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Genome Génome / Conseil National de Recherches Canada

Blake Matthews, Rebecca J Best, Philine G D Feulner, Anita Narwani, Romana Limberger
Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics...
December 14, 2017: Genome Génome / Conseil National de Recherches Canada
Michael Francki, Esther Walker, Dora Li, Kerrie Forrest
The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074 and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively...
December 13, 2017: Genome Génome / Conseil National de Recherches Canada
Si-Won Jin, Md Abdur Rahim, Hoy-Taek Kim, Jong-In Park, Jong-Goo Kang, Ill-Sup Nou
Ornamental cabbage (Brassica oleracea var. acephala) is a winter-grown and important decorative plant of the Brassicaceae family, which displays an exceptional coloration in the central leaves of the rosette. Anthocyanins are the key determinant of the red, purple and blue colors of vegetative and reproductive parts of many plant species including ornamental cabbage. Total anthocyanin content was measured spectrophotometrically and the highest anthocyanin content detected in the red followed by light-red and white ornamental cabbage lines...
December 12, 2017: Genome Génome / Conseil National de Recherches Canada
Nick Barts, Ryan Greenway, Courtney N Passow, Lenin Arias-Rodriguez, Joanna L Kelley, Michael Tobler
Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated ten lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S - along with related lineages from non-sulfidic environments - to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context...
December 11, 2017: Genome Génome / Conseil National de Recherches Canada
Ekaterina D Badaeva, Alevtina S Ruban, Alexandra A Shishkina, Sergei N Sibikeev, Alexander E Druzhin, Sergei A Surzhikov, Alexandra Yu Dragovich
<i>Aegilops columnaris</i> is tetraploid <i>Aegilops</i> species originated from <i>Ae. umbellulata </i>(2n=2x=14, UU) and yet unknown diploid grass species. Although <i>Ae. columnaris </i>possesses some agronomically valuable traits, such as heat and drought tolerance, resistance to pests, it has never been used in wheat breeding due to difficulties of hybrid production and lack of information on the relationships between <i>Ae. columnaris </i>and common wheat chromosomes...
December 7, 2017: Genome Génome / Conseil National de Recherches Canada
Xiao-Ming Zheng, Tingting Gong, Hong-Ling Ou, Dayuan Xue, Weihua Qiao, Junrui Wang, Sha Liu, Qingwen Yang, Kenneth M Olsen
Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (<i>Oryza sativa</i>) to perform a large scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1...
December 1, 2017: Genome Génome / Conseil National de Recherches Canada
Xiaomei Luo, Nicholas A Tinker, Yong-Hong Zhou, Charlene P Wight, Juncheng Liu, Wenlin Wan, Liang Chen, Yuanying Peng
Knowledge of the locations of repeat elements could be very important in the assembly of genome sequences and assignment to physical chromosomes. Genomic and species relationships among sixteen species were investigated using fluorescence in situ hybridization (FISH) with the Am1 and (ACT)6 probes. The Am1 oligonucleotide probe was particularly enriched in the C genomes, whereas the (ACT)6 trinucleotide repeat probe showed a diverse distribution of hybridization patterns in the A, AB, C, AC, and ACD genomes but might not be present in the B and D genomes...
November 30, 2017: Genome Génome / Conseil National de Recherches Canada
Joana Teixeira Sousa, Standish Allen, Brittany M Wolfe, Jessica Moss Small
For commercial oyster aquaculture, triploidy has significant advantages. To produce triploids, the principal technology uses diploid x tetraploid crosses. The development of tetraploid brood stock for this purpose has been successful, but as more is understood about tetraploids, it seems clear that chromosome instability is a principal feature in oysters. This paper is a continuation of work to investigate chromosome instability in polyploid Crassostrea virginica. We established families between tetraploids - apparently stable (non-mosaic) and unstable (mosaic) - and normal reference diploids, creating triploid groups, as well as tetraploids between mosaic and non-mosaic tetraploids...
