the ripe stage as compared to unripe and mid-ripe stages of tomato fruit. The transgenic tomato plants also produced adventitious roots. Our results suggest that the overexpression of MiADH1 in tomato plants induced the fermentative pathway in roots, and mimicked hypoxic response by development of adventitious roots from the stem as an adaptive mechanism.

      PubDate: 2017-11-15T03:45:55Z
      DOI: 10.1016/j.aggene.2017.10.003
      Issue No: Vol. 7 (2017)
  • Identification of differentially expressed genes in two grape varieties
           cultivated in semi-arid and temperate regions from West-Bank, Palestine
    • Authors: Omar Saleh; Jamil Harb; Ali Karrity; M. Asif Arif; Wolfgang Frank
      Pages: 34 - 42
      Abstract: Publication date: March 2018
      Source:Agri Gene, Volume 7
      Author(s): Omar Saleh, Jamil Harb, Ali Karrity, M. Asif Arif, Wolfgang Frank
      Plants respond to stress conditions by altering genetic pathways. In this study, we aimed to identify and analyze differentially expressed genes in leaves of two grape varieties (genotypes) that were grown in Palestine either in a semi-arid region with a prolonged drought and high temperature stress or in a temperate region with moderate stress levels. In total, twelve transcripts with altered expression patterns, either by stress or genotype, were identified with the differential display RT-PCR (DDRT-PCR) technique and validated via quantitative real-time PCR (qRT-PCR). Eight transcripts represent genes that are down-regulated by stress in the leaves of at least one variety, among of which are members of the DEAD-box RNA helicase, Haloacid Dehalogenase (HAD) hydrolase, kinesin-like, and mitochondrial Adenine nucleotide transporter (ANT) gene families. Two genes encoding for members of the GDSL Lipase/Esterase and Multiprotein Bridging Factor (MBF) gene families were found to be up-regulated in stressed leaves. Two transcripts coding for a NAC-domain containing protein and a WD-repeat containing protein, respectively, were found to be non-responsive to those abiotic stresses but are differentially expressed in a genotype-dependent manner.

      PubDate: 2017-11-15T03:45:55Z
      DOI: 10.1016/j.aggene.2017.11.001
      Issue No: Vol. 7 (2017)
  • Paenibacillus larvae subspecies with dissimilar virulence patterns also
           group by vegetative growth characteristics and enolase isozyme biochemical
    • Authors: Bryan W. Lehner; Neil P. Schultes; Douglas W. Dingman
      Pages: 31 - 36
      Abstract: Publication date: December 2017
      Source:Agri Gene, Volume 6
      Author(s): Bryan W. Lehner, Neil P. Schultes, Douglas W. Dingman
      Paenibacillus larvae – the causal agent of American foul brood disease in Honey bees – group to different subspecies based upon disease progression and virulence as well as by molecular genotype. Vegetative growth studies reveal that virulence-grouped subspecies arrive at different saturated cell densities. In addition, strains segregating based upon virulence phenotype contain different genotypes in the locus encoding for the key glycolytic enzyme enolase. DNA sequence comparison of enolase loci from 7 Paenibacillus larvae strains identified 6 single-nucleotide polymorphisms (SNP) that segregated based on subspecies virulence classification. Only one polymorphism represented a change in amino acid coding (glycine or alanine) at position 331 of the protein. The kinetic properties of two recombinant enolase proteins expressed from enolase alleles isolated from different virulence classed strains (P. larvae ATCC 9545 and SAG 10367) yielded a Km and of 4.2μM and 1.5μM and Vmax of 16.2μmolmin−1 mg−1 and 10.8μmolmin−1 mg−1, respectively. Enolase from P. larvae SAG 10367 had a maximum reaction velocity lower than and a specificity constant approximately 1.6× higher than that of P. larvae ATCC 9545.

      PubDate: 2017-09-25T05:39:50Z
      DOI: 10.1016/j.aggene.2017.09.002
      Issue No: Vol. 6 (2017)
  • Expression of cytokine genes and receptors in white blood cells associated
           with divergent body weight gain in beef steers
    • Authors: Amanda K. Lindholm-Perry; Virginia M. Artegoitia; Jeremy R. Miles; Andrew P. Foote
      Pages: 37 - 39
      Abstract: Publication date: December 2017
      Source:Agri Gene, Volume 6
      Author(s): Amanda K. Lindholm-Perry, Virginia M. Artegoitia, Jeremy R. Miles, Andrew P. Foote
      Previous work examining the transcriptome of steer tissue samples from animals with divergent gain have shown a relationship with the expression of genes with functions in immune and inflammatory pathways. The process of mounting an immune or inflammatory response is energetically expensive and variation in cytokine responses may affect cattle production traits. In addition, a previous study has identified variation in the transcript abundance of numerous genes, including the cytokine gene IL6ST, in the circulating white blood cells of pigs associated with high and low residual feed intake (RFI) lines. The aim of this study was to determine whether changes in cytokine expression in the circulating white blood cells (WBC) could also be associated with body weight gain in beef steers. Crossbred steers (n=12) with average feed intake (10.9kg/d), but divergent body weight gain (Low=1.92kg/d; High=2.25kg/d), were selected for the study. The genes CCR3, IL9R, PF4, NAMPT and TNF were associated with gain (P≤0.05); and CSF1, IL2RG, IL6ST, CCL3, and TNFSF13B displayed a trend towards association with gain (P<0.1). The expression of cytokine genes in circulating WBCs may be useful indicators of production traits in cattle.

      PubDate: 2017-10-01T11:45:29Z
      DOI: 10.1016/j.aggene.2017.09.005
      Issue No: Vol. 6 (2017)
  • Associations of single nucleotide polymorphisms in the bovine prolactin
           gene with phenotypic traits in beef cattle
    • Authors: Laura Meyer; Jeremy Powell; Bryan Kutz; Michael Looper; A. Hayden Brown; Charles Rosenkrans
      Pages: 7 - 11
      Abstract: Publication date: September 2017
      Source:Agri Gene, Volume 5
      Author(s): Laura Meyer, Jeremy Powell, Bryan Kutz, Michael Looper, A. Hayden Brown, Charles Rosenkrans
      Fall-calving Angus-based cows (n =170 unique cows; 400 calving records during three years) were used to determine prolactin (Prl) genotype and haplotype effects on phenotypic traits. Genomic DNA, from buffy coat, was genotyped at three Prl SNP sites (C1286T, A1134T, and G8398A). Traits of interest were: pre-breeding body condition score (BCS) and weight, Julian calving date, calf birth weight, cow weight and BCS at weaning, calf weaning weight, adjusted 205-day weight and cow efficiency. Hair coat scores were determined each year in May, June, and July. Heterozygous cows at SNP C1286T had a lower (P <0.05) calving rate when compared to homozygous cows. Calf birth weight was affected (P <0.05) by genotypes at A1134T. Genotype at G8398A did not affect (P >0.10) phenotypic traits. Six haplotypes were identified: CAG (n =107), TAA (n =173), CTG (n =50), TTA (n =32), TAG (n =50), and TTG (n =37); n represents total number of records for that haplotype during 3-year study. Calving percentage for CAG cows was greater (P <0.05) than TTA, TAG, and TTG cows (96 vs. 83%; respectively, CAG vs. mean of TTA, TAG, and TTG). Haplotype CAG cows had earlier hair coat shedding. In addition, CAG cows had a larger calving rate (P <0.05) and greater (P <0.05) cow efficiency (45±0.9%) than TTG cows. Cows with Prl haplotype CTG or TAG cow efficiency decreased from ≤3 to 4–10 and were missing in ≥11years' group, suggesting those cows may have sustainability issues. Our results suggest that mutations associated with the bovine Prl gene may be useful as early selection tools for replacement cattle.

