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Genome wide selection

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https://www.readbyqxmd.com/read/28812720/antagonistic-pleiotropy-and-mutation-accumulation-influence-human-senescence-and-disease
#1
Juan Antonio Rodríguez, Urko M Marigorta, David A Hughes, Nino Spataro, Elena Bosch, Arcadi Navarro
Senescence has long been a public health challenge as well as a fascinating evolutionary problem. There is neither a universally accepted theory for its ultimate causes, nor a consensus about what may be its impact on human health. Here we test the predictions of two evolutionary explanations of senescence-mutation accumulation and antagonistic pleiotropy-which postulate that genetic variants with harmful effects in old ages can be tolerated, or even favoured, by natural selection at early ages. Using data from genome-wide association studies (GWAS), we study the effects of genetic variants associated with diseases appearing at different periods in life, when they are expected to have different impacts on fitness...
January 30, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812021/association-analysis-of-arsenic-induced-straighthead-in-rice-oryza-sativa-l-based-on-the-selected-population-with-a-modified-model
#2
Xiaobai Li, Biaolin Hu, Xuhao Pan, Ning Zhang, Dianxing Wu
A rice physiological disorder makes mature panicle keep erect with empty grains termed as "straighthead." Straighthead causes yield losses and is a serious threat to rice production worldwide. Here, a new study of association mapping was conducted to identify QTL involved in straighthead. A subset of 380 accessions was selected from the USDA rice core collection and genotyped with 72 genome-wide SSR markers. An optimal model implemented with principle components (PCs) was used in this association mapping. As a result, five markers were identified to be significantly associated with straighthead...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28811569/transcriptional-response-to-stress-is-pre-wired-by-promoter-and-enhancer-architecture
#3
Anniina Vihervaara, Dig Bijay Mahat, Michael J Guertin, Tinyi Chu, Charles G Danko, John T Lis, Lea Sistonen
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. Here, to investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Our results globally show that the release of promoter-proximal paused RNA polymerase into elongation functions as a critical switch at which a gene's response to stress is determined...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811387/selection-constrains-high-rates-of-tandem-repetitive-dna-mutation-in-daphnia-pulex
#4
Jullien M Flynn, Ian Caldas, Melania E Cristescu, Andrew G Clark
A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex in addition to six isolates from a non-MA population originating from the same progenitor to both estimate mutation rates of abundances of repeat sequences and evaluate the selective regime acting upon them...
August 15, 2017: Genetics
https://www.readbyqxmd.com/read/28810834/multiple-trait-qtl-mapping-and-genomic-prediction-for-wool-traits-in-sheep
#5
Sunduimijid Bolormaa, Andrew A Swan, Daniel J Brown, Sue Hatcher, Nasir Moghaddar, Julius H van der Werf, Michael E Goddard, Hans D Daetwyler
BACKGROUND: The application of genomic selection to sheep breeding could lead to substantial increases in profitability of wool production due to the availability of accurate breeding values from single nucleotide polymorphism (SNP) data. Several key traits determine the value of wool and influence a sheep's susceptibility to fleece rot and fly strike. Our aim was to predict genomic estimated breeding values (GEBV) and to compare three methods of combining information across traits to map polymorphisms that affect these traits...
August 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28810830/annotating-long-intergenic-non-coding-rnas-under-artificial-selection-during-chicken-domestication
#6
Yun-Mei Wang, Hai-Bo Xu, Ming-Shan Wang, Newton Otieno Otecko, Ling-Qun Ye, Dong-Dong Wu, Ya-Ping Zhang
BACKGROUND: Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process. RESULTS: We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome...
August 15, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28809852/the-snp-set-based-association-study-identifies-itga1-as-a-susceptibility-gene-of-attention-deficit-hyperactivity-disorder-in-han-chinese
#7
L Liu, L Zhang, H M Li, Z R Wang, X F Xie, J P Mei, J L Jin, J Shi, L Sun, S C Li, Y L Tan, L Yang, J Wang, H M Yang, Q J Qian, Y F Wang
Genome-wide association studies, which detect the association between single-nucleotide polymorphisms (SNPs) and disease susceptibility, have been extensively applied to study attention-deficit/hyperactivity disorder (ADHD), but genome-wide significant associations have not been found yet. Genetic heterogeneity and insufficient genomic coverage may account for the missing heritability. We performed a two-stage association study for ADHD in the Han Chinese population. In the discovery stage, 1033 ADHD patients and 950 healthy controls were genotyped using both the Affymetrix Genome-Wide Human SNP Array 6...
