G3: Genes, Genomes, Genetics

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A New Chicken Genome Assembly Provides Insight into Avian Genome Structure
G3: Genes, Genomes, Genetics - Tập 7 Số 1 - Trang 109-117 - 2017
Wesley C. Warren, LaDeana W. Hillier, Chad Tomlinson, Patrick Minx, Milinn Kremitzki, Tina Graves, Chris Markovic, Nathan Bouk, Kim D. Pruitt, Françoise Thibaud‐Nissen, Valérie Schneider, Tamer Mansour, C. Titus Brown, Aleksey V. Zimin, Rachel Hawken, Mitch Abrahamsen, Alexis Black Pyrkosz, Mireille Morisson, Valérie Fillon, Alain Vignal, William Chow, Kerstin Howe, Janet E. Fulton, Marcia M. Miller, Peter V. Lovell, Claudio V. Mello, Morgan Wirthlin, Andrew S. Mason, Richard Kuo, David W. Burt, Jerry B. Dodgson, Hans H. Cheng
Abstract The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved phy...... hiện toàn bộ
Single-Step BLUP with Varying Genotyping Effort in Open-Pollinated Picea glauca
G3: Genes, Genomes, Genetics - Tập 7 Số 3 - Trang 935-942 - 2017
Blaise Ratcliffe, Omnia Gamal El‐Dien, Eduardo P. Cappa, Ilga Porth, Jaroslav Klápště, Charles Chen, Yousry A. El‐Kassaby
Abstract Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and ...... hiện toàn bộ
A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata
G3: Genes, Genomes, Genetics - Tập 7 Số 7 - Trang 2353-2361 - 2017
Jacob A. Tennessen, Stephanie R. Bollmann, Michael S. Blouin
Abstract The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cr...... hiện toàn bộ
Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
G3: Genes, Genomes, Genetics - Tập 1 Số 3 - Trang 171-182 - 2011
Julian Catchen, Angel Amores, Paul A. Hohenlohe, William A. Cresko, John H. Postlethwait
Abstract Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the calling of tens of thousands of genotypes over hundreds of individuals has hindered progress. Stacks is a software system that uses short-read sequence data to identify and genotype loci i...... hiện toàn bộ
A Genetic Map BetweenGossypium hirsutumand the Brazilian EndemicG. mustelinumand Its Application to QTL Mapping
G3: Genes, Genomes, Genetics - Tập 6 Số 6 - Trang 1673-1685 - 2016
Baohua Wang, Liu Li-mei, Dong Zhang, Zhimin Zhuang, Hui Guo, Xin Qiao, Lijuan Wei, Junkang Rong, O. Lloyd May, Andrew H. Paterson, Peng W. Chee
AbstractAmong the seven tetraploid cotton species, little is known about transmission genetics and genome organization in Gossypium mustelinum, the species most distant from the source of most cultivated cotton, G. hirsutum. In this research, an F2 population was developed from an interspecific cross between G. hirsutum and G. mustelinum (HM). A genetic linkage map...... hiện toàn bộ
Genomic Selection in Multi-environment Crop Trials
G3: Genes, Genomes, Genetics - Tập 6 Số 5 - Trang 1313-1326 - 2016
Helena Oakey, B. R. Cullis, R. Thompson, Jordi Comadran, Claire Halpin, Robbie Waugh
AbstractGenomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that re...... hiện toàn bộ
Nuclear Gene Variation in Wild Brown Rats
G3: Genes, Genomes, Genetics - Tập 2 Số 12 - Trang 1661-1664 - 2012
Rob W. Ness, Yao‐Hua Zhang, Lin Cong, Yu Wang, Peter D. Keightley
AbstractAlthough the brown rat (Rattus norvegicus) is widely used as a model mammal throughout biological sciences, little is known about genetic variation in wild rat populations or the relationship of commonly used inbred strains to their wild relatives. We sampled wild brown rats from the species’ presumed ancestral range in NW China and from a derived populatio...... hiện toàn bộ
Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (Solanum tuberosum L.)
G3: Genes, Genomes, Genetics - Tập 5 Số 11 - Trang 2357-2364 - 2015
Alicia N. Massa, Norma C. Manrique‐Carpintero, Joseph Coombs, Daniel G. Zarka, Anne E Boone, W. W. Kirk, Christine A. Hackett, Glenn J. Bryan, David S. Douches
Abstract The objective of this study was to construct a single nucleotide polymorphism (SNP)-based genetic map at the cultivated tetraploid level to locate quantitative trait loci (QTL) contributing to economically important traits in potato (Solanum tuberosum L.). The 156 F1 progeny and parents of a cross (MSL603) between “Jacqueline Lee” and “MSG22...... hiện toàn bộ
Aspergillus fumigatusMADS-Box Transcription FactorrlmAIs Required for Regulation of the Cell Wall Integrity and Virulence
G3: Genes, Genomes, Genetics - Tập 6 Số 9 - Trang 2983-3002 - 2016
Marina Campos Rocha, João Henrique Tadini Marilhano Fabri, Krissia Franco de Godoy, Patrícia Alves de Castro, Juliana Issa Hori, Anderson Ferreira da Cunha, Mark Arentshorst, Arthur F. J. Ram, Cees A. M. J. J. van den Hondel, Gustavo H. Goldman, Iran Malavazi
AbstractThe Cell Wall Integrity (CWI) pathway is the primary signaling cascade that controls the de novo synthesis of the fungal cell wall, and in Saccharomyces cerevisiae this event is highly dependent on the RLM1 transcription factor. Here, we investigated the function of RlmA in the fungal pathogen Aspergillus fumigatus. We show that the ΔrlmA strain exhibits an...... hiện toàn bộ
Influence of Genetic Interactions on Polygenic Prediction
G3: Genes, Genomes, Genetics - Tập 10 Số 1 - Trang 109-115 - 2020
Zhijun Dai, Norton E. Long, Wen Huang
Abstract Prediction of phenotypes from genotypes is an important objective to fulfill the promises of genomics, precision medicine and agriculture. Although it’s now possible to account for the majority of genetic variation through model fitting, prediction of phenotypes remains a challenge, especially across populations that have diverged in the pas...... hiện toàn bộ
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