      PubDate: 2017-07-03T08:57:13Z
      DOI: 10.1016/j.aggene.2017.06.002
      Issue No: Vol. 5 (2017)
  • Comparative transcriptome analysis reveals potential gene targets for
           ovipositional inhibition by diallyl trisulfide against female Sitotroga
    • Authors: Min Ma; Yi-Yi Ying; Zhi-Ya He; Yan Lu; Xue-Gang Li; Chao-Liang Lei; Feng-Lian Yang
      Pages: 12 - 18
      Abstract: Publication date: September 2017
      Source:Agri Gene, Volume 5
      Author(s): Min Ma, Yi-Yi Ying, Zhi-Ya He, Yan Lu, Xue-Gang Li, Chao-Liang Lei, Feng-Lian Yang
      The angoumois grain moth, Sitotroga cerealella Olivier, is a serious stored-grain pest worldwide. In previous studies, we demonstrated that diallyl trisulfide (DATS), one of active substances from garlic essential oil, inhibited oviposition of S. cerealella, but the mechanism for this inhibition remains unclear. We suspected that DATS-regulated gene expression changes in S. cerealella may be a reason for the modulation of fertility and reproductive behaviors of the moth. Comparative transcriptomes of female S. cerealella were built by RNA-sequencing to detect differences between DATS exposure and background air with special lights on the key genes related to the fecundity. A total of 304 differentially expressed genes (DEGs) were detected in female moth after exposure to DATS, of which 120 were up-regulated, and 184 were down-regulated. Sixty-two of these DEGs encoding proteins involved in growth and development of eggs and regulation of hormones and mating behavior were identified, and of these, 49 were annotated as chorion protein. Meanwhile, quantitative real-time PCR verified that DEG data were reliable for further transcriptional analysis. Additionally, the results of ovarian dissection and oviposition activity bioassay suggest that DATS has negative effects on ovarian development and fecundity of S. cerealella. Our comprehensive sequence resource with desirable quality enriched the genomic platform of S. cerealella, and the DEGs that were identified will facilitate understanding of the molecular mechanism of ovipositional inhibition by DATS.