November 30, 2017: Genome Génome / Conseil National de Recherches Canada
Conxita Arenas, Goran Zivanovic, Francisco Mestres
<i>Drosophila </i>has demonstrated to be an excellent model to study the adaptation of organisms to global warming, with inversion chromosomal polymorphism having a key role in this adaptation. Here, we introduce a new index (Chromosomal Thermal Index or CTI) to quantify the thermal adaptation of a population according to its composition of 'warm' and 'cold' adapted inversions. This index is intuitive, has good statistical properties and can be used to hypothesis on the effect of global warming on natural populations...
November 30, 2017: Genome Génome / Conseil National de Recherches Canada
Allison Anjos, Andressa Paladini, Tatiane Casagrande Mariguela, Diogo Cavalcanti Cabral-de-Mello
Spittlebugs, which belong to the Cercopidae family (Auchenorrhyncha, Hemiptera), form a large group of xylem-feeding insects that are best known for causing damage to plantations and pasture grasses. The holocentric chromosomes of these insects remain poorly studied regarding to the organization of different classes of repetitive DNA. To improve chromosomal maps based on repetitive DNAs and to better understand the chromosomal organization and evolutionary dynamics of multigene families in spittlebugs, we physically mapped U1 snRNA gene with fluorescence in situ hybridization (FISH) in ten Cercopidae species belonging to three different genera...
November 29, 2017: Genome Génome / Conseil National de Recherches Canada
Xiaofei Yang, Xin Li, Changyou Wang, Chunhuan Chen, Zengrong Tian, Wanquan Ji
A common wheat - Leymus mollis (2n = 4x = 28, NsNsXmXm) double monosomic addition line, M11003-4-3-8/13/15 (2n = 44 = 42T.a + L.m2 + L.m3), with stripe rust resistance was developed (where T.a represents Triticum aestivum chromosome, L.m represents L. mollis chromosome, and L.m2/3 represents L. mollis chromosome of homoeologous groups 2 and 3). The progenies of line M11003-4-3-8/13/15 were characterized by cytological observation, specific molecular markers, fluorescence in situ hybridization (FISH), and genomic in situ hybridization (GISH)...
November 10, 2017: Genome Génome / Conseil National de Recherches Canada
Yan Zhong, Cong Guo, Jinjin Chu, Hui Liu, Max Zong-Ming Cheng
VQ motif-containing proteins play crucial roles in plant growth, development, and stress responses. However, no information of VQ motif-containing proteins has been studied at microevolution level in Fragaria species. In this study, a total of 19, 21, 23, 23, 23, and 25 genes containing the VQ motif were identified from the genomes of F. nipponica, F. iinumae, F. orientalis, F. vesca, F. nubicola, and F. x ananassa, respectively. We classified the VQs into 15 clades with grapevine VQs, which indicated that at least 15 ancient VQ genes existed before the divergence of the six Fragaria species...
October 30, 2017: Genome Génome / Conseil National de Recherches Canada
Stephanie Pedersen, Lei Liu, Brian Glebe, Steven Leadbeater, Sigbjørn Lien, Elizabeth G Boulding
Little is known about the genetic architecture of traits important for salmonid restoration ecology. We mapped quantitative trait loci (QTL) using single nucleotide polymorphisms (SNPs) for juvenile body length, weight, shape, and vertical skin pigmentation patterns (parr marks) within three hybrid backcross families between European and North American subspecies of Atlantic salmon. Amounts of variation in skin colour and pattern quantified in the two second-generation transAtlantic families exceeded the ranges seen in purebred populations...
October 16, 2017: Genome Génome / Conseil National de Recherches Canada
Wanxu Wang, Ting Shi, Xiaopeng Ni, Yanshuai Xu, Shenchun Qu, Zhihong Gao
The microRNAs (miRNAs) comprise a broad class of non-coding small endogenous RNAs that are associated with many biological processes through the regulation of target genes, such as leaf morphogenesis and polarity, biotic and abiotic stress responses, root and flower development. We identified a miRNA that affects flower development, miR319a, in Prunus mume. The Pm-miR319a target, Pm-TCP4, was validated by 5'RACE. The higher expression of Pm-TCP4 in imperfect flowers showed that the Pm-TCP4 might promote pistil abortion...
