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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/28785867/scmed7-a-sugarcane-mediator-subunit-gene-acts-as-a-regulator-of-plant-immunity-and-is-responsive-to-diverse-stress-and-hormone-treatments
#1
Xu Zhang, Yuting Yang, Jiake Zou, Yun Chen, Qibin Wu, Jinlong Guo, Youxiong Que, Liping Xu
The Mediator complex, is an essential component of the RNA polymerase II general transcriptional machinery in eukaryotes. Mediator subunit 7 (MED7), a key subunit in the central module of this complex, plays an important role in gene transcriptional regulation. The present study isolated the full-length cDNA of the MED7 gene of sugarcane, hereby designated as ScMED7, which was characterized to harbor a 525-bp open reading frame that is predicted to encode a 174-amino acid protein with a molecular mass of 19...
August 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28785866/whole-genome-comparative-analysis-of-four-georgian-grape-cultivars
#2
V Tabidze, I Pipia, M Gogniashvili, N Kunelauri, L Ujmajuridze, M Pirtskhalava, B Vishnepolsky, A G Hernandez, C J Fields, Tengiz Beridze
Grapevine is the one of the most important fruit species in the world. Comparative genome sequencing of grape cultivars is very important for the interpretation of the grape genome and understanding its evolution. The genomes of four Georgian grape cultivars-Chkhaveri, Saperavi, Meskhetian green, and Rkatsiteli, belonging to different haplogroups, were resequenced. The shotgun genomic libraries of grape cultivars were sequenced on an Illumina HiSeq. Pinot Noir nuclear, mitochondrial, and chloroplast DNA were used as reference...
August 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28766017/pmk-1-p38-mapk-promotes-cadmium-stress-resistance-the-expression-of-skn-1-nrf-and-daf-16-target-genes-and-protein-biosynthesis-in-caenorhabditis-elegans
#3
Alex Keshet, Ansgar Mertenskötter, Sarah A Winter, Vanessa Brinkmann, Ramona Dölling, Rüdiger J Paul
The mechanisms of cadmium (Cd) resistance are complex and not sufficiently understood. The present study, therefore, aimed at assessing the roles of important components of stress-signaling pathways and of ABC transporters under severe Cd stress in Caenorhabditis elegans. Survival assays on mutant and control animals revealed a significant promotion of Cd resistance by the PMK-1 p38 MAP kinase, the transcription factor DAF-16/FoxO, and the ABC transporter MRP-1. Transcriptome profiling by RNA-Seq on wild type and a pmk-1 mutant under control and Cd stress conditions revealed, inter alia, a PMK-1-dependent promotion of gene expression for the translational machinery...
August 1, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28748394/association-mapping-analysis-of-fiber-yield-and-quality-traits-in-upland-cotton-gossypium-hirsutum-l
#4
Mulugeta Seyoum Ademe, Shoupu He, Zhaoe Pan, Junling Sun, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Dongyong Xu, Jinlong Yang, Zhiying Ma, Jinbiao Zhang, Zhikun Li, Zhongmin Cai, Xuelin Zhang, Xin Zhang, Aifen Huang, Xianda Yi, Guanyin Zhou, Lin Li, Haiyong Zhu, Baoyin Pang, Liru Wang, Yinhua Jia, Xiongming Du
Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China...
July 26, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28733817/enriching-an-intraspecific-genetic-map-and-identifying-qtl-for-fiber-quality-and-yield-component-traits-across-multiple-environments-in-upland-cotton-gossypium-hirsutum-l
#5
Xueying Liu, Zhonghua Teng, Jinxia Wang, Tiantian Wu, Zhiqin Zhang, Xianping Deng, Xiaomei Fang, Zhaoyun Tan, Iftikhar Ali, Dexin Liu, Jian Zhang, Dajun Liu, Fang Liu, Zhengsheng Zhang
Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population...
July 21, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28710562/significant-and-unique-changes-in-phosphorylation-levels-of-four-phosphoproteins-in-two-apple-rootstock-genotypes-under-drought-stress
#6
Jing Ren, Juan Mao, Cunwu Zuo, Alejandro Calderón-Urrea, Mohammed Mujitaba Dawuda, Xin Zhao, Xinwen Li, Baihong Chen
Drought stress is a major problem around the world and there is still little molecular mechanism about how fruit crops deal with moderate drought stress. Here, the physiological and phosphoproteomic responses of drought-sensitive genotype (M26) and drought-tolerant genotype (MBB) under moderate drought stress were investigated. Our results of the physiology analysis indicated that the MBB genotype could produce more osmosis-regulating substances. Furthermore, phosphoproteins from leaves of both genotypes under moderate drought stress were analyzed using the isobaric tags for relative and absolute quantification technology...