      PubDate: 2017-07-13T12:12:31Z
      DOI: 10.1016/j.aggene.2017.07.001
      Issue No: Vol. 5 (2017)
  • Long noncoding RNAs: Unexplored players in the drug response of the sea
           louse Caligus rogercresseyi
    • Authors: Diego Valenzuela-Miranda; Kayvan Etebari; Sassan Asgari; Cristian Gallardo-Escárate
      Pages: 1 - 7
      Abstract: Publication date: June 2017
      Source:Agri Gene, Volume 4
      Author(s): Diego Valenzuela-Miranda, Kayvan Etebari, Sassan Asgari, Cristian Gallardo-Escárate
      Long non-coding RNAs (lncRNAs), endogenous RNAs with restricted or null coding potential, are emerging as key regulators of multiple biological processes in several species. Despite the importance of these transcripts, few studies have characterized marine crustacean lncRNAs or the modulation of these in response to chemical exposure. Therefore, the present study mainly focused on identifying lncRNAs in the sea louse Caligus rogercresseyi, an ectoparasite of primary concern to the Chilean salmon industry. A bioinformatics pipeline for lncRNAs discovery was designed, revealing 1835 putative lncRNA sequences in the C. rogercresseyi transcriptome. Furthermore, C. rogercresseyi lncRNAs evidenced features classical of lncRNAs, such as lower values of GC content, length, transcription activity, and minimum free energy as compared with coding transcripts. Furthermore, since developed resistance against delousing drugs is a major threat to the management and control of sea lice, the transcriptional modulation of C. rogercresseyi lncRNAs during exposure to delousing drugs was also evaluated. Unlike coding transcripts, lncRNAs were mainly downregulated after exposure to either deltamethrin or azamethiphos, showing transcription patterns similar to other, better studied non-coding RNAs in arthropods. Finally, a subset of lncRNAs exhibited a strong transcriptional correlation to genes commonly associated with the drug response, such as ABC transporters, cytochrome p450, and glutathione S-transferase, among others. Our findings provide one of the first comprehensive lncRNA characterizations in a crustacean, contributing towards understandings on the regulatory role of lncRNAs during the drug response in Caligus rogercresseyi.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2017.03.001
      Issue No: Vol. 4 (2017)
  • The Caligus rogercresseyi miRNome: Discovery and transcriptome profiling
           during the sea lice ontogeny
    • Authors: C. Gallardo-Escárate; V. Valenzuela-Muñoz; S. Boltaña; G. Nuñez-Acuña; D. Valenzuela-Miranda; A.T. Gonçalves; C. Détrée; E. Tarifeño-Saldivia; R. Farlora; S. Roberts; H.M. Putnam
      Pages: 8 - 22
      Abstract: Publication date: June 2017
      Source:Agri Gene, Volume 4
      Author(s): C. Gallardo-Escárate, V. Valenzuela-Muñoz, S. Boltaña, G. Nuñez-Acuña, D. Valenzuela-Miranda, A.T. Gonçalves, C. Détrée, E. Tarifeño-Saldivia, R. Farlora, S. Roberts, H.M. Putnam
      Small RNA sequencing in the copepod ectoparasite Caligus rogercresseyi was conducted to evidence putative roles of non-coding RNAs during the sea louse ontogeny. Here, differentially expressed miRNAs and mRNAs for each developmental stage were analyzed in parallel with bioinformatic gene target predictions. Based on sequence analysis, C. rogercresseyi miRNome comprises 673 conserved miRNAs, including precursors, 5′ and 3′ isomiRs. The conserved miRNAs include 40 families found in twelve different arthropods species. The results also showed that C. rogercresseyi miRNome exhibit stage-specific expression patterns, with miRNA-996-4 and miRNA-124 displaying sex-biased expression. Target prediction of these miRNAs identifies possible silencing mechanism of sex-related genes. Furthermore, bantam isomiRs were highly transcribed during the infective stage of copepodid and target prediction using differentially expressed genes in Atlantic salmon infested with sea lice, suggests a putative role of these miRNAs in the host-pathogen interaction. This is the first study reporting a miRNA repertoire in a marine copepod ectoparasite that affects the salmon aquaculture worldwide.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2017.03.002
      Issue No: Vol. 4 (2017)
  • Comparison of complete mitochondrial DNA sequences between old and new
           world strains of the cowpea aphid, Aphis craccivora (Hemiptera: Aphididae)
    • Authors: Weilin Sun; Bao-Lam Huynh; James Adebayo Ojo; Brad S. Coates; Francis Kusi; Philip A. Roberts; Barry R. Pittendrigh
      Pages: 23 - 29
      Abstract: Publication date: June 2017
      Source:Agri Gene, Volume 4
      Author(s): Weilin Sun, Bao-Lam Huynh, James Adebayo Ojo, Brad S. Coates, Francis Kusi, Philip A. Roberts, Barry R. Pittendrigh
      Mitochondrial DNA provides useful tools for inferring population genetic structure within a species and phylogenetic relationships between species. The complete mitogenome sequences were assembled from strains of the cowpea aphids, Aphis craccivora, from the old (15,308bp) and new world (15,305bp) using shotgun Illumina HiSeq 2500 sequence reads. The A. craccivora mitogenomes have 13 protein coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs in the same order and orientation found among Insecta. The two A. craccivora mitogenomes do not contain long intergenic repeats as found in other members of the family Aphididae. Comparisons between strains indicated a 99.7% sequence identity, wherein 57 and 11 substitutions were respectively predicted among reads from new and old world strains. Among these substitutions, 31 and 2 were in PCGs of new world and old world aphids, respectively, and out of which 28 and 2 were nonsynonymous. A majority of the substitutions were in NADH Dehydrogenase subunit 1. Phylogenetic analysis of full mitogenomes sequences predicted that Aphididae as monophyletic and clustered with Pterocommatinae and Aphidinae at subfamily level.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2017.03.003
      Issue No: Vol. 4 (2017)
  • Genome wide analysis of NAC gene family ‘sequences’ in sugarcane and
           its comparative phylogenetic relationship with rice, sorghum, maize and
           Arabidopsis for prediction of stress associated NAC genes
    • Authors: Manimekalai Ramaswamy; Jini Narayanan; Gokul Manickavachagam; Selvi Athiappan; Meena Arun; Gomathi R; Bakshi Ram
      Pages: 1 - 11
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Manimekalai Ramaswamy, Jini Narayanan, Gokul Manickavachagam, Selvi Athiappan, Meena Arun, Gomathi R, Bakshi Ram
      A total of 85 NAC genes of sugarcane (ScNAC) were retrieved from GRASSIUS (grass regulatory information server). An overview of this gene family is presented including conserved domains, phylogenies, comparative analysis of NAC genes of sugarcane with its closest relative sorghum and with other monocot species. Among the Poaceae family, the NAC genes from sugarcane showed high sequence identity with most of the NAC genes of Sorghum bicolor. A highly conserved two proline residues, a glycine, phenyl alanine and leucine residues are present in N-terminal domain. Conserved amino acid residues and phylogeny helps us to classify the ScNAC gene family into two major groups (Group I and II) and five subgroups (A–E). The analysis of phylogenetic tree of NAC protein sequences of sugarcane with sorghum, rice, maize and Arabidopsis reveals distinct clades with several orthologs and paralogs. A total of 30 pairs of paralogous NAC genes were identified in sugarcane. Based on the orthology, putative stress associated NAC genes were predicted in sugarcane. These stress associated NAC genes of sugarcane and their orthologs from other species were clustered in the phylogenetic tree and shared common motifs, revealing the possibility of functional similarities within this subgroup.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.10.003
      Issue No: Vol. 3 (2017)
  • Genome-wide identification, cloning and characterization of SNARE genes in
           bread wheat (Triticum aestivum L.) and their response to leaf rust
    • Authors: S. Chandra; P. Halder; M. Kumar; K. Mukhopadhyay
      Pages: 12 - 20
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): S. Chandra, P. Halder, M. Kumar, K. Mukhopadhyay
      SNAREs (soluble N-ethylmaleimide sensitive factor adaptor protein receptors) are small polypeptides characterized by a particular domain called the SNARE motif. Compared with the genome of other eukaryotes, monocotyledonous and dicotyledonous plants have more SNAREs indicating their important roles in higher plant species. Higher plants have the capability to form SNARE complexes that are important in determining the precise process of vesicle fusion for intracellular trafficking pathways. SNAREs have been reported to be engaged in the delivery of cell wall precursors to the newly formed cell plate during cytokinesis. The role of SNARE genes in response to plant-pathogen interaction is still not well understood. We found 35 SNARE genes in the wheat genome using a Hidden Markov Model. In this study with combined usage of in silico and molecular cloning technologies, we identified and characterized three SNARE genes (SNARE3, SNARE5 and SNARE6). The deduced amino acid sequences of these SNARE genes contained two characteristic conserved domains – a SNARE motif and a transmembrane domain, and they showed a high degree of homology with other eukaryotic SNARE genes. Phylogenetic analysis and three dimensional structures built with the help of Modeller software confirmed the presence of SNARE motifs in the proteins. The spatio-temporal expression profiling studies exemplify the positive role of SNARE transcripts have in resistant and susceptible wheat plants during incompatible and compatible interaction respectively, in response to Puccinia triticina induced leaf-rust infection. Taken together, our study suggests a role for SNARE genes in vesicle mediated resistance to leaf rust in wheat.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.11.002
      Issue No: Vol. 3 (2017)
  • Ontogeny and expression analysis of tube (interleukin-1
           receptor-associated kinase-4 homolog) from Penaeus monodon in response to
           white spot syndrome virus infection and on exposure to ligands
    • Authors: K. Sreedharan; A. Deepika; Anutosh Paria; P.P. Suresh Babu; M. Makesh; K.V. Rajendran
      Pages: 21 - 31
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): K. Sreedharan, A. Deepika, Anutosh Paria, P.P. Suresh Babu, M. Makesh, K.V. Rajendran
      Tube, an IRAK- 4 (Interleukin-1 receptor-associated kinase-4) homolog, is a key component in the Toll signalling pathway that has diverse role in the innate immunity of organisms including the ontogenic development. In the present study, Tube from Penaeus monodon (PmIRAK-4) was studied in response to infection with white spot syndrome virus (WSSV) and on exposure to various ligands. The ontogenic expression pattern of PmIRAK-4 in different developmental stages of P. monodon showed that the gene was constitutively expressed in all the stages tested with the maximum expression detected in egg. Immune-modulation of PmIRAK-4 in response to WSSV was studied in post-larvae, juveniles and adult P. monodon in vivo, and in primary haemocyte cultures at different time-points post-infection in vitro. PmIRAK-4 displayed significant up-regulation in haemocytes, gill, lymphoid organ and stomach at all time-points in vivo as well as in primary haemocyte cultures in vitro. To understand the post-injection stress on the immune-modulation, we have compared the expression level of PmIRAK-4 using zero hour (un-injected) and phosphate buffered saline (PBS)-injected controls, wherein the trend in expression was found to be similar. Following in vitro stimulation with ligands such as lipopolysaccharide and peptidoglycan, significant up-regulation of the gene could be observed at all time-points. However, poly I:C induction resulted in down-regulation of the same at early time-points. The ubiquitous expression of PmIRAK-4 in different larval and post-larval stages implies the involvement of the gene in defense mechanism during early developmental stages of P. monodon. Further, the modulation of expression of PmIRAK-4 in response to WSSV and different ligands indicates its possible role in immune responses in shrimp.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.10.002
      Issue No: Vol. 3 (2017)
  • De novo sequencing and comparative analysis of peduncle transcriptomes in
           Hovenia acerba
    • Authors: Shu-Dong Zhang; Li-Zhen Ling
      Pages: 32 - 36
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Shu-Dong Zhang, Li-Zhen Ling
      The fresh fleshy peduncles of Hovenia acerba have been used as a food supplement and traditional herbal medicine (i.e. immunostimulatory and antialcoholism) for a long time. However, little is known about the genetic factors underlying peduncle development. Here, we presented the first transcriptome-wide peduncle development research at two developmental stages using Illumina's Genome Analyzer. Our results indicated that a total of 146,206 unigenes were identified and their functional annotation and classification revealed that the unigenes involved in energy catabolism and genetic information processing were necessary to the developing of peduncle in H. acerba. The comparison of Gene Ontology (GO) annotation between two developmental stages indicated that the term of oxidation-reduction process exhibited the big difference in unigene number, in which the possible relative transcription factors were identified. However, we found that these transcription factors were partly involved in oxidation-reduction process and most of them were involved in regulation of transcription. The metabolic process was classified into the second different GO term when compared unigene number between two stages. Combined with the KEGG pathway annotation, we found that carbohydrate metabolism showed the major difference in unigene number, which might contribute to the biosynthesis of polysaccharides as immunostimulatory agent. Finally, 54 candidate genes encoding 14 enzymes were found to biosynthesize flavonoid that has the antialcoholism effect. This study is the first report on transcriptome information in H. acerba and will promote to understand the genetic mechanism of peduncle development.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.11.001
      Issue No: Vol. 3 (2017)
  • miRNA mediated gene regulatory network analysis of Cichorium intybus
    • Authors: Swati Srivastava; Noopur Singh; Gaurava Srivastava; Ashok Sharma
      Pages: 37 - 45
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Swati Srivastava, Noopur Singh, Gaurava Srivastava, Ashok Sharma
      Cichorium intybus commonly known as chicory, is an important medicinal plants having different therapeutic properties. Several studies have been done on plant miRNAs for understanding their role in biological functions. However, no miRNAs are reported in miRBase for the genus C. intybus. In the present study, we used a homology based search and in-silico approach for identifying miRNA in C. intybus. Twenty eight potential miRNA families were predicted. Out of 28 predicted miRNA families, 17 were found to regulate 349 target transcripts and play important role in different biological, cellular and metabolic process. To understand the miRNA mediated gene regulatory control and to validate predicted miRNA targets, a biological network was also constructed. Further study of C. intybus miRNA regulation mechanisms may help us to know more about the important roles of miRNAs in C. intybus.
      Graphical abstract image

