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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/28710562/significant-and-unique-changes-in-phosphorylation-levels-of-four-phosphoproteins-in-two-apple-rootstock-genotypes-under-drought-stress
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/28620757/a-novel-homozygous-complex-deletion-in-cftr-caused-cystic-fibrosis-in-a-chinese-patient
#16
Keqiang Liu, Yaping Liu, Xue Li, Kai-Feng Xu, Xinlun Tian, Xue Zhang
Cystic fibrosis (CF) is the most frequent lethal genetic disorder among Caucasians, but is considered to be a very rare disease in Chinese population. Here, we present an 11-year-old Chinese CF patient with disseminated bronchiectasis and salty sweat, for whom exon sequencing followed by multiplex ligation-dependent probe amplification analysis of the CFTR gene was applied for mutation screening. A homozygous deletion involving exon 20 of CFTR was observed in the patient's genome. Molecular characterization of the breakpoints indicated that both alleles of this locus had an identical novel complex rearrangement (c...
June 15, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28612167/efficient-identification-of-snps-in-pooled-dna-samples-using-a-dual-mononucleotide-addition-based-sequencing-method
#17
Changchang Cao, Rongfang Pan, Jun Tan, Xiao Sun, Pengfeng Xiao
Identifying single nucleotide polymorphism (SNPs) from pooled samples is critical for many studies and applications. SNPs determined by next-generation sequencing results may suffer from errors in both base calling and read mapping. Taking advantage of dual mononucleotide addition-based pyrosequencing, we present Epds, a method to efficiently identify SNPs from pooled DNA samples. On the basis of only five patterns of non-synchronistic extensions between the wild and mutant sequences using dual mononucleotide addition-based pyrosequencing, we employed an enumerative algorithm to infer the mutant locus and estimate the proportion of mutant sequence...
June 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28601922/the-landscape-and-structural-diversity-of-ltr-retrotransposons-in-musa-genome
#18
Faisal Nouroz, Shumaila Noreen, Habib Ahmad, J S Pat Heslop-Harrison
Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated, and a great number of partial copies/remnants from GenBank database...
June 10, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28597316/substrate-translocation-involves-specific-lysine-residues-of-the-central-channel-of-the-conjugative-coupling-protein-trwb
#19
Delfina Larrea, Héctor D de Paz, Inmaculada Matilla, Dolores L Guzmán-Herrador, Gorka Lasso, Fernando de la Cruz, Elena Cabezón, Matxalen Llosa
Conjugative transfer of plasmid R388 requires the coupling protein TrwB for protein and DNA transport, but their molecular role in transport has not been deciphered. We investigated the role of residues protruding into the central channel of the TrwB hexamer by a mutational analysis. Mutations affecting lysine residues K275, K398, and K421, and residue S441, all facing the internal channel, affected transport of both DNA and the relaxase protein in vivo. The ATPase activity of the purified soluble variants was affected significantly in the presence of accessory protein TrwA or DNA, correlating with their behaviour in vivo...
June 8, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28567704/fission-yeast-ctf1-a-cleavage-and-polyadenylation-factor-subunit-is-required-for-the-maintenance-of-genomic-integrity
#20
Amit Sonkar, Sachin Gaurav, Shakil Ahmed
Accurate segregation of chromosome during mitosis requires the coordinated action of several cell cycle checkpoints that monitor replication of the genome and the attachment of sister chromatids to the mitotic spindle apparatus. Here we have characterized the fission yeast Ctf1, an ortholog of S. cerevisiae Rna15 in the maintenance of genomic integrity. The ctf1 is nonessential for the cell survival and its deletion strain exhibit cold sensitivity. The ctf1 deleted cells exhibit genetic interaction with spindle checkpoint protein Mad2 and Bub1...
May 31, 2017: Molecular Genetics and Genomics: MGG
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