August 15, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28808686/a-conformational-checkpoint-between-dna-binding-and-cleavage-by-crispr-cas9
#8
Yavuz S Dagdas, Janice S Chen, Samuel H Sternberg, Jennifer A Doudna, Ahmet Yildiz
The Cas9 endonuclease is widely used for genome engineering applications by programming its single-guide RNA, and ongoing work is aimed at improving the accuracy and efficiency of DNA targeting. DNA cleavage of Cas9 is controlled by the conformational state of the HNH nuclease domain, but the mechanism that governs HNH activation at on-target DNA while reducing cleavage activity at off-target sites remains poorly understood. Using single-molecule Förster resonance energy transfer, we identified an intermediate state of Streptococcus pyogenes Cas9, representing a conformational checkpoint between DNA binding and cleavage...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28808654/genome-wide-identification-and-transcriptional-expression-analysis-of-cucumber-superoxide-dismutase-sod-family-in-response-to-various-abiotic-stresses
#9
Yong Zhou, Lifang Hu, Hao Wu, Lunwei Jiang, Shiqiang Liu
Superoxide dismutase (SOD) proteins are widely present in the plant kingdom and play important roles in different biological processes. However, little is known about the SOD genes in cucumber. In this study, night SOD genes were identified from cucumber (Cucumis sativus) using bioinformatics-based methods, including 5 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Phylogenetic analyses with SODs from cucumber and several other species revealed that these SOD proteins can be traced back to two ancestral SODs before the divergence of monocot and dicot plants...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28806931/draft-de-novo-transcriptome-assembly-and-proteome-characterization-of-the-electric-lobe-of-tetronarce-californica-a-molecular-tool-for-the-study-of-cholinergic-neurotransmission-in-the-electric-organ
#10
Maria Stavrianakou, Ricardo Perez, Cheng Wu, Matthew S Sachs, Rodolfo Aramayo, Mark Harlow
BACKGROUND: The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of this preparation, we have performed a transcriptome assembly of the presynaptic component of the electric organ (the electric lobe). We combined our assembled transcriptome with a previous transcriptome of the postsynaptic electric organ, to define a MetaProteome containing pre- and post-synaptic components of the electric organ...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28806733/the-interaction-between-endogenous-30s-ribosomal-subunit-protein-s11-and-cucumber-mosaic-virus-ls2b-protein-affects-viral-replication-infection-and-gene-silencing-suppressor-activity
#11
Ruilin Wang, Zhiyou Du, Zhenqing Bai, Zongsuo Liang
Cucumber mosaic virus (CMV) is a model virus for plant-virus protein interaction and mechanism research because of its wide distribution, high-level of replication and simple genome structure. The 2b protein is a multifunctional protein encoded by CMV that suppresses RNA silencing-based antiviral defense and contributes to CMV virulence in host plants. In this report, 12 host proteins were identified as CMV LS2b binding partners using the yeast two-hybrid screen system from the Arabidopsis thaliana cDNA library...
2017: PloS One
https://www.readbyqxmd.com/read/28805926/multiple-trait-genomewide-mapping-and-gene-network-analysis-for-scrotal-circumference-growth-curves-in-brahman-cattle
#12
A C C Soares, S E F Guimarães, M J Kelly, M R S Fortes, F F E Silva, L L Verardo, R Mota, S Moore
Fertility traits are economically important in cattle breeding programs. Scrotal circumference (SC) measures are repeatable, easily obtained, highly heritable, and positively correlated with female fertility traits and sperm quality traits in males. A useful approach to summarize SC measures over time is using nonlinear models, which summarize specific measures of SC in a few parameters with biological interpretation. This approach facilitates the selection of bulls with larger SC and maturity index (K), that is, early maturing animals...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28804651/pharmacogenetic-biomarkers-to-predict-treatment-response-in-multiple-sclerosis-current-and-future-perspectives
#13
REVIEW
Patricia K Coyle
Disease-modifying therapies (DMTs) have significantly advanced the treatment of relapsing multiple sclerosis (MS), decreasing the frequency of relapses, disability, and magnetic resonance imaging lesion formation. However, patients' responses to and tolerability of DMTs vary considerably, creating an unmet need for biomarkers to identify likely responders and/or those who may have treatment-limiting adverse reactions. Most studies in MS have focused on the identification of pharmacogenetic markers, using either the candidate-gene approach, which requires prior knowledge of the genetic marker and its role in the target disease, or genome-wide association, which examines multiple genetic variants, typically single nucleotide polymorphisms (SNPs)...
2017: Multiple Sclerosis International
https://www.readbyqxmd.com/read/28803809/improved-androgen-specificity-of-ar-ecoscreen-by-crispr-based-glucocorticoid-receptor-knockout
#14
Nick Zwart, Dave Andringa, Willem-Jan de Leeuw, Hiroyuki Kojima, Mitsuru Iida, Corine Houtman, Jacob de Boer, Jeroen Kool, Marja Lamoree, Timo Hamers
The AR-EcoScreen is a widely used reporter assay for the detection of androgens and anti-androgens. Endogenous expression of glucocorticoid receptors and their affinity for the androgen responsive element that drives reporter expression, however, makes the reporter cells sensitive to interference by glucocorticoids and less specific for (anti-)androgens. To create a glucocorticoid insensitive derivative of the AR-EcoScreen, CRISPR/Cas9 genome editing was used to develop glucocorticoid receptor knockout mutants by targeting various sites in the glucocorticoid gene...