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.11.003
      Issue No: Vol. 3 (2017)
  • Cloning of invertebrate gonadotropin-releasing hormone receptor
           (GnRHR)-like gene in Yesso scallop, Patinopecten yessoensis
    • Authors: Kazue Nagasawa; Kouta Muroi; Tongchai Thitiphuree; Yuki Minegishi; Naoki Itoh; Makoto Osada
      Pages: 46 - 56
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Kazue Nagasawa, Kouta Muroi, Tongchai Thitiphuree, Yuki Minegishi, Naoki Itoh, Makoto Osada
      Although the invGnRH peptide was characterized from the nerve ganglia in bivalves, its signaling mechanism is nevertheless unclear. The objective of this paper was to identify the invGnRHR cDNA from Yesso scallop as a first step for understanding of invGnRH in bivalve neuroendocrine system. We performed PCR cloning mediated with transcriptome survey and expression analysis with various tissues of the scallop. Our results showed that we identified an invGnRHR-like cDNAs from not only Yesso scallop Patinopecten yessoensis but also Pacific oyster Crassostrea gigas. In addition, we subsequently identified an adipokinetic hormone receptor (AKHR)-like and AKH-like cDNA pair from the scallop. Comparison of the tissue distributions of both receptor mRNAs suggested functional divergence of two homologous neuropeptides. In brief, py-GnRHR-like mRNA showed broad distribution in various tissues including the nerve ganglia, while py-AKHR-like mRNA was expressed in the nerve ganglia and restricted to some limited peripheral tissues. The findings suggested that both py-GnRH and py-AKH signals were utilized via their own receptors. qPCR assays revealed their receptor mRNA expression in the gonads during a maturation, showing that py-GnRHR-like mRNA in the pre-mature gonads was higher than other mature stages.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.11.005
      Issue No: Vol. 3 (2017)
  • Genetic and environmental effect on the growth characteristics and
           bioactive components of eight-year-old Glycyrrhiza uralensis Fisch
    • Authors: Xiaosu Miao; Rongxiu Liu; Hongpei Liu; Fulai Yu; Jiyong Wang; Wenquan Wang; Shengli Wei
      Pages: 57 - 62
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Xiaosu Miao, Rongxiu Liu, Hongpei Liu, Fulai Yu, Jiyong Wang, Wenquan Wang, Shengli Wei
      Licorice derived from Glycyrrhiza uralensis Fisch is an important traditional Chinese medicine. The cultivated licorice has gradually replaced the wild licorice, becoming the main source, while its quality is unstable. To explore the influence of genetic and environment on the quality of cultivated licorice, the growth characteristics and the contents of glycyrrhizin and liquiritin of eight-year-old licorice were analyzed. The growth characteristics and contents of glycyrrhizin and liquiritin of eight-year-old licorice varied in different provenances. Especially, the contents of lycyrrhizin and liquiritin of different sources existed significant variation owing to genetic expression. Further, the growth characteristics were negatively correlated with temperature and moisture, while the contents of glycyrrhizin and liquiritin were positively correlated with temperature and negatively correlated with moisture. It indicated that there were significant geographic variations in the growth of eight-year-old licorice, which was associated with genetic expression and the ecological environment.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.11.004
      Issue No: Vol. 3 (2017)
  • Estimation of dominance effects related to mastitis and production traits
           for CXCR1 gene using logistic regression analysis in dairy cattle
    • Authors: Masoumeh Bagheri; Azadeh Zahmatkesh
      Pages: 63 - 66
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Masoumeh Bagheri, Azadeh Zahmatkesh
      The dominance effect is important for mastitis, which is the major source of economic loss in dairy herds. The objective of this study was to evaluate dominance effects of CXCR1 gene for clinical mastitis and production traits in Holstein dairy cattle using the selective genotyping method. Records of 305-day lactation were obtained for production traits and for the number of cases of clinical mastitis per lactation. Cows were selected based on extreme values (highest and lowest CMR values) for clinical mastitis residuals (CMR) from mixed model analyses. Each of the two extreme groups of cowswas genotyped for CXCR1 gene and then, associations between genotypes and CMR and also breeding values for traits of interest were estimated by applying logistic regression analyses. Allele G of CXCR1 gene was associated with fewer cases for clinical mastitis (CM), and showed desired effects on production traits, especially on milk, protein and fat yield. Effects of dominance ranged from −0.03 SD to 0.55 SD for the production traits and CM. For milk production traits, positive values for dominance indicated a surplus in these traits. Result showed that CXCR1 gene may be a valuable candidate gene for improvement of mastitis resistance as well as production traits in dairy cattle herds and the dominance effects may not be negligible.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.11.006
      Issue No: Vol. 3 (2017)
  • Population structuring of selected mungbean landraces of the Odisha State
           of India via DNA marker-based genetic diversity analysis
    • Authors: Ram Chandra Jena; Khusbu Agarwal; Tarini Shankar Ghosh; Pradeep Kumar Chand
      Pages: 67 - 86
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Ram Chandra Jena, Khusbu Agarwal, Tarini Shankar Ghosh, Pradeep Kumar Chand
      Ever-increasing demands of mungbean consumption, wide eco-geographical variations and inadequate achievements through conventional breeding necessitate comprehensive assessment of genetic variability coupled with population patterning. In the present work 30 mungbean landraces of the Odisha State of India representing four different geographical regions (populations) along with some Indian genotypes were used for elucidation of genetic diversity and population structure analysis using 52 SCoT (gene-targeted) and 45 RAPD (arbitrary) markers. SCoT markers proved to be more effective than RAPD in ascertaining genetic diversity at genotype level (% polymorphism, Rp, PIC, EMR, MI, GI and I) and population level (Na, Ne, H, I, Ht and Hs). Unique bands (23 RAPD and 47 SCoT) were generated which enabled identification of 16 and 25 genotypes respectively. Genetic diversity parameters of East Odisha revealed high genetic variability compared to other populations. AMOVA revealed >95% variation within the populations which is further supported by high gene flow and low level of genetic differentiation. UPGMA dendrogram and population structure grouped genotypes into 8 major clusters irrespective of their geographical affiliations. However, genotypes belonging to certain clusters exhibited significant geographical and morphological preferences using the cumulative strategy. The study illustrated the importance of combined marker analysis, which uses complementary information from two distinct and analogous markers and in the process, offers accurate and reliable results. Further, the applicability of in silico analysis in performing a high resolution patterning of genetic divergence and population structure was demonstrated.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.11.007
      Issue No: Vol. 3 (2017)
  • Genomic organization and structural diversity of germin-like protein
           coding genes in foxtail millet (Setaria italica L.)
    • Authors: Dipnarayan Saha; Rajeev Singh Rana; Lalit Arya; Tapan Kumar Mondal
      Pages: 87 - 98
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Dipnarayan Saha, Rajeev Singh Rana, Lalit Arya, Tapan Kumar Mondal
      Germin-like protein (GLP) genes in plants constitute a multigene family that functions in a variety of biological processes, such as plant growth and development and respond to abiotic and biotic stresses. Available genome sequences of foxtail millet (Setaria italica) have facilitated the identification and delineation of the GLP gene family, which is perhaps the first report in any millet crop. A total of 20 SiGLP genes were mapped in six of the nine foxtail millet chromosomes. The majority of these SiGLP genes, except six, clustered into five known germin (GER) groups and revealed group-specific variations in their gene structure and conserved protein motifs. The SiGLP genes shared homologous relationship within and across plant genomes as per their syntenic chromosomal regions, indicating gene duplication and expansion in course of plant evolution. Gene expression dynamics revealed four out of the 20 SiGLP genes having a putative functional role in different tissues. The presence of diverse cis-acting regulatory elements in the putative SiGLP promoter sequences and homology-based 3-D protein structure predictions revealed their possible functional diversity. The present work encompasses a molecular insight into the organization and functions of SiGLP gene family members. This may serve as a platform for functional analysis and their efficient utilizations in genetic improvement of foxtail millet and other related crops.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.12.001
      Issue No: Vol. 3 (2017)
  • Phylogenetic analysis and drought-responsive expression profiles of the
           WRKY transcription factor family in maize
    • Authors: Ting Zhang; Dengfeng Tan; Li Zhang; Xiaoyan Zhang; Zhaoxue Han
      Pages: 99 - 108
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Ting Zhang, Dengfeng Tan, Li Zhang, Xiaoyan Zhang, Zhaoxue Han
      WRKY transcription factors play diverse roles in biotic and abiotic stresses. However, little comprehensive study has been presented about maize WRKY genes in drought stress response. In the present study, the phylogenetic relationships between ZmWRKYs and known WRKYs were analyzed, and it was shown that the gene structure and motif compositions were conserved within a group or a subgroup identified. And then, the expression profiling of ZmWRKY genes based on the global microarray data revealed eight genes responded to drought stress. Additionally, RNA-Seq profiling showed that 58 ZmWRKY genes were induced in drought stress. Real-time quantitative RT-PCR was used to verify the expression patterns of several candidate drought-responsive ZmWRKY genes. The cis-elements analysis of ten candidate ZmWRKY genes showed that the putative promoter of each gene includes at least a drought-responsive MBS element. Furthermore, the protein-protein interaction analyses revealed the intricate co-regulatory and co-expression network, which was consistent with the drought-responsive expression profiles of ZmWRKYs. Thus, these results provide a fundamental clue for cloning functional maize WRKY genes.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2017.01.001
      Issue No: Vol. 3 (2017)
  • Eukaryotic initiation factor 4E binding protein family members are widely
           expressed in fish tissues: Cloning and distribution of 4E-BPs in
           Schizothorax prenanti
    • Authors: Fangjun Lin; Dengyue Yuan; Defang Chen; Zhiqiong Li
      Pages: 109 - 115
      Abstract: Publication date: March 2017
      Source:Agri Gene, Volume 3
      Author(s): Fangjun Lin, Dengyue Yuan, Defang Chen, Zhiqiong Li
      Schizothorax prenanti (Cypriniformes, Cyprinidae, Schizothoracinae) is an endemic, valuable fish in the southwest of China. Although a series of studies concerning the genetic and endocrine control of feeding and growth in S. prenanti have been examined in our laboratory, the mechanism is still unclear. To better understand these mechanisms, complete coding sequences of the eukaryotic initiation factor 4E binding proteins (4E-BP1, 4E-BP2 and 4E-BP3) were isolated in S. prenanti and their mRNA distributions examined in different tissues. S. prenanti 4E-BP1, 4E-BP2 and 4E-BP3 consisted of 120, 113 and 111 amino acids and exhibited a quite high degree of amino acid identity, respectively, to their cyprinid fish homologs. Phylogenetic analysis of the 4E-BPs sequences showed three main branches of vertebrate 4E-BPs. However, it was of interest that teleost 4E-BP1 clustered with vertebrate 4E-BP3, while the tetrapod 4E-BP1 formed a distinct clade. The mRNAs of all 4E-BPs were ubiquitously expressed in S. prenanti tissues, including brain, pituitary, eye, heart, gut, hepatopancreas, kidney, spleen, gonad, muscle, skin and gill. The widespread distributions suggest that 4E-BPs might have distinct physiological actions in S. prenanti, in particular on the brain, pituitary, gut, hepatopancreas and muscle, which involved feeding and growth regulation. This preliminary study opens the way for further functional studies on the mechanisms of the regulation of feeding and growth in S. prenanti and other teleost.

