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Genetic diversity

Luciano Rogério Braatz de Andrade, Roberto Fritsche Neto, Ítalo Stefanine Correia Granato, Gustavo César Sant'Ana, Pedro Patric Pinho Morais, Aluízio Borém
A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection...
2016: PloS One
Daniel M Bear, Jean-Marc Lassance, Hopi E Hoekstra, Sandeep Robert Datta
Evolution sculpts the olfactory nervous system in response to the unique sensory challenges facing each species. In vertebrates, dramatic and diverse adaptations to the chemical environment are possible because of the hierarchical structure of the olfactory receptor (OR) gene superfamily: expansion or contraction of OR subfamilies accompanies major changes in habitat and lifestyle; independent selection on OR subfamilies can permit local adaptation or conserved chemical communication; and genetic variation in single OR genes can alter odor percepts and behaviors driven by precise chemical cues...
October 24, 2016: Current Biology: CB
G E B Wright, B Carleton, M R Hayden, C J D Ross
Differences in response to medications have a strong genetic component. By leveraging publically available data, the spectrum of such genomic variation can be investigated extensively. Pharmacogenomic variation was extracted from the 1000 Genomes Project Phase 3 data (2504 individuals, 26 global populations). A total of 12 084 genetic variants were found in 120 pharmacogenes, with the majority (90.0%) classified as rare variants (global minor allele frequency <0.5%), with 52.9% being singletons. Common variation clustered individuals into continental super-populations and 23 pharmacogenes contained highly differentiated variants (FST>0...
October 25, 2016: Pharmacogenomics Journal
J L Baker, D Shriner, A R Bentley, C N Rotimi
As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations...
October 25, 2016: Pharmacogenomics Journal
Rachel B Spigler, Konstantinos Theodorou, Shu-Mei Chang
Inbreeding depression is a major driver of mating system evolution and has critical implications for population viability. Theoretical and empirical attention has been paid to predicting how inbreeding depression varies with population size. Lower inbreeding depression is predicted in small populations at equilibrium, primarily due to higher inbreeding rates facilitating purging and/or fixation of deleterious alleles (drift load), but predictions at demographic and genetic disequilibrium are less clear. In this study, we experimentally evaluate how lifetime inbreeding depression and drift load, estimated by heterosis, vary with census (Nc ) and effective (estimated as genetic diversity, He ) population size across six populations of the biennial Sabatia angularis as well as present novel models of inbreeding depression and heterosis under varying demographic scenarios at disequilibrium (fragmentation, bottlenecks, disturbances)...
October 25, 2016: Evolution; International Journal of Organic Evolution
Anne Julie Overgaard, Simranjeet Kaur, Flemming Pociot
Metabolomics is the snapshot of all detectable metabolites and lipids in biological materials and has potential in reflecting genetic and environmental factors contributing to the development of complex diseases, such as type 1 diabetes. The progression to seroconversion to development of type 1 diabetes has been studied using this technique, although in relatively small cohorts and at limited time points. Overall, three observations have been consistently reported; phospholipids at birth are lower in children developing type 1 diabetes early in childhood, methionine levels are lower in children at seroconversion, and triglycerides are increased at seroconversion and associated to microbiome diversity, indicating an association between the metabolome and microbiome in type 1 diabetes progression...
December 2016: Current Diabetes Reports
Armando Arias, Lucy Thorne, Elsa Ghurburrun, Dalan Bailey, Ian Goodfellow
Intrahost genetic diversity and replication error rates are intricately linked to RNA virus pathogenesis, with alterations in viral polymerase fidelity typically leading to attenuation during infections in vivo. We have previously shown that norovirus intrahost genetic diversity also influences viral pathogenesis using the murine norovirus model, as increasing viral mutation frequency using a mutagenic nucleoside resulted in clearance of a persistent infection in mice. Given the role of replication fidelity and genetic diversity in pathogenesis, we have now investigated whether polymerase fidelity can also impact virus transmission between susceptible hosts...
