Top 6 Biorxiv Papers Today in Genetics


2.04 Mikeys
#1. Characterization of genes and alleles involved in the control of flowering time in grapevine
Nadia Kamal, Iris Ochßner, Anna Schwandner, Prisca Viehöver, Ludger Hausmann, Reinhard Töpfer, Bernd Weisshaar, Daniela Luise Holtgräwe
Grapevine (Vitis vinifera) is one of the most important perennial crop plants in worldwide. Understanding of developmental processes like flowering, which impact quality and quantity of yield in this species is therefore of high interest. This gets even more important when considering some of the expected consequences of climate change. Earlier bud burst and flowering, for example, may result in yield loss due to spring frost. Berry ripening under higher temperatures will impact wine quality. Knowledge of interactions between a genotype or allele combination and the environment can be used for the breeding of genotypes that are better adapted to new climatic conditions. To this end, we have generated a list of more than 500 candidate genes that may play a role in the timing of flowering. The grapevine genome was exploited for flowering time control gene homologs on the basis of functional data from model organisms like A. thaliana. In a previous study, a mapping population derived from early flowering GF.GA-47-42 and late...
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biorxivpreprint: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/yeE0RNi64F #bioRxiv
biorxiv_genetic: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/u1jGRUfxMP #biorxiv_genetic
boas_pucker: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/h5OZRrAad5 #bioRxiv #genetics #plants @CeBiTec @JKI_Bund https://t.co/FAk59woZeL
JKI_Bund: RT @boas_pucker: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/h5OZRrAad5 #…
tomilloberlin: RT @boas_pucker: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/h5OZRrAad5 #…
swagayathri: RT @biorxivpreprint: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/yeE0RNi64F…
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Sample Sizes : None.
Authors: 8
Total Words: 16980
Unqiue Words: 5166

2.0 Mikeys
#2. Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective
Joseph H Marcus, Cosimo Posth, Harald Ringbauer, Luca Lai, Robin Skeates, Carlo Sidore, Jessica Beckett, Anja Furtwängler, Anna Olivieri, Charleston Chiang, Hussein Al-Asadi, Kushal Dey, Tyler A Joseph, Clio Der Sarkissian, Rita Radzeviciute, Maria Giuseppina Gradoli, Wolfgang Haak, David Reich, David Schlessinger, Francesco Cucca, Johannes Krause, John Novembre
Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies -- Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinia's Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA...
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PromPreprint: Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective https://t.co/hLbGnvLnPC
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Sample Sizes : [43, 972, 18, 87, 75, 84, 419, 72, 289, 41, 492, 1000]
Authors: 22
Total Words: 13767
Unqiue Words: 4440

1.998 Mikeys
#3. Neuro-genetic plasticity of Caenorhabditis elegans behavioral thermal tolerance
Gregory W Stegeman, Denise Medina, Asher D Cutter, William S Ryu
Background: Animal responses to thermal stimuli involve intricate contributions of genetics, neurobiology and physiology, with temperature variation providing a pervasive environmental factor for natural selection. Thermal behavior thus exemplifies a dynamic trait that requires non-trivial phenotypic summaries to appropriately capture the trait in response to a changing environment. To characterize the deterministic and plastic components of thermal responses, we developed a novel micro-droplet assay of nematode behavior that permits information-dense summaries of dynamic behavioral phenotypes as reaction norms in response to increasing temperature (thermal tolerance curves, TTC). Results: We found that C. elegans TTCs shift predictably with rearing conditions and developmental stage, with significant differences between distinct wildtype genetic backgrounds. Moreover, after screening TTCs for 58 C. elegans genetic mutant strains, we determined that genes affecting thermosensation, including cmk-1 and tax-4, potentially play...
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asherdcutter: RT @biorxiv_genetic: Neuro-genetic plasticity of Caenorhabditis elegans behavioral thermal tolerance https://t.co/nyfFlnsCU9 #biorxiv_gene…
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Sample Sizes : None.
Authors: 4
Total Words: 10111
Unqiue Words: 3028