      PubDate: 2017-04-20T19:06:16Z
      DOI: 10.1016/j.aggene.2016.10.001
      Issue No: Vol. 3 (2017)
  • Identification of BABY BOOM homolog in bread wheat
    • Authors: Andriy Bilichak; Justin Luu; Fengying Jiang; Franҫois Eudes
      Abstract: Publication date: Available online 21 November 2017
      Source:Agri Gene
      Author(s): Andriy Bilichak, Justin Luu, Fengying Jiang, Franҫois Eudes
      Modern breeding practice of small grain cereals necessitates the development of an efficient system for the large scale and reproducible production of the doubled haploid (DH) lines. It is believed that among the available DH generation techniques, only isolated microspore culture (IMC) can satisfy the demand of public and private breeding programs. Unfortunately, the IMC method is prone to several challenges that jeopardizes its large scale adoption. One of the approaches to limit the variation in DH plant production and increase the efficiency of the method is manipulation of embryogenesis-related genes. Here we set up a study to map BABY BOOM in a bread wheat genome. The gene is one of the morphogenic regulators of somatic embryogenesis in plants. To achieve this task, we used amino acid sequences of Zea mays BBM-like proteins. TaBBM homoeologs were mapped to chromosomes 6AL, 6BL and 6DL. Amino acid sequence analysis revealed the presence of two AP2 domains and bbm-1 motif in the A and D copies and only one AP2 domain and bbm-1 motif in the B copy. This, along with the absence of both gene expression and predictable TATA-box, suggests that TaBBM-gB is a pseudogene. The expression pattern of the identified A and D homoeologs was similar to that for the BBM-like genes in other species and presence of the transcript was detected in an embryogenic microspore population. Identification of the TaBBM homolog can have application in elevating the efficiency of DH production, tissue culture, plant transformation and genome editing for wheat improvement.