August 10, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28802249/high-resolution-mapping-of-chromatin-conformation-in-cardiac-myocytes-reveals-structural-remodeling-of-the-epigenome-in-heart-failure
#15
Manuel Rosa-Garrido, Douglas J Chapski, Anthony D Schmitt, Todd H Kimball, Elaheh Karbassi, Emma Monte, Enrique Balderas, Matteo Pellegrini, Tsai-Ting Shih, Elizabeth Soehalim, David A Liem, Peipei Ping, Niels J Galjart, Shuxun Ren, Yibin Wang, Bing Ren, Thomas M Vondriska
Background -Cardiovascular disease is associated with epigenomic changes in the heart, however the endogenous structure of cardiac myocyte chromatin has never been determined. Methods -To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype...
August 11, 2017: Circulation
https://www.readbyqxmd.com/read/28801756/segregation-distortion-and-genome-wide-digenic-interactions-affect-transmission-of-introgressed-chromatin-from-wild-cotton-species
#16
Rahul Chandnani, Baohua Wang, Xavier Draye, Lisa K Rainville, Susan Auckland, Zhimin Zhuang, Edward L Lubbers, O Lloyd May, Peng W Chee, Andrew H Paterson
This study reports transmission genetics of chromosomal segments into Gossypium hirsutum from its most distant euploid relative, Gossypium mustelinum . Mutilocus interactions and structural rearrangements affect introgression and segregation of donor chromatin. Wild allotetraploid relatives of cotton are a rich source of genetic diversity that can be used in genetic improvement, but linkage drag and non-Mendelian transmission genetics are prevalent in interspecific crosses. These problems necessitate knowledge of transmission patterns of chromatin from wild donor species in cultivated recipient species...
August 11, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28801564/evolution-of-hemoglobin-genes-in-codfishes-influenced-by-ocean-depth
#17
Helle Tessand Baalsrud, Kjetil Lysne Voje, Ole Kristian Tørresen, Monica Hongrø Solbakken, Michael Matschiner, Martin Malmstrøm, Reinhold Hanel, Walter Salzburger, Kjetill S Jakobsen, Sissel Jentoft
Understanding the genetic basis of adaptation is one of the main enigmas of evolutionary biology. Among vertebrates, hemoglobin has been well documented as a key trait for adaptation to different environments. Here, we investigate the role of hemoglobins in adaptation to ocean depth in the diverse teleost order Gadiformes, with species distributed at a wide range of depths varying in temperature, hydrostatic pressure and oxygen levels. Using genomic data we characterized the full hemoglobin (Hb) gene repertoire for subset of species within this lineage...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800357/identification-of-differentially-expressed-genes-through-rna-sequencing-in-goats-capra-hircus-at-different-postnatal-stages
#18
Yaqiu Lin, Jiangjiang Zhu, Yong Wang, Qian Li, Sen Lin
Intramuscular fat (IMF) content and fatty acid composition of longissimus dorsi muscle (LM) change with growth, which partially determines the flavor and nutritional value of goat (Capra hircus) meat. However, unlike cattle, little information is available on the transcriptome-wide changes during different postnatal stages in small ruminants, especially goats. In this study, the sequencing reads of goat LM tissues collected from kid, youth, and adult period were mapped to the goat genome. Results showed that out of total 24 689 Unigenes, 20 435 Unigenes were annotated...
2017: PloS One
https://www.readbyqxmd.com/read/28799009/genome-wide-survey-and-characterization-of-fatty-acid-desaturase-gene-family-in-brassica-napus-and-its-parental-species
#19
Yufei Xue, Baojun Chen, Rui Wang, Aung Naing Win, Jiana Li, Yourong Chai
Rapeseed (Brassica napus) is an important oilseed crop worldwide, and fatty acid (FA) compositions determine the nutritional and economic value of its seed oil. Fatty acid desaturases (FADs) play a pivotal role in regulating FA compositions, but to date, no comprehensive genome-wide analysis of FAD gene family in rapeseed and its parent species has been reported. In this study, using homology searches, 84, 45, and 44 FAD genes were identified in rapeseed, Brassica rapa, and Brassica oleracea genomes, respectively...
August 10, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28798766/toward-genomics-based-breeding-in-c3-cool-season-perennial-grasses
#20
REVIEW
Shyamal K Talukder, Malay C Saha
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind...
2017: Frontiers in Plant Science
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