1.997 Mikeys
#4. variant2literature: full text literature search for genetic variants
Yin-Hung Lin, Yu-Chen Lu, Jacob Shujui Hsu, Ko-Han Lee, Yi-Wei Cheng, Yi-Chieh Chen, Ting-Fu Chen, Chien-Ta Tu, Chen-Ming Hsu, Chih-Chen Chou, Pei-Lung Chen, Yi-Chin Ethan Tu, Chien-Yu Chen
Whole genome sequencing (WGS) by next-generation sequencing produces millions of variants for an individual. The retrieval of biomedical literature for such a large number of genetic variants remains challenging, because in many cases the variants are only present in figures or tables as images, or in the supplementary documents of which the file formats are diverse. The proposed tool named variant2literature from the TaiGenomics (Toolkits for AI genomics) resolves the problem by incorporating image processing in text recognition. In addition to the adoption of text retrieval by image processing, the recall rate of finding the literature containing the variants of interest is further improved by employing the skill of variant normalization. Different variant presentations are transformed into chromosome coordinates (standard VCF format) such that false negatives can be largely avoided. variant2literature is available in two ways. First, a web-based interface is provided to search all the PMC literatures. Second, the command-line...
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TayazaFadason: RT @biorxivpreprint: variant2literature: full text literature search for genetic variants https://t.co/Jgbxj3otFn #bioRxiv
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Sample Sizes : None.
Authors: 13
Total Words: 1615
Unqiue Words: 778

1.997 Mikeys
#5. A meta-analysis of genome-wide association studies of epigenetic age acceleration
Jude Gibson, Tom Russ, Toni-Kim Clarke, David M Howard, Kathryn Evans, Rosie M Walker, Mairead Bermingham, Stewart Morris, Archie Campbell, Caroline Hayward, Alison Murray, David Porteous, Steve Horvath, Ake Lu, Andrew McIntosh, Heather Whalley, Riccardo Marioni
'Epigenetic age acceleration' is a valuable biomarker of ageing, predictive of morbidity and mortality, but for which the underlying biological mechanisms are not well established. Two commonly used measures, derived from DNA methylation, are Horvath-based (Horvath-EAA) and Hannum-based (Hannum-EAA) epigenetic age acceleration. We conducted genome-wide association studies of Horvath-EAA and Hannum-EAA in 13,493 unrelated individuals of European ancestry, to elucidate genetic determinants of differential epigenetic ageing. We identified ten independent SNPs associated with Horvath-EAA, five of which are novel. We also report 21 Horvath-EAA-associated genes including several involved in metabolism (NHLRC, TPMT) and immune system pathways (TRIM59, EDARADD). GWAS of Hannum-EAA identified one associated variant (rs1005277), and implicated 12 genes including several involved in innate immune system pathways (UBE2D3, MANBA, TRIM46), with metabolic functions (UBE2D3, MANBA), or linked to lifespan regulation (CISD2). Both measures had...
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biorxivpreprint: A meta-analysis of genome-wide association studies of epigenetic age acceleration https://t.co/YqYKH4eSHz #bioRxiv
biorxiv_genetic: A meta-analysis of genome-wide association studies of epigenetic age acceleration https://t.co/lEWpZXCjYc #biorxiv_genetic
EvidenceRobot: RT @biorxiv_genetic: A meta-analysis of genome-wide association studies of epigenetic age acceleration https://t.co/lEWpZXCjYc #biorxiv_ge…
EvidenceRobot: RT @biorxivpreprint: A meta-analysis of genome-wide association studies of epigenetic age acceleration https://t.co/YqYKH4eSHz #bioRxiv
evogen_p: RT @biorxiv_genetic: A meta-analysis of genome-wide association studies of epigenetic age acceleration https://t.co/lEWpZXCjYc #biorxiv_ge…
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Sample Sizes : [5100, 5091, 10, 8393, 13493]
Authors: 17
Total Words: 14477
Unqiue Words: 4638

1.996 Mikeys
#6. Genetic admixture patterns in Argentinian Patagonia
María Laura Parolin, Ulises F Toscanini, Irina F Velázquez, Cintia Llull, Gabriela L Berardi, Alfredo Holley, Camila Tamburrini, Sergio Avena, Francisco R Carnese, José L Lanata, Noela Sánchez Carnero, Lucas F Arce, Néstor G Basso, Rui Pereira, Leonor Gusmão
As for other Latin American populations, Argentinians are the result of the admixture amongst different continental groups, mainly from America and Europe, and to a lesser extent from Sub-Saharan Africa. However, it is known that the admixture processes did not occur homogeneously throughout the country. Therefore, considering the importance for anthropological, medical and forensic researches, this study aimed to investigate the population genetic structure of the Argentinian Patagonia, through the analysis of 46 ancestry informative markers, in 433 individuals from five different localities. Overall, in the Patagonian sample, the average individual ancestry was estimated as 35.8% Native American (95% CI: 32.2-39.4%), 62.1% European (58.5-65.7%) and 2.1% African (1.7-2.4%). Comparing the five localities studied, statistically significant differences were observed for the Native American and European contributions, but not for the African ancestry. The admixture results combined with the genealogical information revealed...
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MiguelSieck: RT @biorxivpreprint: Genetic admixture patterns in Argentinian Patagonia https://t.co/aOMS25YOep #bioRxiv
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Sample Sizes : None.
Authors: 15
Total Words: 8311
Unqiue Words: 2830

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