      PubDate: 2017-11-25T10:07:08Z
      DOI: 10.1016/j.aggene.2017.11.002
  • Identification of a maize (Zea mays) chitinase allele sequence suitable
           for a role in ear rot fungal resistance
    • Authors: Patrick F. Dowd; Todd A. Naumann; Neil P.J. Price; Eric T. Johnson
      Abstract: Publication date: Available online 14 October 2017
      Source:Agri Gene
      Author(s): Patrick F. Dowd, Todd A. Naumann, Neil P.J. Price, Eric T. Johnson
      Chitinases are thought to play a role in plant resistance to pathogens, but the extent of this role is unknown. The gene for a maize (Zea mays) chitinase “chitinase 2” previously reported to be induced by two ear rot pathogens in one maize inbred, was cloned from mRNA isolated from milk stage kernels of several different inbreds reported to be susceptible or resistant to ear rot pathogens. The chitinase gene sequence of some of the susceptible inbreds had frame shifts which would result in a nonfunctional protein. Other susceptible inbreds, and a few resistant inbreds, were missing regions that would contribute to chitin binding. A putative functional clone from a resistant inbred was expressed in yeast, and produced a protein with chitinase activity against different oligomers of N-acetyl glucosamine and modified chitin. The yeast-produced chitinase was also resistant to degradation by proteases from maize ear rot fungi, and enhanced antifungal activity of miconazole towards Fusarium graminearum. When introduced in maize callus transgenically, the callus expressing the chitinase 2 gene had significantly less growth of the ear rot pathogen, F. graminearium, than callus which did not express the gene. This information suggests susceptibility and resistance to ear rot pathogens is influenced not only by expression levels, but also by the sequence of putative resistance genes. Previous reports of increased expression of putative resistance genes need to be tempered with the realization that they may play no role in resistance if the genes code for nonfunctional or reduced function proteins.

      PubDate: 2017-10-18T00:29:04Z
      DOI: 10.1016/j.aggene.2017.10.001
  • Study of microRNA mediated gene regulation in Striga hermonthica through
           in-silico approach
    • Authors: Swati Srivastava; Ashok Sharma
      Abstract: Publication date: Available online 28 September 2017
      Source:Agri Gene
      Author(s): Swati Srivastava, Ashok Sharma
      Striga hermonthica is a parasitic plant that attacks mostly cereal crops for its growth and development. S. hermonthica parasitism affects two thirds of the arable land and over 100 milion people. It is also well known as a folk medicine due to presence of flavonoids, terpenes, saponins, cardiac glycosides, alkaloids, tannins and coumarins miRNAs are important gene regulatory elements involved in almost all biological processes during different biotic and abiotic stresses in plants. Mobile small RNA are reported to move bidrection between parasitic plant and host plants. The study was to investigate the miRNA of S. hermonthica and miRNA mediated regulation of host plant Oryza sativa genes. In-silico identification of miRNAs revealed 13 conserved miRNA families (miR1846c-3p, miR1848, miR1851, miR1857-5p, miR2102-3p, miR2864.1, miR417, miR437, miR444e, miR529a, miR810b.2, miR156e, miR5564b). Approximately, 185 genes playing diverse roles have been predicted as targets for the identified 12 miRNA families (miR1848, miR1851, miR1857-5p, miR2102-3p, miR2864.1, miR417, miR437, miR444e, miR529a, miR810b.2, miR156e, miR5564b). Manipulation in miRNAs or their targets may be utilized for developing better crop protection strategies.
      Graphical abstract image

      PubDate: 2017-10-01T11:45:29Z
      DOI: 10.1016/j.aggene.2017.09.004
  • Haplotype variation of Badh2 gene, unearthing of a new fragrance allele
           and marker development for non-basmati fragrant rice ‘Velchi’ (Oryza
           sativa L.)
    • Authors: Kiran S. Khandagale; Rahul L. Zanan; Sarika V. Mathure; Altafhusain B. Nadaf
      Abstract: Publication date: Available online 28 September 2017
      Source:Agri Gene
      Author(s): Kiran S. Khandagale, Rahul L. Zanan, Sarika V. Mathure, Altafhusain B. Nadaf
      In the present study, selected indica rice accessions (basmati, non-basmati fragrant, and non-fragrant) were screened for mutations in betaine aldehyde dehydrogenase 2 (badh2) gene to investigate the allelic differences using previously reported functional markers. This screening experiment revealed that non-basmati fragrant accession ‘Velchi’ does not harbour any reported mutation in coding region of badh2. While working with badh2-p-UTR marker we got deviating results. All the non-basmati fragrant and basmati types gave amplicon of 203bp except Velchi, whereas all non-fragrant and ‘Velchi’ gave 456 and 461bp amplicons respectively. The new allele has 253bp deletion in the promoter region of fragrant indica rice accessions compared to non-fragrant rice. Further, the fragrant accession ‘Velchi’ has additional 5bp duplication as compared to non-fragrant accessions. To distinguish Velchi from other non-fragrant indica accessions, a new marker (velbadh2-p-UTR) has been designed to identify this 5bp difference, which could distinguish ‘Velchi’ from non-fragrant rice accessions and can be useful in breeding for development of fragrant rice varieties via marker-assisted selection. The 2AP biosynthesis related metabolites, gene expression and enzyme assay confirmed deletion in badh2 and expression of fragrance in Velchi.

      PubDate: 2017-10-01T11:45:29Z
      DOI: 10.1016/j.aggene.2017.09.003
  • Overexpression of a heat stress inducible, wheat myo-inositol-1-phosphate
           synthase 2 (TaMIPS2) confers tolerance to various abiotic stresses in
           Arabidopsis thaliana
    • Authors: Neetika Khurana; Naveen Sharma; Paramjit Khurana
      Abstract: Publication date: Available online 13 September 2017
      Source:Agri Gene
      Author(s): Neetika Khurana, Naveen Sharma, Paramjit Khurana
      Myo-Inositol phosphate synthase (MIPS) enzyme catalyses rate limiting step of myo-inositol (MI) biosynthesis. MIPS by-products are involved in many plant processes. In this study, TaMIPS2 identified from a heat subtractive cDNA library from wheat has been functionally characterized. To investigate the importance of TaMIPS2 during heat stress tolerance, TaMIPS2 overexpression transgenics were raised in Arabidopsis which were analysed physiologically and morphologically under different abiotic stress conditions. MIPS enzyme assay revealed the level of inositol in transgenics and of other soluble sugars as quantified by HPLC. Analysis of overexpression transgenics under different stress condition revealed that TaMIPS2 transgenic have reduced sensitivity to heat stress. This is the first report indicating a role of myo-Inositol during heat stress. The analysis of transgenic lines of TaMIPS2 suggests its additional role under other environmental stresses.

