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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/28534238/a-fast-algorithm-for-bayesian-multi-locus-model-in-genome-wide-association-studies
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28389699/ion-channelopathies-and-migraine-pathogenesis
#12
REVIEW
Cassie L Albury, Shani Stuart, Larisa M Haupt, Lyn R Griffiths
Migraine is a common neurological disorder that affects approximately 12-20% of the general adult population. Migraine pathogenesis is complex and not wholly understood. Molecular genetic investigations, imaging and biochemical studies, have unveiled a number of interconnected neurological pathways which seem to have a cause and effect component integral to its cause. Much weight of migraine attack initiation can be placed on the initial trigger and the pathways involved in its neuronal counter reaction. Ion channels play a large role in the generation, portrayal and mitigation of the brains response to external triggers...
April 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28389698/evolution-of-the-duplicated-intracellular-lipid-binding-protein-genes-of-teleost-fishes
#13
REVIEW
Ananda B Venkatachalam, Manoj B Parmar, Jonathan M Wright
Increasing organismal complexity during the evolution of life has been attributed to the duplication of genes and entire genomes. More recently, theoretical models have been proposed that postulate the fate of duplicated genes, among them the duplication-degeneration-complementation (DDC) model. In the DDC model, the common fate of a duplicated gene is lost from the genome owing to nonfunctionalization. Duplicated genes are retained in the genome either by subfunctionalization, where the functions of the ancestral gene are sub-divided between the sister duplicate genes, or by neofunctionalization, where one of the duplicate genes acquires a new function...
April 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28386641/mathematical-deconvolution-uncovers-the-genetic-regulatory-signal-of-cancer-cellular-heterogeneity-on-resistance-to-paclitaxel
#14
Ian Morilla, Juan A Ranea
Drug resistance remains a major problem in combating malignancies, resulting critical the resistance to paclitaxel used in the treatment of many different cancers. Elucidating the cellular heterogeneity composition of tumours may be relevant to designing more effective treatment strategies on drug resistance. In particular, such heterogeneity correlates with the measurement of gene expression below the population level. However, experimental assays capturing differential response are limited and cannot discern the variation in gene expression specific to different cellular types in tumour populations...
April 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28386640/newly-developed-ssr-markers-reveal-genetic-diversity-and-geographical-clustering-in-spinach-spinacia-oleracea
#15
Şurhan Göl, Mehmet Göktay, Jens Allmer, Sami Doğanlar, Anne Frary
Spinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected...
April 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28357596/combined-sense-antisense-alu-elements-activate-the-egfp-reporter-gene-when-stable-transfection
#16
Zhihong Ma, Xianglong Kong, Shufeng Liu, Shuxian Yin, Yuehua Zhao, Chao Liu, Zhanjun Lv, Xiufang Wang
Alu elements in the human genome are present in more than one million copies, accounting for 10% of the genome. However, the biological functions of most Alu repeats are unknown. In this present study, we detected the effects of Alu elements on EGFP gene expression using a plasmid system to find the roles of Alu elements in human genome. We inserted 5'-4TMI-Alus-CMV promoter-4TMI-Alus (or antisense Alus)-3' sequences into the pEGFP-C1 vector to construct expression vectors. We altered the copy number of Alus, the orientation of the Alus, and the presence of an enhancer (4TMI) in the inserted 5'-4TMI-Alus-CMV promoter-4TMI-Alus (or antisense Alus)-3' sequences...
March 29, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28357595/increasing-the-yield-of-middle-silk-gland-expression-system-through-transgenic-knock-down-of-endogenous-sericin-1
#17
Sanyuan Ma, Xiaojuan Xia, Yufeng Li, Le Sun, Yue Liu, Yuanyuan Liu, Xiaogang Wang, Run Shi, Jiasong Chang, Ping Zhao, Qingyou Xia
Various genetically modified bioreactor systems have been developed to meet the increasing demands of recombinant proteins. Silk gland of Bombyx mori holds great potential to be a cost-effective bioreactor for commercial-scale production of recombinant proteins. However, the actual yields of proteins obtained from the current silk gland expression systems are too low for the proteins to be dissolved and purified in a large scale. Here, we proposed a strategy that reducing endogenous sericin proteins would increase the expression yield of foreign proteins...
March 29, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28352959/inheritance-fine-mapping-and-candidate-gene-analyses-of-resistance-to-soybean-mosaic-virus-strain-sc5-in-soybean
#18
Adhimoolam Karthikeyan, Kai Li, Hua Jiang, Rui Ren, Cui Li, Haijian Zhi, Shouyi Chen, Junyi Gai
Soybean mosaic virus (SMV) is one of the most devastating pathogens for soybeans in China. Among the country-wide 22 strains, SC5 dominates in Huang-Huai and Changjiang valleys. For controlling its damage, the resistance gene was searched through Mendelian inheritance study, gene fine-mapping, and candidate gene analysis combined with qRT-PCR (quantitative real-time polymerase chain reaction) analysis. The parents F1, F2, and RILs (recombinant inbred lines) of the cross Kefeng-1 (Resistance, R) × NN1138-2 (Susceptible, S) were used to examine the inheritance of SC5-resistance...
March 28, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28349297/molecular-identification-of-differential-expression-genes-associated-with-sex-pheromone-biosynthesis-in-spodoptera-exigua
#19
Ya-Nan Zhang, Long-Wa Zhang, Da-Song Chen, Liang Sun, Zhao-Qun Li, Zhan-Feng Ye, Mei-Yan Zheng, Jin-Bu Li, Xiu-Yun Zhu
Species-specific sex pheromone is biosynthesized and released in most female moths as a chemical cue in mating communication. However, information on genes involved in this pathway is limited. The beet armyworm, Spodoptera exigua, is a cosmopolitan agricultural pest that causes severe economic losses to many crops. In China, the female sex pheromones in sex pheromone glands (PGs) of S. exigua have been measured which comprises (Z,E)-9,12-tetradecadienyl acetate, (Z)-9-tetradecen-l-ol, (Z)-9-tetradecenyl acetate, and (Z,E)-9,12-tetradecadien-1-ol in a ratio of 47:18:18:17...
March 27, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28342042/genetic-variant-of-bnc2-gene-is-functionally-associated-with-adolescent-idiopathic-scoliosis-in-chinese-population
#20
Leilei Xu, Chao Xia, Xiaodong Qin, Weixiang Sun, Nelson Leung-Sang Tang, Yong Qiu, Jack Chun-Yiu Cheng, Zezhang Zhu
Adolescent idiopathic scoliosis (AIS) is a structural curvature of the spine that was estimated to affect millions of children worldwide. Recent study shows that the functional variant rs10738445 could add to the risk of AIS through the regulation of BNC2 gene. This study aims to investigate whether the rs10738445 of BNC2 gene is a functional susceptible locus for AIS in the Chinese population and to further clarify the association of the BNC2 expression with the curve severity. SNP rs10738445 was genotyped in 1952 patients and 2492 controls, and further replicated in 693 patients and 254 controls...
March 25, 2017: Molecular Genetics and Genomics: MGG
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