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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/28634826/tai-vacuolar-invertase-orthologs-the-interspecific-variability-in-tomato-plants-solanum-section-lycopersicon
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28534238/a-fast-algorithm-for-bayesian-multi-locus-model-in-genome-wide-association-studies
#10
Weiwei Duan, Yang Zhao, Yongyue Wei, Sheng Yang, Jianling Bai, Sipeng Shen, Mulong Du, Lihong Huang, Zhibin Hu, Feng Chen
Genome-wide association studies (GWAS) have identified a large amount of single-nucleotide polymorphisms (SNPs) associated with complex traits. A recently developed linear mixed model for estimating heritability by simultaneously fitting all SNPs suggests that common variants can explain a substantial fraction of heritability, which hints at the low power of single variant analysis typically used in GWAS. Consequently, many multi-locus shrinkage models have been proposed under a Bayesian framework. However, most use Markov Chain Monte Carlo (MCMC) algorithm, which are time-consuming and challenging to apply to GWAS data...
May 22, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28523359/arginine-cga-codons-as-a-source-of-nonsense-mutations-a-possible-role-in-multivariant-gene-expression-control-of-mrna-quality-and-aging
#11
Georgy A Romanov, Victor S Sukhoverov
Methylation of cytosine residues in DNA of higher eukaryotes, including humans, creates "hot spots" of C→T transitions in the genome. The predominantly methylated sequence in mammalian DNAs is CG (CpG). Among CG-containing codons, CGA codons for arginine are unique due to their ability to create stop codons TGA (UGA in mRNA) upon epigenetic-mediated mutation. As such nonsense mutations can have a strong adverse effect on the cell and organism, we have performed a study, on the example of human genes, aimed to characterise the anticipated effects of epigenetic-mediated nonsense mutations CGA→TGA in somatic cells...
May 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28500374/exploring-the-genetics-of-feed-efficiency-and-feeding-behaviour-traits-in-a-pig-line-highly-selected-for-performance-characteristics
#12
Henry Reyer, Mahmoud Shirali, Siriluck Ponsuksili, Eduard Murani, Patrick F Varley, Just Jensen, Klaus Wimmers
The consideration of feed efficiency traits is highly relevant in animal breeding due to economic and ecologic impacts of the efficient usage and utilization of feed resources. In pigs, corresponding observations are recorded using automatic feeding stations and serve as one of the main criteria in most pig selection programmes. Simultaneously, feeding stations also generate feeding behaviour data which represent a nearly unused resource and provide a valuable proxy measure of health status, animal welfare, and management practices...
May 12, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28497168/relationship-between-geographical-origin-seed-size-and-genetic-diversity-in-faba-bean-vicia-faba-l-as-revealed-by-ssr-markers
#13
Şurhan Göl, Sami Doğanlar, Anne Frary
Faba bean (Vicia faba L.) is an important legume species because of its high protein and starch content. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the nitrogen fixing bacteria in its roots. In this work, 255 faba bean germplasm accessions were characterized using 32 SSR primers which yielded 302 polymorphic fragments. According to the results, faba bean individuals were divided into two main groups based on the neighbor-joining algorithm (r = 0.91) with some clustering based on geographical origin as well as seed size...
May 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28492984/comparative-transcript-profiling-of-fertile-and-sterile-flower-buds-from-multiple-allele-inherited-male-sterility-in-chinese-cabbage-brassica-campestris-l-ssp-pekinensis
#14
Xue Zhou, Zhiyong Liu, Ruiqin Ji, Hui Feng
We studied the underlying causes of multiple-allele-inherited male sterility in Chinese cabbage (Brassica campestris L. ssp. pekinensis) by identifying differentially expressed genes (DEGs) related to pollen sterility between fertile and sterile flower buds. In this work, we verified the stages of sterility microscopically and then performed transcriptome analysis of mRNA isolated from fertile and sterile buds using Illumina HiSeq 2000 platform sequencing. Approximately 80% of ~229 million high-quality paired-end reads were uniquely mapped to the reference genome...