      PubDate: 2017-09-18T18:53:31Z
      DOI: 10.1016/j.aggene.2017.09.001
  • Superoxide dismutases in bread wheat (Triticum aestivum L.): Comprehensive
           characterization and expression analysis during development and, biotic
           and abiotic stresses
    • Authors: Shivi Tyagi; Shailesh Sharma; Mehak Taneja; Shumayla; Rohit Kumar; Jaspreet K. Sembi; Santosh Kumar Upadhyay
      Abstract: Publication date: Available online 19 August 2017
      Source:Agri Gene
      Author(s): Shivi Tyagi, Shailesh Sharma, Mehak Taneja, Shumayla, Rohit Kumar, Jaspreet K. Sembi, Santosh Kumar Upadhyay
      Reactive oxygen species (ROS) induce oxidative stress at high concentrations and act as signaling molecules at low concentrations. Superoxide dismutases (SOD) are defence-related proteins, which are involved in detoxifying ROS. SODs have been characterized in various plants, but their comprehensive characterization has not been performed in Triticum aestivum. Herein, a total of 23 TaSOD genes were identified, which were classified into fourteen TaCu-ZnSOD and nine TaFe-MnSOD genes based on their domain organization. These genes were located on various homeologous chromosomes of each A, B and D-subgenome. Higher number of genes on each subgenome than their progenitor genome indicated the role of duplication events during the evolution of TaSODs. The phylogenetic analysis indicated evolutionary conservation in SODs from various plant species. Gene structure in terms of exon/intron organization and intron-phase, and physico-chemical properties like molecular weight and pI was variably conserved in homeologous TaSODs. Most of the Cu-ZnSODs were predicted as cytoplasmic, while Fe-MnSODs were chloroplastic and mitochondrial. Both TaCu-ZnSODs and TaFe-MnSODs were found structurally conserved in terms of various metal binding and active sites, and secondary and tertiary structures as well. They showed putative interaction with each other and other ROS detoxifying enzymes like catalases and peroxidases. Specifically high expression of a few TaSODs in certain tissue developmental stages suggested their precise role in those tissues. TaFe-MnSOD1 group genes were highly expressed during development of grain. Constitutive expression of certain genes indicated their role during all developmental stages. The modulated expression of a few genes during biotic (TaCu-ZnSOD3-A, TaFe-MnSOD2-A) and abiotic stresses (heat; TaCu-ZnSOD3-B, TaFe-MnSOD1-B, drought; TaFe-MnSOD1-A, salt; TaFe-MnSOD2-A) suggested their function in a stress response. The present study provided inclusive characterization of SOD proteins in T. aestivum, which extends the opportunity for future functional characterization of each individual protein.

      PubDate: 2017-08-20T07:21:43Z
      DOI: 10.1016/j.aggene.2017.08.003
  • Genome-wide identification and expression analysis of transcription
           factors in Solanum lycopersicum
    • Authors: Rui Geng; Xubo Ke; Chenglong Wang; Yong He; Huasen Wang; Zhujun Zhu
      Abstract: Publication date: Available online 12 August 2017
      Source:Agri Gene
      Author(s): Rui Geng, Xubo Ke, Chenglong Wang, Yong He, Huasen Wang, Zhujun Zhu
      Transcription factors (TFs) are essential regulators during gene expression. To better understand TF genes in tomato (Solanum lycopersicum L.), a silico genomic analysis of TF prediction was performed through the tomato genome. A total of 2026 TF genes were identified in the tomato genome, and they account for approximately 5.83% of its estimated total number of genes. These genes can be also classified into 57 families. The largest family is famous for the MYB superfamily and comprises 220 MYB TF genes. Predicted TFs were distributed across all 12 chromosomes with different densities. Chromosome 01 possesses 241 TFs, accounting for the largest number of TFs. According to microarray and expressed sequence tag data, expression patterns of 298 TFs showed that many of these TFs play roles in growth, development, diverse biological processes and responses to various stresses of S. lycopersicum L. Eight TF genes were further analyzed by reverse transcription polymerase chain reaction analysis in different tissues (root, stem, leaf, flower, and fruit). To the best of our knowledge, this study is the first to report genome-wide analysis of tomato TF gene families. This study provides valuable information regarding classification and putative functions of TFs in Solanaceae.

      PubDate: 2017-08-20T07:21:43Z
      DOI: 10.1016/j.aggene.2017.08.002
  • The differentially expressed genes identification in dwarf mutant of
           Gossypium hirsutum by RNA-Seq approach
    • Authors: Zhao Liang; Di Jiachun; Guo Qi; Zhao Jun; Zhou Xiangyang; Chen Xusheng
      Abstract: Publication date: Available online 4 August 2017
      Source:Agri Gene
      Author(s): Zhao Liang, Di Jiachun, Guo Qi, Zhao Jun, Zhou Xiangyang, Chen Xusheng
      Demands for dwarf plants are increasing, because dwarfism is one of the most important traits in modern crop breeding. Gibberellin (GA) is an essential hormone that is involved in many aspects of plant growth and development. A cotton mutant shows that ultra-dwarf (average plant height is 10cM), blade twisting and cannot grow normally, but the mutant could change to normal plant with GA treatment in the process of growth. To comprehensively survey the patterns of gene expression, RNA-Seq was used in this paper. Approximately 93.5% of all tags could be mapped reference sequences. 77,686 genes could detect expression level by the map. A total of 11,403 DEGs between the samples were detected. Quantitative real-time PCR was used to evaluate the results of RNA-Seq for gene expression profiles. Based on KEGG analysis, a total of 425 genes involved in plant hormone biosynthesis and signal transduction. Among those genes, 27 DEGs involved in GA biosynthesis and 20 in signal transduction. Gh_A06G1386 and Gh_D06G1730, a pair of homoeologous genes, may be candidate genes based on results of fine mapping and RNA-Seq analysis.