July 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28710561/genetic-architecture-of-wild-soybean-glycine-soja-response-to-soybean-cyst-nematode-heterodera-glycines
#7
Hengyou Zhang, Qijian Song, Joshua D Griffin, Bao-Hua Song
The soybean cyst nematode (SCN) is one of the most destructive pathogens of soybean plants worldwide. Host-plant resistance is an environmentally friendly method to mitigate SCN damage. To date, the resistant soybean cultivars harbor limited genetic variation, and some are losing resistance. Thus, a better understanding of the genetic mechanisms of the SCN resistance, as well as developing diverse resistant soybean cultivars, is urgently needed. In this study, a genome-wide association study (GWAS) was conducted using 1032 wild soybean (Glycine soja) accessions with over 42,000 single-nucleotide polymorphisms (SNPs) to understand the genetic architecture of G...
July 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28707092/the-determinants-of-alternative-rna-splicing-in-human-cells
#8
REVIEW
Tatsiana V Ramanouskaya, Vasily V Grinev
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body...
July 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28699001/identification-classification-and-transcriptional-profiles-of-dirigent-domain-containing-proteins-in-sugarcane
#9
Paula Macedo Nobile, Alexandra Bottcher, Juliana L S Mayer, Michael S Brito, Ivan A Dos Anjos, Marcos Guimarães de Andrade Landell, Renato Vicentini, Silvana Creste, Diego Mauricio Riaño-Pachón, Paulo Mazzafera
Dirigent (DIR) proteins, encoded by DIR genes, are referred to as "dirigent" because they direct the outcome of the coupling of the monolignol coniferyl alcohol into (+) or (-) pinoresinol, the first intermediates in the enantiocomplementary pathways for lignan biosynthesis. DIR domain-containing or DIR-like proteins are, thus, termed for not having a clear characterization. A transcriptome- and genome-wide survey of DIR domain-containing proteins in sugarcane was carried out, in addition to phylogenetic, physicochemical and transcriptional analyses...
July 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28688048/susceptibility-background-for-type-2-diabetes-in-eleven-mexican-indigenous-populations-hnf4a-gene-analysis
#10
M A Granados-Silvestre, M G Ortiz-López, J Granados, S Canizales-Quinteros, Rosenda I Peñaloza-Espinosa, C Lechuga, V Acuña-Alonzo, K Sánchez-Pozos, M Menjivar
The genetic risk of developing type 2 diabetes (T2D) increases in parallel with the proportion of Native American ancestry. Mestizo Mexicans have a 70% Native Amerindian genetic background. The T130I polymorphism in the HNF4A gene has been associated with early-onset T2D in mestizo Mexicans. Thus, the aim of the present study was to evaluate the frequency and relationship of the T130I variant in the HNF4A gene with risk factors for developing T2D in eleven indigenous groups from Mexico. In two groups, all exons of the HNF4A gene were directly sequenced; in the remaining the T130I polymorphism was analyzed by restriction fragment length polymorphism...
July 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28674743/whole-genome-duplication-enhances-the-photosynthetic-capacity-of-chrysanthemum-nankingense
#11
Bin Dong, Haibin Wang, Tao Liu, Peilei Cheng, Yun Chen, Sumei Chen, Zhiyong Guan, Weimin Fang, Jiafu Jiang, Fadi Chen
Whole genome duplication has a major effect on the phenotype and physiology of higher plants. A comparison between the diploid and tetraploid forms of Chrysanthemum nankingense showed that the latter's leaf contained a higher content of chlorophyll a/b and harbored a larger number of chloroplasts per cell, leading to an enhancement in its photosynthetic capacity and an improved level of productivity with respect to biomass. A transcriptomic analysis of the two ploidy level forms revealed 21,559 differentially transcribed genes...
July 3, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28668975/marker-assisted-introgression-of-resistance-to-fusarium-wilt-race-2-in-pusa-256-an-elite-cultivar-of-desi-chickpea
#12
Aditya Pratap, Sushil K Chaturvedi, Rakhi Tomar, Neha Rajan, Nupur Malviya, Mahender Thudi, P R Saabale, Umashanker Prajapati, Rajeev K Varshney, N P Singh
Fusarium wilt caused by F. oxysporum f. sp. ciceris causes extensive damage to chickpea (Cicer arietinum L.) in many parts of the world. In the central part of India, pathogen race 2 (Foc 2) causes severe yield losses. We initiated molecular marker-assisted backcrossing (MABC) using desi cultivar, Vijay, as a donor to introgress resistance to this race (Foc2) in Pusa 256, another elite desi cultivar of chickpea. To confirm introgression of resistance for this race, foreground selection was undertaken using two SSR markers (TA 37 and TA110), with background selection to observe the recovery of recurrent parent genome using 45 SSRs accommodated in 8 multiplexes...
