TY  - JOUR
A1  - Togninalli, Matteo
A1  - Seren, Ümit
A1  - Meng, Dazhe
A1  - Fitz, Joffrey
A1  - Nordborg, Magnus
A1  - Weigel, Detlef
A1  - Borgwardt, Karsten
A1  - Korte, Arthur
A1  - Grimm, Dominik G.
T1  - The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog
JF  - Nucleic Acids Research
N2  - The abundance of high-quality genotype and phenotype data for the model organism Arabidopsis thaliana enables scientists to study the genetic architecture of many complex traits at an unprecedented level of detail using genome-wide association studies (GWAS). GWAS have been a great success in A. thaliana and many SNP-trait associations have been published. With the AraGWAS Catalog (https://aragwas.1001genomes.org) we provide a publicly available, manually curated and standardized GWAS catalog for all publicly available phenotypes from the central A. thaliana phenotype repository, AraPheno. All GWAS have been recomputed on the latest imputed genotype release of the 1001 Genomes Consortium using a standardized GWAS pipeline to ensure comparability between results. The catalog includes currently 167 phenotypes and more than 222 000 SNP-trait associations with P < 10\(^{-4}\), of which 3887 are significantly associated using permutation-based thresholds. The AraGWAS Catalog can be accessed via a modern web-interface and provides various features to easily access, download and visualize the results and summary statistics across GWAS.
KW  - model organism
KW  - genotype
KW  - phenotype
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-158727
VL  - 46
IS  - D1
ER  - 
TY  - JOUR
A1  - Seren, Ümit
A1  - Grimm, Dominik
A1  - Fitz, Joffrey
A1  - Weigel, Detlef
A1  - Nordborg, Magnus
A1  - Borgwardt, Karsten
A1  - Korte, Arthur
T1  - AraPheno: a public database for Arabidopsis thaliana phenotypes
JF  - Nucleic Acids Research
N2  - Natural genetic variation makes it possible to discover evolutionary changes that have been maintained in a population because they are advantageous. To understand genotype–phenotype relationships and to investigate trait architecture, the existence of both high-resolution genotypic and phenotypic data is necessary. Arabidopsis thaliana is a prime model for these purposes. This herb naturally occurs across much of the Eurasian continent and North America. Thus, it is exposed to a wide range of environmental factors and has been subject to natural selection under distinct conditions. Full genome sequencing data for more than 1000 different natural inbred lines are available, and this has encouraged the distributed generation of many types of phenotypic data. To leverage these data for meta analyses, AraPheno (https://arapheno.1001genomes.org) provide a central repository of population-scale phenotypes for A. thaliana inbred lines. AraPheno includes various features to easily access, download and visualize the phenotypic data. This will facilitate a comparative analysis of the many different types of phenotypic data, which is the base to further enhance our understanding of the genotype–phenotype map.
KW  - phenotype
KW  - arabidopsis
KW  - genotype
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147909
VL  - 45
IS  - D1
ER  - 
TY  - JOUR
A1  - Künstner, Axel
A1  - Hoffmann, Margarete
A1  - Fraser, Bonnie A.
A1  - Kottler, Verena A.
A1  - Sharma, Eshita
A1  - Weigel, Detlef
A1  - Dreyer, Christine
T1  - The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population
JF  - PLoS ONE
N2  - For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well as local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such as ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources and predation regime shape these traits, and barrier waterfalls often separate contrasting environments in the same river. We have assembled and annotated the genome of an inbred single female from a high-predation site in the Guanapo drainage. The final assembly comprises 731.6 Mb with a scaffold N50 of 5.3 MB. Scaffolds were mapped to linkage groups, placing 95% of the genome assembly on the 22 autosomes and the X-chromosome. To investigate genetic variation in the population used for the genome assembly, we sequenced 10 wild caught male individuals. The identified 5 million SNPs correspond to an average nucleotide diversity (π) of 0.0025. The genome assembly and SNP map provide a rich resource for investigating adaptation to different predation regimes. In addition, comparisons with the genomes of other Poeciliid species, which differ greatly in mechanisms of sex determination and maternal resource allocation, as well as comparisons to other teleost genera can begin to reveal how live bearing evolved in teleost fish.
KW  - Trinidadian guppy
KW  - Poecilia reticulata
KW  - genetics
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166755
VL  - 11
IS  - 12
ER  -