September 2016: MSphere
Marie Collet, Chloé Vayssade, Alexandra Auguste, Laurence Mouton, Emmanuel Desouhant, Thibaut Malausa, Xavier Fauvergue
Sex determination is ruled by haplodiploidy in Hymenoptera, with haploid males arising from unfertilized eggs and diploid females from fertilized eggs. However, diploid males with null fitness are produced under complementary sex determination (CSD), when individuals are homozygous for this locus. Diploid males are expected to be more frequent in genetically eroded populations (such as islands and captive populations), as genetic diversity at the csd locus should be low. However, only a few studies have focused on the relation between population size, genetic diversity, and the proportion of diploid males in the field...
September 2016: Ecology and Evolution
Ronan Becheler, Constance Xhaard, Etienne K Klein, Katherine J Hayden, Pascal Frey, Stéphane De Mita, Fabien Halkett
The genetic consequences of range expansions have generally been investigated at wide geographical and temporal scales, long after the colonization event. A unique ecological system enabled us to both monitor the colonization dynamics and decipher the genetic footprints of expansion over a very short time period. Each year an epidemic of the poplar rust (Melampsora larici-populina) expands clonally and linearly along the Durance River, in the Alps. The colonization dynamics observed in 2004 showed two phases with different genetic outcomes...
September 2016: Ecology and Evolution
Alesandro S Santos, Eliana Cazetta, Pavel Dodonov, Deborah Faria, Fernanda A Gaiotto
Habitat loss represents one of the main threats to tropical forests, which have reached extremely high rates of species extinction. Forest loss negatively impacts biodiversity, affecting ecological (e.g., seed dispersal) and genetic (e.g., genetic diversity and structure) processes. Therefore, understanding how deforestation influences genetic resources is strategic for conservation. Our aim was to empirically evaluate the effects of landscape-scale forest reduction on the spatial genetic structure and gene flow of Euterpe edulis Mart (Arecaceae), a palm tree considered a keystone resource for many vertebrate species...
September 2016: Ecology and Evolution
Julie B Hébert, Sonja J Scheffer, David J Hawthorne
Evolutionary radiations have been well documented in plants and insects, and natural selection may often underly these radiations. If radiations are adaptive, the diversity of species could be due to ecological speciation in these lineages. Agromyzid flies exhibit patterns of repeated host-associated radiations. We investigated whether host-associated population divergence and evidence of divergent selection exist in the leaf miner Phytomyza glabricola on its sympatric host plants, the holly species, Ilex coriacea and I...
September 2016: Ecology and Evolution
Helge-Ansgar Giebel, Franziska Klotz, Sonja Voget, Anja Poehlein, Katrin Grosser, Andreas Teske, Thorsten Brinkhoff
The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community...
2016: Standards in Genomic Sciences
Aline Assis Cardoso, Michel de Paula Andraus, Tereza Cristina de Oliveira Borba, Claudia Cristina Garcia Martin-Didonet, Enderson Petrônio de Brito Ferreira
This study aimed to evaluate the tolerance to salinity and temperature, the genetic diversity and the symbiotic efficiency of rhizobia isolates obtained from wild genotypes of common bean cultivated in soil samples from the States of Goiás, Minas Gerais and Paraná. The isolates were subjected to different NaCl concentrations (0%, 1%, 2%, 4% and 6%) at different temperatures (28°C, 33°C, 38°C, 43°C and 48°C). Genotypic characterization was performed based on BOX-PCR, REP-PCR markers and 16S rRNA sequencing...
October 4, 2016: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
Mark A Hanson, Phineas T Hamilton, Steve J Perlman
BACKGROUND: Drosophila is an important model for studying the evolution of animal immunity, due to the powerful genetic tools developed for D. melanogaster. However, Drosophila is an incredibly speciose lineage with a wide range of ecologies, natural histories, and diverse natural enemies. Surprisingly little functional work has been done on immune systems of species other than D. melanogaster. In this study, we examine the evolution of immune genes in the speciose subgenus Drosophila, which diverged from the subgenus Sophophora (that includes D...
