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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
Suzy Cp Renn, Heather E Machado, Nina Unterwaditzer, Rayna M Harris, Anna K Sessa, Hans A Hofmann
The diversity of mating systems among animals is astounding. Importantly, similar mating systems have evolved even across distantly related taxa. However, our understanding of the mechanisms underlying these convergently evolved phenotypes is limited. Here, we examine on a genomic scale the neuromolecular basis of social organization in Ectodini cichlids from Lake Tanganyika. Using field collected males and females of four closely related species representing two independent evolutionary transitions from polygyny to monogamy, we take a comparative transcriptomic approach to test the hypothesis that these independent transitions have recruited similar gene sets...
September 25, 2017: Genome Génome / Conseil National de Recherches Canada
Bohao Zhao, Yang Chen, Xiaorong Yan, Ye Hao, Jie Zhu, Qiiaoqing Weng, Xinsheng Wu
Fur is an important economic trait in rabbits. The identification of genes that influence fur development and knowledge regarding the actions of these genes provides useful tools for improving fur quality. However, the mechanism of fur development is unclear. To obtain candidate genes related to fur development, the transcriptomes of tissues from backs and bellies of Chinchilla rex rabbits were compared. Of the genes analyzed, 336 showed altered expression in the two groups (285 upregulated and 51 downregulated), P≤0...
August 29, 2017: Genome Génome / Conseil National de Recherches Canada
Jian Ma, Wei Luo, Han Zhang, Xiao-Hong Zhou, Na-Na Qin, Yu-Ming Wei, Yaxi Liu, Qian-Tao Jiang, Guo-Yue Chen, You-Liang Zheng, Xiu-Jin Lan
As a primitive hexaploid wheat resource distributed only in Tibet, Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) possesses unique characteristics that could be exploited in wheat breeding program. A good root system could offer a stable platform for the above-ground components. Aiming at detecting possible excellent locus for root traits from Tibetan semi-wild wheat, we here identified QTLs for root traits using a recombinant inbred line population derived from a cross between Tibetan semi-wild wheat Q1028 and Zhengmai 9023...
August 25, 2017: Genome Génome / Conseil National de Recherches Canada
Weixiao Yin, Peng Cui, Wei Wei, Yang Lin, Chaoxi Luo
The basic leucine zipper (bZIP) transcription factor (TF) family is one of the largest and most diverse TF families widely distributed across the eukaryotes. The bZIP TF family play important roles in growth, development, and response to abiotic or biotic stresses, which have been well characterized in plants, but not in plant pathogenic fungi. In this study, we performed genome-wide and systematic bioinformatics analysis of bZIP genes in the fungus <i>Ustilaginoidea virens</i>, the causal agent of rice false smut disease...
August 25, 2017: Genome Génome / Conseil National de Recherches Canada
Hiroshi Shinozuka, Noel Cogan, German Spangenberg, John Forster
RNA-Seq methodology has been used to generate a comprehensive transcriptome sequence resource for perennial ryegrass, an important temperate pasture grass species. A total of 931,547,255 reads were obtained from libraries corresponding to 19 distinct tissue samples, including both vegetative and reproductive stages of development. Assembly of data generated a final filtered reference set of 48,713 contigs and scaffolds. The transcriptome resource will support whole genome sequence assembly, comparative genomics, implementation of genotyping-by-sequencing (GBS) methods based on transcript sampling and identification of candidate genes for multiple biological functions...
August 25, 2017: Genome Génome / Conseil National de Recherches Canada
Wei Xu, Nai-Yong Liu, Yalin Liao, Alisha Anderson
Insects utilize sugars as their essential energy and nutrient sources; therefore, the sense of sugar detection plays a critical role in insect behaviours. Previously using genomic and transcriptomic approaches, we identified eight putative sugar gustatory receptor (GR) genes from the cotton bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). Here we further validated these annotated sugar receptor genes (HarmGr4-8 and 10-12) and found HarmGr10 may be a pseudogene carrying a stop codon in the open reading frame (ORF)...
