The polymerase chain reaction (PCR): General methods

The polymerase chain reaction (PCR) converts very low quantities of DNA into very high quantities and is the foundation of many specialized techniques of molecular biology. PCR utilizes components of the cellular machinery of mitotic cell division in vitro which respond predictably to user inputs. This chapter introduces the principles of PCR and discusses practical considerations from target sequence definition through to optimization and application

Association Mapping and Marker Development of Genes for Starch Lysophospholipid Synthesis in Rice

Phospholipids are a major kind of lipids in rice grains and have fundamental nutritional and functional benefits to the plant. Their lyso forms (lysophospholipids, LPLs) often form inclusion complexes with amylose or independently influence the physicochemical and functional properties of rice starch. However, the genetic basis for LPL synthesis in rice endosperm is largely unknown. Here, we performed a preliminary association test of 13 LPL compositions among 20 rice accessions, and identified 22 putative main-effect quantitative trait loci responsible for all LPLs except for LPC14:0 and LPE14:0. Five derived cleaved amplified polymorphic sequences and one insertion/deletion marker for three LPL-synthesis-related candidate genes were developed. Association analysis revealed two markers significantly associated with starch LPL traits. These results provide an insight into the genetic basis of phospholipid biosynthesis in rice and may contribute to the rice quality breeding programs using functional markers

Analysis of adaptive ribosomal gene diversity in wild plant populations from contrasting climatic environments

Plant populations may contain variation that reflects adaptation to local environmental conditions. Clues to adaptive evolution of plants may be found in the genomes of species growing in diverse environments or across steep environmental gradients, and under stress. We have examined populations of wild relatives of barley and rice across diverse environmental gradients. Greater diversity, in a nuclear biotic stress defense gene and in chloroplast genes, was found in the more stressed, hotter and dryer environments. This may reflect the greater heterogeneity of these environments. Adaptation of plants to different abiotic stresses (temperatures and levels of water availability) may also require significant adaptation to the different biotic (pest and disease) pressures in these environments.(1

A perfect marker for fragrance genotyping in rice

Allele specific amplification (ASA) is a low-cost, robust technique that can be utilised to discriminate between alleles that differ by SNP's, insertions or deletions, within a single PCR tube. Fragrance in rice, a recessive trait, has been shown to be due to an eight bp deletion and three SNP's in a gene on chromosome 8 which encodes a putative betaine aldehyde dehydrogenase 2 (BAD2). Here we report a single tube ASA assay which allows discrimination between fragrant and non-fragrant rice varieties and identifies homozygous fragrant, homozygous non-fragrant and heterozygous non-fragrant individuals in a population segregating for fragrance. External primers generate a fragment of approximately 580 bp as a positive control for each sample. Internal and corresponding external primers produce a 355 bp fragment from a non-fragrant allele and a 257 bp fragment from a fragrant allele, allowing simple analysis on agarose gels

Agricultural Information Worldwide, vol. 6, 2014

Agricultural Information Worldwide, Volume 6, 2014In this issue: FROM THE EDITOR’S DESK / Jim Morris-Knower (3); Conference Reflections / Antoinette Paris Greider (4). ARTICLES: Keynote Address: The State of Information Literacy Policy: A Global Priority / Sharon Weiner (5); Framing of Climate Change News in Four National Daily Newspapers in Southern Nigeria / Agwu Ekwe Agwu, Chiebonam Justina Amu (11); Access and Use of Information Communication Technologies by Women Staff of Public Extension Service in the North Central Zone of Nigeria / Agwu Ekwe Agwu, Elizabeth Ene Ogbonnah (18); Providing User Preferred Information Resources for a New Faculty of Agriculture, Nnamdi Azikiwe Univeristy, Awka, Nigeria / Chinwe V. Anunobi, Andrew U. Ogbonna (25); Diffusion of Scientific Knowledge in Agriculture: The Case for Africa / Shimelis Assefa, Daniel Gelaw Alemneh, Abebe Rorissa (34); The Use of Social Media in Agricultural Research Workflows in Ghana and Kenya / Justin Chisenga, Richard Kedemi, Joel Sam (48); Towards Mobile Agricultural Information Services in Zimbabwean Libraries: Challenges and Opportunities for Small Sacle Farmers in Utilizing ICTs for Sustainable Food Production / Collence Takaingenhamo Chisita, Thembani Malapela (58); Agriculture and Natural Resource Scientists' Biodiversity Information Needs: Barriers and Facilitators to Use and Access in the U.S. Southeast / Miriam L.E. Steiner Davis, Carol Tenopir, Suzie Allard (66); French Agricultural Research Institute Paves the Way to Open Access: Feedback from CIRAD / Marie-Claude Deboin, Cécile Fovet-Rabot (77); Exploring Relevance of Agro Input Dealers in Disseminating and Communicating of Soil Fertility Management Knowledge: The Case of Siaya and Trans Nzoia Counties, Kenya / T. B. Etyang, J. J. Okello, S. Zingore, P. F. Okoth, F. S. Mairura, A. Mureithi, B. S. Waswa (82); Plantwise Knowledge Bank: Building Sustainable Data and Information Processes to Support Plant Clinics in Kenya / Cambria Finegold, MaryLucy Oronje, Margo C. Leach, Teresia Karanja, Florence Chege, Shaun L.A. Hobbs (96); Innovation in Extension Services for Improved Farmer Access to Agricultural Information in Uganda / Patrick Kasangaki (102); Managing a Web Portal Adapting to New Technologies / Soonho Kim, Kathryn Pace Kincheloe, Yuan Gao, Valdete Berisha (107); Library Outreach to University Farm Staff / Emily MacKenzie, Natalie Waters (114); Enhancing Access to Research in Institutional Repositiories through API / Ryan Miller, Indira Yerramareddy (118); Building Capacity of Smallholder Farmers in Agribusiness and Entrepreneurship Skills in Northern Uganda / Basil Mugonola, Callistus Baliddawa (122); The Data Landscpe of the Coral Triangle / Jeanette Norris (127); Agricultural Information Access Among Smallholder Farmers: Comparative Assessment of Peri-Urban and Rural Settings in Kenya / Dorine Odongo (133); From Local to Global: Launching the New Rangelands West Portals and Database / Jeanne L. Pfander, Barbara S. Hutchinson, Valeria Pesce, Matt Rahr (138); Seed Village Programme: An Innovative Approach for Small Farmers / Dheeraj Singh, M. K. Chaudhary, M. L. Meena, M. M. Roy (143); Transformation of Indian Agricultural Libraries in a Digital and Collaborative Era: A Case Study / Neena Singh, Anil Chikate (147); Collaboration for Impact / Indira Yerramareddy, Luz Marina Alvaré, Katarlah Taylor (157

Multi-messenger Observations of a Binary Neutron Star Merger

International audienceOn 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of $\sim 1.7\,{\rm{s}}$ with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg(2) at a luminosity distance of ${40}_{-8}^{+8}$ Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 $\,{M}_{\odot }$. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at $\sim 40\,{\rm{Mpc}}$) less than 11 hours after the merger by the One-Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ∼10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position $\sim 9$ and $\sim 16$ days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC 4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta