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Genome Génome / Conseil National de Recherches Canada

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https://www.readbyqxmd.com/read/29447476/sequencing-and-characterization-of-lncrnas-in-the-breast-muscle-of-gushi-and-arbor-acres-chicken
#1
Tuanhui Ren, Zhuanjian Li, Yu Zhou, Xuelian Liu, Ruili Han, Yongcai Wang, Fengbin Yan, Guirong Sun, Hong Li, Xiangtao Kang
Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development-related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens...
February 15, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29447453/in-silico-genome-wide-identification-and-characterization-of-glutathione-s-transferase-gene-family-in-vigna-radiata-l-wilczek
#2
Swati Vaish, Praveen Awasthi, Siddharth Tiwari, Shailesh Kumar Tiwari, Divya Gupta, Mahesh Kumar Basantani
Plant glutathione S-transferases are integral to normal plant metabolism, and biotic and abiotic stress tolerance. GST gene family has been characterized in diverse plant species using molecular biology and bioinformatics approaches. In the current study, in silico analysis identified 44 GSTs in Vigna radiata. Of the total 44 GSTs identified, chromosomal locations of 31 GSTs were confirmed. The pI value of GST proteins ranged from 5.10 to 9.40. The predicted molecular weights ranged from 13.12 to 50 kDa. Subcellular localization analysis revealed that all GSTs were predominantly localized in the cytoplasm...
February 15, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29432699/population-genomics-of-sorghum-sorghum-bicolor-across-diverse-agroclimatic-zones-of-niger
#3
Fanna Maina, Sophie Bouchet, Sandeep Marla, Zhenbin Hu, Jianan Wang, Aissata Mamadou, Magagi Abdou, Abdoul-Aziz Saïdou, Geoffrey Preston Morris
Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known...
February 12, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29425468/identifying-small-rnas-derived-from-maternal-and-somatic-type-rrnas-in-zebrafish-development
#4
Mauro D Locati, Johanna F B Pagano, Farah Abdullah, Wim A Ensink, Marina van Olst, Selina van Leeuwen, Ulrike Nehrdich, Herman P Spaink, Han Rauwerda, Martijs J Jonker, Rob J Dekker, Timo Breit
rRNAs are non-coding RNAs present in all prokaryotes and eukaryotes. In eukaryotes there are four rRNAs: 18S, 5.8S, 28S, originating from a common precursor (45S), and 5S. We have recently discovered the existence of two distinct developmental types of rRNA: a maternal-type, present in eggs and a somatic-type, expressed in adult tissues. Lately, next-generation sequencing has allowed the discovery of new small-RNAs deriving from longer non-coding RNAs, including small-RNAs from rRNAs (srRNAs). Here, we systemically investigated srRNAs of maternal- or somatic-type 18S, 5...
February 9, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29420906/development-of-an-indel-polymorphism-database-for-jute-via-comparative-transcriptome-analysis
#5
Zemao Yang, Zhigang Dai, Dongwei Xie, Jiquan Chen, Qing Tang, Chaohua Cheng, Ying Xu, Tingzhang Wang, Jianguang Su
Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31...
February 8, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29401409/alternative-splicing-results-in-a-lack-of-starch-synthase-iia-d-in-chinese-wheat-landrace
#6
Yan-Jie Zhou, Qiang Yang, Xiao-Juan Zhong, Mei Deng, Jian Ma, Peng-Fei Qi, Ji-Rui Wang, Guo-Yue Chen, Yaxi Liu, Zhen-Xiang Lu, Wei Li, Xiu-Jin Lan, Yu-Ming Wei, Youliang Zheng, Qian-Tao Jiang
We evaluated the SGP-1 protein composition of 368 Chinese wheat landraces using SDS-PAGE. The SGP-D1 null type was identified in three accessions (Xiaoqingmang, Pushanbamai, and P119). An 18-bp deletion and 9-bp variation were found at the junction region of the 7th intron and 8th exon, leading to deletion of the intron-exon junction recognition site AG when aligned the 8261-bp DNA sequence of TaSSIIa-D in Pushanbamai with that of Chinese Spring. Four cDNA types with mis-spliced isoforms were subsequently detected though amplification of TaSSIIa-D cDNAs...
February 5, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29401405/molecular-analyses-of-the-agouti-allele-in-the-japanese-house-mice-identify-a-novel-variant-of-the-agouti-gene
#7
Masahiro A Iwasa, Sayaka Kawamura, Hikari Myoshu, Taichi A Suzuki
It has been thought that Japanese house mice carry the Aw allele at the agouti locus causing light-colored bellies, but they do not always show this coloration. Thus, the presence of the Aw allele seems to be doubtful in them. To ascertain whether the Aw allele is present, a two-pronged approach was used. First, we compared lengths of DNA fragments obtained from three PCRs conducted on them to the known fragment sizes generated from mouse strains exhibiting homozygosities of either a/a, A/A, or Aw/Aw. PCRs I, II, and III can amplify only in the A and Aw alleles, the a and Aw alleles, and the a allele, respectively, and we detected amplifications in strains with A/A and Aw/Aw by PCR I, in those with a/a and Japanese house mice by PCR II, and in those with a/a by PCR III...
February 5, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29394492/influence-of-5-flanking-sequence-on-4-5si-rna-gene-transcription-by-rna-polymerase-iii
#8
Irina Gogolevskaya, Danil Stasenko, Karina Tatosyan, Dmitri Kramerov
Short nuclear 4.5SI RNA can be found in three related rodent families. Its function remains unknown. The genes of 4.5SI RNA contain an internal promoter of RNA polymerase III composed of the boxes A and B. Here, the effect of the sequence immediately upstream of the mouse 4.5SI RNA on its transcription was studied. The gene with deletions and substitutions in the 5'-flanking sequence was used to transfect HeLa cells and its transcriptional activity was evaluated from the cellular level of 4.5SI RNA. Single-nucleotide substitutions in the region adjacent to the transcription start site (positions -2 to -8) decreased the expression activity of the gene down to 40-60% of the control...
February 2, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29373804/quantitative-trait-loci-qtl-analysis-of-root-traits-under-phosphorus-deficiency-at-the-seedling-stage-in-wheat
#9
Xilan Yang, Yaxi Liu, Fangkun Wu, Xiaojun Jiang, Yu Lin, Zhiqiang Wang, Zhengli Zhang, Jian Ma, Guangdeng Chen, Yuming Wei, Youliang Zheng
Deficiency of available phosphorus (P) in soil limits wheat production and creates a need to develop P-deficiency-tolerant cultivars. Plant roots, important organs for absorbing nutrients and synthesizing growth regulators, are good candidates for P-efficiency screening. In this study, we evaluated five root traits under hydroponic culture conditions either with (AP) or without (NP) applied P in a recombinant inbred line population H461/CM107 of <i>Triticum aestivum </i>L. at the seedling stage...
January 26, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29365289/comparative-genome-analysis-to-identify-snps-associated-with-high-oleic-acid-and-elevated-protein-content-in-soybean
#10
Krishnanand Kulkarni, Gunvant Patil, Babu Valliyodan, Tri Vuong, Grover Shannon, Henry Nguyen, Jeong-Dong Lee
The objective of this study was to determine the genetic relationship between the oleic acid and protein content. The genotypes having high oleic acid and elevated protein (HOEP) content were crossed with five elite lines having normal oleic acid and average protein (NOAP) content. The selected accessions were grown at six environments in three different locations and phenotyped for protein, oil and fatty acid components. The mean protein content of parents, HOEP, and NOAP lines was 34.6%, 38%, and 34.9%, respectively...
January 24, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29338359/characterization-of-moso-bamboo-phyllostachys-edulis-dof-factors-in-floral-development-and-abiotic-stress-responses
#11
Zhanchao Cheng, Dan Hou, Jun Liu, Xiangyu Li, Lihua Xie, Yanjun Ma, Jian Gao
The Dof transcription factor (TF) family belongs to a class of plant-specific TFs, and is involved in plant growth, development, and response to abiotic stresses. However, there are only very limited reports on the characterization of Dof TFs in moso bamboo. In the present research, PheDofs showed specific expression profiles based on RNA-seq data analyses. The co-experssion network indicated that PheDof12, PheDof14 and PheDof16 might play vital roles during flower development. Cis-regulatory element analysis of these PheDof genes suggested diverse functions...
January 16, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29338343/molecular-analysis-of-anthocyanin-biosynthesis-pathway-genes-and-their-differential-expression-in-mango-peel
#12
Anju Bajpai, Kasim Khan, M Muthukumar, S Rajan, Nagendra Kumar Singh
Mango fruit is cherished by masses for its taste and nutrition, contributed by color, flavor and aroma. Among these, peel color is an important trait contributing to fruit quality and market value. We attempted to elucidate the role of key genes of anthocyanin biosynthesis pathway related to fruit peel color from the leaf transcriptome of cv. Amrapali. A total of 108 mined transcript sequences were assigned to phenylpropanoid flavonoid pathway from which 15 contigs representing anthocyanin biosynthesis genes were annotated...
January 16, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29338341/rna-sequencing-on-amomum-villosum-lour-induced-by-meja-identifies-the-genes-of-wrky-and-terpene-synthases-involved-in-terpene-biosynthesis
#13
Xueying He, Huan Wang, Jinfen Yang, Ke Deng, Teng Wang
Amomum villosum Lour. is an important Chinese medicine that has diverse medicinal functions, and mainly contains volatile terpenes This study aimed to explore the WRKY transcription factors (TFs) and terpene synthases (TPS) unigenes, which might be involved in terpene biosynthesis in A. villosum for providing some new information on the regulation of terpenes in plants. RNA sequencing of A.villosum-induced by methyl jasmonate (MeJA) revealed WRKY family was the second biggest TF family in the transcriptome...
January 16, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29304291/genome-wide-identification-and-expression-analysis-of-calax-and-capin-gene-families-in-pepper-capsicum-annuum-l-under-various-abiotic-stresses-and-hormones-treatments
#14
Chenghao Zhang, Wenqi Dong, Zong-An Huang, MyeongCheoul Cho, Qingcang Yu, Chuanyu Wu, Chenliang Yu
Auxin plays key roles in regulating plant growth and development as well as in responses to environmental stresses. The intercellular transport of auxin is mediated by four gene families, with the ATP-binding cassette family B (ABCB), the Auxin resistant1/ like (AUX1AUX/LAX) family, the pin-formed(PIN)families, and the PIN-LIKES (PILS) family. Here, the latest assembled pepper genome was used to characterise and analyse the CaLAX and CaPIN families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships and intron/exon structures, were performed...
January 5, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29268034/genome-wide-searches-and-molecular-analyses-highlight-the-unique-evolutionary-path-of-flavone-synthase-i-fnsi-in-apiaceae
#15
Qi Zhi Wang, Stephen R Downie, Zhen Xi Chen
Flavone synthase is a key enzyme for flavone biosynthesis and is encoded by two gene families, flavone synthase I (FNSI) and flavone synthase II (FNSII). FNSII is widely distributed in plants, while FNSI has been reported in rice (Oryza sativa) and seven species of Apiaceae. FNSI has likely evolved from the duplication of flavanone 3β-hydroxylase (F3H). In this study, we used multiple bioinformatics tools to identify putative FNSI and F3H genes from 42 publicly available genome and transcriptome datasets. Results showed that rice FNSI does not share a common ancestral sequence with other known FNSI genes and that FNSI is absent from non-Apiaceae species...
December 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29268023/whole-genome-sequencing-reveals-the-extent-of-heterozygosity-in-a-preferentially-self-fertilizing-hermaphroditic-vertebrate
#16
Luana S F Lins, Shawn Trojahn, Alexandra Sockell, Muh-Ching Yee, Andrey Tatarenkov, Carlos D Bustamante, Ryan L Earley, Joanna L Kelley
The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus but overall there is a low rate of outcrossing and therefore, low heterozygosity. In this study, we used whole-genome data to assess the level of genetic diversity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages...
December 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29265885/corrigendum-exploiting-alpine-glaciers-as-biological-archives-dna-metabarcoding-of-ice-cores-extracted-from-the-largest-and-deepest-southern-alps-glacier-adamello-italy
#17
Cristiano Vernesi, Matteo Girardi, Matteo Montagna, Daniela Festi, Christian Casarotto, Valter Maggi, Antonella Cristofori
No abstract text is available yet for this article.
December 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29241022/evolution-as-an-ecosystem-process-insights-from-genomics
#18
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
https://www.readbyqxmd.com/read/29237140/high-density-snp-mapping-reveals-closely-linked-qtl-for-resistance-to-stagonospora-nodorum-blotch-snb-in-flag-leaf-and-glume-of-hexaploid-wheat
#19
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
https://www.readbyqxmd.com/read/29232522/molecular-analysis-of-anthocyanin-related-genes-in-ornamental-cabbage
#20
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
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