August 21, 2017: Genome Génome / Conseil National de Recherches Canada
Acga Cheng, Ismanizan Ismail, Mohamad Osman, Habibuddin Hashim, Nur Samahah Mohd Zainual
While it is crucial for developing countries like Malaysia to achieve self-sufficiency in rice (Oryza sativa L.), it is equally critical to be able to produce high-quality rice, specifically fragrant rice, which demands are often met through importation. The present study was aimed at developing high-yielding fragrant rice, in a timely and cost-effective manner. A marker-assisted backcross (MABC) approach was optimised to introgress the fragrance gene (fgr) into two high-yielding Malaysian varieties; MR84 and MR219, within two years utilising less than fifty molecular markers...
August 16, 2017: Genome Génome / Conseil National de Recherches Canada
M H Ye, H Bao, Y Meng, L L Guan, P Stothard, G Plastow
While some research has looked into the host genetic response in pigs challenged with specific viruses or bacteria, few studies have explored the expression changes of transcripts in the peripheral blood of sick pigs which may be infected with multiple pathogens on farms. In this study, peripheral blood transcriptome architecture in 64 Duroc sired commercial pigs, including 18 healthy animals at entry to a growing facility (set as a control) and 23 pairs of samples from healthy and sick pen mates, was generated using RNA-Seq technology...
August 1, 2017: Genome Génome / Conseil National de Recherches Canada
Nastasia R Merceron, Thibault Leroy, Emilie Chancerel, Jeanne Romero-Severson, Daniel Borkowski, Alexis Ducousso, Arnaud Monty, Annabel J Porté, Antoine Kremer
Quercus rubra has been introduced in Europe since the end of the seventeenth century. It is widely distributed today across this continent and considered invasive in some countries. Here, we investigated the distribution of genetic diversity of both native and introduced populations with the aim of tracing the origin of introduced populations. A large sampling of 883 individuals from 73 native and 38 European locations were genotyped at 69 SNPs. In the natural range, we found a continuous geographic gradient of variation with a predominant latitudinal component...
July 27, 2017: Genome Génome / Conseil National de Recherches Canada
Kaikai Wu, Zhiying Jia, Qi'ai Wang, Zhenlin Wei, Zunchun Zhou, Xiaolin Liu
Accumulating evidence indicates that Krüppel-like factors (KLFs) play important roles in fat biology via the regulation of CCAAT/enhancer binding proteins (C/EBPs). However, KLFs and C/EBPs have not been identified from Strongylocentrotus nudus, and their roles in this species are not clear. In this study, the full-length cDNA of S. nudus KLF10 (SnKLF10) and three cDNA fragments of S. nudus C/EBPs (SnC/EBPs) were obtained. Examination of tissue distribution and expression patterns during gonadal development implied that SnKLF10 and SnC/EBPs play important roles in gonadal lipogenesis...
October 2017: Genome Génome / Conseil National de Recherches Canada
Chen Zhu, Yanzhen Wang, Chunhuan Chen, Changyou Wang, Aicen Zhang, Nana Peng, Yajuan Wang, Hong Zhang, Xinlun Liu, Wanquan Ji
Thinopyrum ponticum (Th. ponticum) (2n = 10x = 70) is an important breeding material with excellent resistance and stress tolerance. In this study, we characterized the derivative line CH1113-B13-1-1-2-1 (CH1113-B13) through cytological, morphological, genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), expressed sequence tag (EST), and PCR-based landmark unique gene (PLUG) marker analysis. The GISH analysis revealed that CH1113-B13 contained 20 pairs of common wheat chromosomes and one pair of J(St) genomic chromosomes...
October 2017: Genome Génome / Conseil National de Recherches Canada
J Vierna, J Doña, A Vizcaíno, D Serrano, R Jovani
High-throughput DNA barcoding has become essential in ecology and evolution, but some technical questions still remain. Increasing the number of PCR cycles above the routine 20-30 cycles is a common practice when working with old-type specimens, which provide little amounts of DNA, or when facing annealing issues with the primers. However, increasing the number of cycles can raise the number of artificial mutations due to polymerase errors. In this work, we sequenced 20 COI libraries in the Illumina MiSeq platform...
October 2017: Genome Génome / Conseil National de Recherches Canada
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