      PubDate: 2017-08-10T01:26:28Z
      DOI: 10.1016/j.aggene.2017.08.001
  • Identification of a type I interferon (IFN) gene from Japanese eel and its
           expression analysis in vivo and in vitro
    • Authors: Jianjun Feng; Peng Lin; Yilei Wang; Songlin Guo; Ziping Zhang; Lili Yu
      Abstract: Publication date: Available online 18 July 2017
      Source:Agri Gene
      Author(s): Jianjun Feng, Peng Lin, Yilei Wang, Songlin Guo, Ziping Zhang, Lili Yu
      Type I interferon (IFN) is a key cytokine of innate immune response for viral infection in teleost fish. In present study we report the identification of a type I IFN gene (AjIFN) from Japanese eel (Anguilla japonica) and provide evidence that AjIFN has been involved in Japanese eel host response against not only the virus but also the bacterial infection. The full-length cDNA of AjIFN (826bp) has an ORF of 531bp. The analysis of NCBI CDD showed that the AjIFN protein had the typical conserved domains, including IFabd conserved domain, and two conserved cysteine residues potentially forming disulphide bridges. Based on the phylogenetic analysis, AjIFN was classified into type I IFNs families belonging to the subgroup-a of the 2Cys group. In vivo, the AjIFN expressions in liver and kidney were induced following injection with LPS, the viral mimic poly I:C, and Aeromonas hydrophila infection. In vitro, the AjIFN transcripts of Japanese eel liver cells were enhanced by LPS, poly I:C and CpG-DNA stimulation and no change of the expression level was found post PGN treatment. Following A. hydrophila infection, the low concentration of 1×106 cfu/mL failed to induce the expression of AjIFN whereas the concentration of 1×107 cfu/mL and 1×108 cfu/mL successfully induced the expression of AjIFN. These results collectively suggested AjIFN is an inducible gene possibly involved in Japanese eel defense against viral and bacterial infection.

      PubDate: 2017-07-24T16:12:30Z
      DOI: 10.1016/j.aggene.2017.07.003
  • The mitogenome of the brown pod-sucking bug Clavigralla tomentosicollis
           Stäl (Hemiptera: Coreidae)
    • Authors: Laura D. Steele; Weilin Sun; M. Carmen Valero; James Adebayo Ojo; Keon Mook Seong; Brad S. Coates; Venu M. Margam; Manuele Tamò; Barry R. Pittendrigh
      Abstract: Publication date: Available online 16 July 2017
      Source:Agri Gene
      Author(s): Laura D. Steele, Weilin Sun, M. Carmen Valero, James Adebayo Ojo, Keon Mook Seong, Brad S. Coates, Venu M. Margam, Manuele Tamò, Barry R. Pittendrigh
      The brown pod-sucking bug, Clavigralla tomentosicollis Stäl (Hemiptera: Coreidae), causes significant damage to cultivated cowpea, Vigna unguiculata Walp, a staple crop in sub-Saharan Africa. C. tomentosicollis pierce and suck sap from cowpea pods, resulting in reduced grain yield and quality. The complete, 16,089bp mitogenome of C. tomentosicollis encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and an A+T rich control region, with gene order and orientation identical to that of the insect ancestral gene order. The initiation and termination codons for the PCGs used standard ATN codons and TAA or TAG codons respectively. All predicted tRNAs fold into a clover-leaf secondary structures with the exception of tRNA-Ser (AGN) with a semi-loop dihydrouridine arm. The 1509bps A+T rich region contains a single 89bp tandem repeat unit duplicated 3.7 times. When compared with other published Coreoidea mitogenomes, C. tomentosicollis was also highly A−T skewed, and similar in both size and A−T%; however, its longer tandem repeat within the A+T rich region was unique. The C. tomentosicollis mitogenome can serve as a foundation to combine molecular marker data with pest monitoring strategies to better understand the population dynamics of this species.

      PubDate: 2017-07-24T16:12:30Z
      DOI: 10.1016/j.aggene.2017.07.002
  • Metagenome analysis of antibiotic resistance genes in fecal microbiota of
    • Authors: Panpan Tong; Xue Ji; Lizhi Chen; Jun Liu; Lizhi Xu; Lingwei Zhu; Wei Zhou; Guo Liu; Shujuan Wang; Xuejun Guo; Shuzhang Feng; Yang Sun
      Abstract: Publication date: Available online 15 June 2017
      Source:Agri Gene
      Author(s): Panpan Tong, Xue Ji, Lizhi Chen, Jun Liu, Lizhi Xu, Lingwei Zhu, Wei Zhou, Guo Liu, Shujuan Wang, Xuejun Guo, Shuzhang Feng, Yang Sun
      Numerous environmental reservoirs contribute to the problem of acquired antibiotic resistance of human pathogens. One environmental reservoir of particular importance is the intestinal bacteria of poultry. Antibiotics are often used to prevent sickness and improve production in chicken farms. Hence, the intestinal microbial community of chickens as a reservoir for antibiotic resistance genes (ARGs) has received increasing attention. Therefore, the aim of this study was to investigate the occurrence, diversity, and abundance of ARGs and mobile genetic elements (MGEs), and the distribution of plasmids in layer and broiler feces using Illumina high-throughput sequencing. Metagenomic analysis showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were predominate in chicken feces. At the genus level, Escherichia coli may be predominant in chicken feces with a relative abundance of plasmids. Sequencing reads revealed differences in the distribution of plasmids in microbial communities between layer and broiler feces. Genes coding for antibiotic resistance were identified in both communities. BLAST analysis against the Antibiotic Resistance Genes Database (ARDB) further revealed that layer and broiler feces contained various ARGs with high abundances, among which vancomycin (van) was the most abundant, accounting for >36% of all reads of ARGs. Beta-lactam resistance genes (bl) were highly enriched in the broiler feces, among which bl2e_cbla was the most abundant, but was absent in layer feces. Over 20 types of insertion sequences were detected in each fecal sample. These results highlight the prevalence of ARGs, plasmids, and MGEs in chicken feces, which warrants further studies to better elucidate the risk to public health.

      PubDate: 2017-06-17T03:18:51Z
      DOI: 10.1016/j.aggene.2017.06.001
  • PCR optimization and allele distribution of SNAC1 gene coding region in
           rice (Oryza sativa L.)
    • Authors: Narjes Tabkhkar; Babak Rabiei; Habibollah Samizadeh Lahiji; Maryam Hosseini Chaleshtori
      Abstract: Publication date: Available online 17 May 2017
      Source:Agri Gene
      Author(s): Narjes Tabkhkar, Babak Rabiei, Habibollah Samizadeh Lahiji, Maryam Hosseini Chaleshtori
      Drought is the most serious abiotic stress that limits crop production in rain-fed environments. In this study genetic diversity of SNAC1 gene investigated in a collection of 83 diverse rice accessions from different geographical origins. Amplification of SNAC1 gene exons was performed by combined hot start-touchdown PCR protocol. The average number of alleles was 9.5 alleles. A total of 6 rare alleles were identified from exons of SNAC1. The average gene diversity index, PIC (Polymorphism information content) and Shannon value were 0.8518, 0.8343 and 2.0469, respectively. Evolutionary study based on Ewens-Watterson test showed that exon 1 of SNAC1 gene was probability under genetic drift. To identify potential SSR markers in SNAC1 gene sequence, SSR distributions within rice SNAC1 gene sequence were mined. Totally 15 microsatellite loci were detected which tri-nucleotide motifs (8) was being most abundant, followed by di- (6) and tetra-nucleotide (1) motifs. Maximum loci were found in 3′ UTR (5) (Untranslated regions), followed by in 5′ UTR (4) and coding sequences (3 for each exon). The present study revealed genetic divergence of SNAC1 gene coding regions and also mined SSR distributions within SNAC1 gene sequence and introduced an optimized PCR method. This information can be used for the development of drought tolerant rice varieties.

      PubDate: 2017-05-19T10:30:23Z
      DOI: 10.1016/j.aggene.2017.05.001
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