G3: Genes, Genomes, Genetics
2160-1836
2160-1836
Mỹ
Cơ quản chủ quản: Genetics Society of America , OXFORD UNIV PRESS INC
Lĩnh vực:
GeneticsGenetics (clinical)Medicine (miscellaneous)Molecular Biology
Phân tích ảnh hưởng
Thông tin về tạp chí
G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 is a peer-reviewed, peer-edited journal. All editorial decisions are made through collaboration of at least two peer-editors.
Các bài báo tiêu biểu
Nuclear Gene Variation in Wild Brown Rats Abstract Although 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 population in the UK and estimated nucleotide diversity and population subdivision, based on the sequences of 30 autosomal protein-coding loci. Neutral genetic diversity was close to 0.2% in both populations, which is about five times lower than diversity at the orthologous sites in a population of wild house mice from the species’ putative ancestral range in India. We found significant population differentiation between UK and Chinese populations, as assessed by Fst and the program STRUCTURE. Based on synonymous diversity and divergence between the brown rat and house mouse, we estimate that the recent effective population size in brown rats is approximately 130,000 (approximate 95% confidence interval 85,000-184,000), about fivefold lower than wild house mice.
Tập 2 Số 12 - Trang 1661-1664 - 2012
Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (<i>Solanum tuberosum</i> L.) 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 “MSG227-2” were genotyped using the Infinium 8303 Potato Array. Furthermore, the progeny and parents were evaluated for foliar late blight reaction to isolates of the US-8 genotype of Phytophthora infestans (Mont.) de Bary and vine maturity. Linkage analyses and QTL mapping were performed using a novel approach that incorporates allele dosage information. The resulting genetic maps contained 1972 SNP markers with an average density of 1.36 marker per cM. QTL mapping identified the major source of late blight resistance in “Jacqueline Lee.” The best SNP marker mapped ∼0.54 Mb from a resistance hotspot on the long arm of chromosome 9. For vine maturity, the major-effect QTL was located on chromosome 5 with allelic effects from both parents. A candidate SNP marker for this trait mapped ∼0.25 Mb from the StCDF1 gene, which is a candidate gene for the maturity trait. The identification of markers for P. infestans resistance will enable the introgression of multiple sources of resistance through marker-assisted selection. Moreover, the discovery of a QTL for late blight resistance not linked to the QTL for vine maturity provides the opportunity to use marker-assisted selection for resistance independent of the selection for vine maturity classifications.
Tập 5 Số 11 - Trang 2357-2364 - 2015
<i>Aspergillus fumigatus</i>MADS-Box Transcription Factor<i>rlmA</i>Is Required for Regulation of the Cell Wall Integrity and Virulence Abstract The 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 altered cell wall organization in addition to defects related to vegetative growth and tolerance to cell wall-perturbing agents. A genetic analysis indicated that rlmA is positioned downstream of the pkcA and mpkA genes in the CWI pathway. As a consequence, rlmA loss-of-function leads to the altered expression of genes encoding cell wall-related proteins. RlmA positively regulates the phosphorylation of MpkA and is induced at both protein and transcriptional levels during cell wall stress. The rlmA was also involved in tolerance to oxidative damage and transcriptional regulation of genes related to oxidative stress adaptation. Moreover, the ΔrlmA strain had attenuated virulence in a neutropenic murine model of invasive pulmonary aspergillosis. Our results suggest that RlmA functions as a transcription factor in the A. fumigatus CWI pathway, acting downstream of PkcA-MpkA signaling and contributing to the virulence of this fungus.
Tập 6 Số 9 - Trang 2983-3002 - 2016
Influence of Genetic Interactions on Polygenic Prediction 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 past. In this study, we designed simulation experiments to specifically investigate the role of genetic interactions in failure of polygenic prediction. We found that non-additive genetic interactions can significantly reduce the accuracy of polygenic prediction. Our study demonstrated the importance of considering genetic interactions in genetic prediction.
Tập 10 Số 1 - Trang 109-115 - 2020
A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise Abstract Barley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv. Golden Promise, the most efficient genotype for genetic transformation. We have developed a barley cv. Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database. A high-quality Golden Promise reference assembly will be useful and utilized by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments.
Tập 10 Số 6 - Trang 1823-1827 - 2020
Linking anthocyanin diversity, hue, and genetics in purple corn Abstract
While maize with anthocyanin-rich pericarp (purple corn) is rising in popularity as a source of natural colorant for foods and beverages, information on color range and stability—factors associated with anthocyanin decorations and compositional profiles—is currently limited. Furthermore, to maximize the scalability and meet growing demands, both anthocyanin concentrations and agronomic performance must improve in purple corn varieties. Using the natural anthocyanin diversity present in a purple corn landrace, Apache Red, we generated a population with variable flavonoid profiles—flavanol–anthocyanin condensed forms (0–83%), acylated anthocyanins (2–72%), pelargonidin-derived anthocyanins (5–99%), C-glycosyl flavone co-pigments up to 1904 µg/g, and with anthocyanin content up to 1598 µg/g. Each aspect of the flavonoid profiles was found to play a role in either the resulting extract hue or intensity. With genotyping-by-sequencing of this population, we mapped aspects of the flavonoid profile. Major quantitative trait loci (QTLs) for anthocyanin type were found near loci previously identified only in aleurone-pigmented maize varieties [Purple aleurone1 (Pr1) and Anthocyanin acyltransferase1 (Aat1)]. A QTL near P1 (Pericarp color1) was found for both flavone content and flavanol–anthocyanin condensed forms. A significant QTL associated with peonidin-derived anthocyanins near a candidate S-adenosylmethionine-dependent methyltransferase was also identified, warranting further investigation. Mapping total anthocyanin content produced signals near Aat1, the aleurone-associated bHLH R1 (Colored1), the plant color-associated MYB, Pl1 (Purple plant1), the aleurone-associated recessive intensifier, In1 (Intensifier1), and several previously unidentified candidates. This population represents one of the most anthocyanin diverse pericarp-pigmented maize varieties characterized to date. Moreover, the candidates identified here will serve as branching points for future research studying the genetic and molecular processes determining anthocyanin profile in pericarp.
Tập 11 Số 2 - 2021
A Resource of Quantitative Functional Annotation for<i>Homo sapiens</i>Genes Abstract The body of human genomic and proteomic evidence continues to grow at ever-increasing rates, while annotation efforts struggle to keep pace. A surprisingly small fraction of human genes have clear, documented associations with specific functions, and new functions continue to be found for characterized genes. Here we assembled an integrated collection of diverse genomic and proteomic data for 21,341 human genes and make quantitative associations of each to 4333 Gene Ontology terms. We combined guilt-by-profiling and guilt-by-association approaches to exploit features unique to the data types. Performance was evaluated by cross-validation, prospective validation, and by manual evaluation with the biological literature. Functional-linkage networks were also constructed, and their utility was demonstrated by identifying candidate genes related to a glioma FLN using a seed network from genome-wide association studies. Our annotations are presented—alongside existing validated annotations—in a publicly accessible and searchable web interface.
Tập 2 Số 2 - Trang 223-233 - 2012