October 16, 2017: Genome Génome / Conseil National de Recherches Canada
Jason Gibbs
There is an ongoing campaign to DNA barcode the world's >20,000 bee species. Recent revisions of <i>Lasioglossum</i> (<i>Dialictus</i>) (Hymenoptera: Halictidae) for Canada and the eastern United States were completed using integrative taxonomy. DNA barcode data from 110 species of <i>L</i>. (<i>Dialictus</i>) are examined for their value in identification and discovering additional taxonomic diversity. Specimen identification success was estimated using the best close match method...
October 3, 2017: Genome Génome / Conseil National de Recherches Canada
Susan Weiner, Amy Geffre, Amy Lynn Toth
RNA-interference (RNAi) is a useful tool to assess gene function by knocking down expression of a target gene, and has been used successfully in domestic and laboratory organisms. However, RNAi for functional genomics has not fully extended into ecological model organisms in natural environments. Assessment of gene function in the wild is important, because gene function can be environmentally and context-dependent. Here, we present a case study using RNAi to assess gene function in wild paper wasps Polistes metricus, to test roles for two candidate genes (NADH dehydrogenase and Retinoid and fatty acid binding protein) in the development of reproductive castes...
October 2, 2017: Genome Génome / Conseil National de Recherches Canada
Shangguo Feng, Kaili Jiao, Yujia Zhu, Hongfen Wang, Mengying Jiang, Huizhong Wang
Physalis L., an important genus of the family Solanaceae, includes many commercially important edible and medicinal species. Traditionally, species identification is based on morphological traits; however, the highly similar morphological traits among Physalis species make this approach difficult. In this study, we evaluated the feasibility of using a popular DNA barcode, the chloroplast psbA-trnH intergenic region, in the identification of Physalis species. Thirty-six psbA-trnH regions of Physalis species and of the closely related plant Nicandra physalodes were analyzed...
September 29, 2017: Genome Génome / Conseil National de Recherches Canada
Saeed S Sohrabi, Mohammadreza Mohammadabadi, Dong-Dong Wu, Ali Esmailizadeh
Copy number variations (CNVs) are important large scale variants that are widespread in the genome and may contribute to phenotypic variation. Detection and characterization of CNVs can provide new insights into the genetic basis of important traits. Here, we performed whole genome short read sequence analysis to identify CNVs in two indigenous and commercial chicken breeds and evaluate the impact of the identified CNVs on breed specific traits. After filtration, a total of 12955 CNVs spanning (on average) about 9...
September 29, 2017: Genome Génome / Conseil National de Recherches Canada
Andrew J Mongue, James Walters
Genes that promote sexual conflict, such as those with a sex-limited fitness benefit, are expected to accumulate differentially on sex chromosomes relative to autosomes. Few tests of this hypothesis exist for male homogametic (ZZ) taxa, however, and most use RNA expression data to identify such genes. Here, we employ a different identification method by using proteomic analysis of sperm cells to identify genes with a sex-limited benefit. We tested for a bias in genomic location of sperm protein genes in two species of Lepidoptera...
September 29, 2017: Genome Génome / Conseil National de Recherches Canada
Frédérique Bélanger-Lépine, Christelle Leung, Hélène Glémet, Bernard Angers
The ribosomal intergenic spacer (IGS), responsible for the rate of transcription of rRNA genes, is associated with the growth and fecundity of individuals. A previous study of IGS length variants in a yellow perch (<i>Perca flavescens</i>) population revealed the presence of two predominant alleles differing by 1 kb due to variation in the number of repeat units. This study aims to assess whether length variation of IGS is the result of selection in natural populations. Length variation of IGS and eleven neutral microsatellite loci were assessed in geographically distant yellow perch populations...
September 26, 2017: Genome Génome / Conseil National de Recherches Canada
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