May 10, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28492983/target-enrichment-sequencing-in-cultivated-peanut-arachis-hypogaea-l-using-probes-designed-from-transcript-sequences
#15
Ze Peng, Wen Fan, Liping Wang, Dev Paudel, Dante Leventini, Barry L Tillman, Jianping Wang
Enabled by the next generation sequencing, target enrichment sequencing (TES) is a powerful method to enrich genomic regions of interest and to identify sequence variations. The objective of this study was to explore the feasibility of probe design from transcript sequences for TES application in calling sequence variants in peanut, an important allotetraploid crop with a large genome size. In this study, we applied an in-solution hybridization method to enrich DNA sequences of seven peanut genotypes. Our results showed that it is feasible to apply TES with probes designed from transcript sequences in polyploid peanut...
May 10, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28447196/the-axon-degeneration-gene-sarm1-is-evolutionarily-distinct-from-other-tir-domain-containing-proteins
#16
Harsha Malapati, Spencer M Millen, William J Buchser
Many forms of neurodegenerative disease are characterized by Wallerian degeneration, an active program of axonal destruction. Recently, the important player which enacts Wallerian degeneration was discovered, the multidomain protein SARM1. Since the SARM1 protein has classically been thought of as an innate immune molecule, its role in Wallerian degeneration has raised questions on the evolutionary forces acting on it. Here, we synthesize a picture of SARM1's evolution through various organisms by examining the molecular and genetic changes of SARM1 and the genes around it...
April 26, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28447195/salivary-mir-16-mir-191-and-mir-223-intuitive-indicators-of-dominant-ovarian-follicles-in-buffaloes
#17
Prashant Singh, Naresh Golla, Pankaj Singh, Vijay Simha Baddela, Subhash Chand, Rubina Kumari Baithalu, Dheer Singh, Suneel Kumar Onteru
Estrus or sexual receptivity determination is utmost important for efficient breeding programs for female buffaloes. Prominent estrus behavioral symptoms are the result of several molecular and neuroendocrine events involving the ovary and the brain. Expression of estrus behavior is poor in buffaloes during the summer season. Hence, the discovery of biomarkers specific to the estrus stage or its related ovarian events, like the presence of dominant ovarian follicle, is helpful for developing an easy estrus determination method...
April 26, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28444444/bioinformatic-and-expression-analyses-on-carotenoid-dioxygenase-genes-in-fruit-development-and-abiotic-stress-responses-in-fragaria-vesca
#18
Yong Wang, Guanqun Ding, Tingting Gu, Jing Ding, Yi Li
Carotenoid dioxygenases, including 9-cis-epoxycarotenoid dioxygenases (NCEDs) and carotenoid cleavage dioxygenases (CCDs), can selectively cleave carotenoids into various apocarotenoid products that play important roles in fleshy fruit development and abiotic stress response. In this study, we identified 12 carotenoid dioxygenase genes in diploid strawberry Fragaria vesca, and explored their evolution with orthologous genes from nine other species. Phylogenetic analyses suggested that the NCED and CCDL groups moderately expanded during their evolution, whereas gene numbers of the CCD1, CCD4, CCD7, and CCD8 groups maintained conserved...
April 25, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28409264/a-study-of-the-bodrogk%C3%A3-z-population-in-north-eastern-hungary-by-y-chromosomal-haplotypes-and-haplogroups
#19
Horolma Pamjav, Á Fóthi, T Fehér, Erzsébet Fóthi
We have determined the distribution of Y chromosomal haplotypes and haplogroups in population samples from one of the most important areas in north-eastern Hungary from many villages in the Bodrogköz. The Bodrogköz region was chosen due to its isolated nature, because this area was a moorland encircled by the Tisza, Bodrog, and Latorca Rivers and inhabitants of this part of Hungary escaped from both Tatar and Ottoman invasions, which decimated the post-Hungarian Conquest populations in many parts of the country...
April 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28405778/verification-and-fine-mapping-of-qgw1-05-a-major-qtl-for-grain-weight-in-maize-zea-mays-l
#20
Qiang Zhou, Yongbin Dong, Qingling Shi, Long Zhang, Huanqing Chen, Chunhui Hu, Yuling Li
Grain weight, one of the important factors to determine corn yield, is a typical quantitative inheritance trait. However, the molecular genetic basis of grain weight still remains limited. In our previous researches, a major QTL associated with grain weight, qGW1.05, has been identified between SSR markers umc1601 and umc1754 at bin locus 1.05-1.06 in maize. Here, its genetic and environmental stabiliteis were verified using a BC3F2 population to identify the effect of qGW1.05 on grain weight. Further, qGW1...
April 12, 2017: Molecular Genetics and Genomics: MGG
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