October 24, 2016: BMC Evolutionary Biology
Félix Javier Jiménez-Jiménez, Hortensia Alonso-Navarro, María Trinidad Herrero, Elena García-Martín, José A G Agúndez
BACKGROUND: The pathogenesis of Parkinson's disease (PD) is not fully understood. Together with some important physiological functions in the Central Nervous System (CNS), nitric oxide (NO) can have both, neuroprotective or neurotoxic actions, depending on its redox state. An important body of evidence suggests the involvement of NO in many of the processes leading to neurodegeneration in several neurological disorders including PD. OBJECTIVE: The main aim of this review is to update the data regarding the possible involvement of NO in the pathogenesis of PD...
2016: Current Medicinal Chemistry
Zhuofeng Yu, Pinjing He, Liming Shao, Hua Zhang, Fan Lü
Since municipal solid waste (MSW) landfill harbours miscellaneous wastes, pollutants and microorganisms, it gradually becomes a huge potential reservoir for breeding antibiotic resistance genes (ARGs). The objective of this study was to determine the prevalence and diversity of ARGs associated with various mobile genetic elements (MGEs) in MSW landfill leachates. The relationship of ARGs with leachate characteristics was also studied to explore the influence of landfill age. Seven sulfonamides (sulfapyridine, sulfadiazine, sulfathiazole, sulfamethoxazole, sulfamerazine, sulfamethazine and sulfaquinoxaline), three encoded ARGs (sul-I, sul-II and sul-III) and four types of MGEs (plasmids, transposons, integrons and insertion sequences) were quantified in leachates with landfill ages ranging from 3 months-6 years...
October 18, 2016: Water Research
Julio Vargas, Vincenzo Landi, Amparo Martínez, Mayra Gómez, María Esperanza Camacho, Luz Ángela Álvarez, Lenin Aguirre, Juan Vicente Delgado
Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered. The present study used molecular genetics tools to investigate the within- and between-breeds diversity, in order to characterize the breed population, define its associations with other breeds, and infer its origin and evolution...
2016: PloS One
Kalle Kipper, Ebba Gregorsson Lundius, Vladimir Curic, Ivana Nikic, Edward A Lemke, Manfred Wiessler, Johan Elf
Small synthetic fluorophores are in many ways superior to fluorescent proteins as labels for imaging. A major challenge is to use them for a protein-specific labeling in living cells. Here, we report on our use of noncanonical amino acids that are genetically encoded via the pyrrolysyl-tRNA/pyrrolysyl-RNA synthetase pair at artificially introduced TAG codons in a recoded E. coli strain. The strain is lacking endogenous TAG codons and the TAG-specific release factor RF1. The amino acids contain bioorthogonal groups that can be clicked to externally supplied dyes, thus enabling protein-specific labeling in live cells...
October 24, 2016: ACS Synthetic Biology
Monika B Dolinska, Nicole Kus, Katie Farney, Paul T Wingfield, Brian P Brooks, Yuri V Sergeev
: Oculocutaneous albinism Type 1 (OCA1) is an autosomal recessive disorder caused by mutations in the tyrosinase gene. Two subtypes of OCA1 have been described: severe OCA1A with complete absence of tyrosinase activity and less severe OCA1B with residual tyrosinase activity. Here, we characterize the recombinant human tyrosinase intra-melanosomal domain and mutant variants, which mimic genetic changes in both subtypes of OCA1 patients. Proteins were prepared using site-directed mutagenesis, expressed in insect larvae, purified by chromatography, and characterized by enzymatic activities- tryptophan fluorescence, and Gibbs free energy changes...
October 24, 2016: Pigment Cell & Melanoma Research
María Muñoz-Amatriaín, Hamid Mirebrahim, Pei Xu, Steve I Wanamaker, MingCheng Luo, Hind Alhakami, Matthew Alpert, Ibrahim Atokple, Benoit Joseph Batieno, Ousmane Boukar, Serdar Bozdag, Ndiaga Cisse, Issa Drabo, Jeffrey D Ehlers, Andrew Farmer, Christian Fatokun, Yong Q Gu, Yi-Ning Guo, Bao-Lam Huynh, Scott A Jackson, Francis Kusi, Cynthia T Lawley, Mitchell R Lucas, Yaqin Ma, Michael P Timko, Jiajie Wu, Frank You, Philip A Roberts, Stefano Lonardi, Timothy J Close
Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4,355 BACs...
October 24, 2016: Plant Journal: for Cell and Molecular Biology
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