July 1, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28667404/identification-of-critical-genes-associated-with-lignin-biosynthesis-in-radish-raphanus-sativus-l-by-de-novo-transcriptome-sequencing
#13
Haiyang Feng, Liang Xu, Yan Wang, Mingjia Tang, Xianwen Zhu, Wei Zhang, Xiaochuan Sun, Shanshan Nie, Everlyne M'mbone Muleke, Liwang Liu
Radish is an important root vegetable crop with high nutritional, economic, and medicinal value. Lignin is an important secondary metabolite possessing a great effect on plant growth and product quality. To date, lignin biosynthesis-related genes have been identified in some important plant species. However, little information on characterization of critical genes involved in plant lignin biosynthesis is available in radish. In this study, a total of 71,148 transcripts sequences were obtained from radish root, of which 66 assembled unigenes and ten candidate genes were identified to be involved in lignin monolignol biosynthesis...
June 30, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28660309/genome-wide-comparative-analysis-of-four-indian-drosophila-species
#14
Sujata Mohanty, Radhika Khanna
Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics...
June 28, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28660308/relationship-between-rage-gene-polymorphisms-and-cardiovascular-disease-prognosis-in-the-chinese-han-population
#15
Jinxiong Gao, Liehua Deng, Ying Wang, Yanke Shi, Xiaohua Xiao, Xueou Zheng, Hao Ren, Dingli Xu
Cardiovascular disease (CVD) is the leading cause of death in China. This study aimed to investigate whether RAGE gene polymorphisms are associated with the prognosis of various cardiovascular diseases in the Chinese Han population. This study was conducted from July 2004 to December 2005 and a total of 425 subjects from Guangdong province were enrolled. Genotyping of the three polymorphisms (-429T/C, 1704G/T, and G82S) in the RAGE gene was performed with polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP)...
June 28, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28647758/a-meta-analysis-of-quantitative-trait-loci-for-abiotic-and-biotic-stress-resistance-in-tetraploid-cotton
#16
Abdelraheem Abdelraheem, Feng Liu, Mingzhou Song, Jinfa F Zhang
The number and location of mapped quantitative trait loci (QTL) depend on genetic populations and testing environments. The identification of consistent QTL across genetic backgrounds and environments is a pre-requisite to marker-assisted selection. This study analyzed a total of 661 abiotic and biotic stress resistance QTL based on our previous work and other publications using the meta-analysis software Biomercator. It identified chromosomal regions containing QTL clusters for different resistance traits and hotspots for a particular resistance trait in cotton from 98 QTL for drought tolerance under greenhouse (DT) and 150 QTL in field conditions (FDT), 80 QTL for salt tolerance in the greenhouse conditions (ST), 201 QTL for resistance to Verticillium wilt (VW, Verticillium dahliae), 47 QTL for resistance to Fusarium wilt (FW, Fusarium oxysporum f...
June 24, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28634826/tai-vacuolar-invertase-orthologs-the-interspecific-variability-in-tomato-plants-solanum-section-lycopersicon
#17
M A Slugina, A V Shchennikova, E Z Kochieva
Understanding the genetic mechanisms underlying carbohydrate metabolism can promote the development of biotechnological advances in fruit plants. The flesh tomato fruit represents an ideal system for examining the role of sucrose cleavage enzymes in fruit development, and wild tomato species differing in storage sugars serve as an excellent research material for this purpose. Plant vacuolar invertase is a key enzyme of sucrose metabolism in the sink organs. In the present study, we identified complete gene sequences encoding the TAI vacuolar invertase in 11 wild and one cultivated tomato accessions of the Solanum section Lycopersicon...
June 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28634825/a-rapid-and-cost-effective-approach-for-the-development-of-polymorphic-microsatellites-in-non-model-species-using-paired-end-rad-sequencing
#18
Dong-Xiu Xue, Yu-Long Li, Jin-Xian Liu
As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective "RAD-seq-Assembly-Microsatellite" approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design...
June 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28631230/sequence-analysis-of-chromosome-1-revealed-different-selection-patterns-between-chinese-wild-mice-and-laboratory-strains
#19
Fuyi Xu, Shixian Hu, Tianzhu Chao, Maochun Wang, Kai Li, Yuxun Zhou, Hongyan Xu, Junhua Xiao
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1...
June 19, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28620758/transcriptome-analysis-of-drought-responsive-genes-regulated-by-hydrogen-sulfide-in-wheat-triticum-aestivum-l-leaves
#20
Hua Li, Min Li, Xingliang Wei, Xia Zhang, Ruili Xue, Yidan Zhao, Huijie Zhao
Drought is an environmental factor that deeply impacts wheat yield and quality. Hydrogen sulfide (H2S) is a known regulator of drought resistance in plants. To preliminarily elucidate the regulatory mechanisms of H2S on drought tolerance, the effects of H2S on drought-responsive genes were investigated by transcriptome analysis. As a result, a total of 7552 transcripts not only responded to drought stress but also exhibited differential expression relative to the polyethylene glycol (PEG) treatment (P) and the NaHS pretreatment with PEG treatment (SP)...
June 15, 2017: Molecular Genetics and Genomics: MGG
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