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Methods for Genotyping-by-Sequencing

Posted on December 01, 2016

A guide to genotyping-by-sequencing, in Methods in Molecular Biology read more

Rowan, B. A., Seymour, D. K., Chae, E., Lundberg, D. S., & Weigel, D. (2017).

A major goal for biologists is to understand the connection between genes and phenotypic traits, and genetic mapping in experimental populations remains a powerful approach for discovering the causal genes underlying phenotypes. For genetic mapping, the process of genotyping was previously a major rate-limiting step. Modern sequencing technology has greatly improved the resolution and speed of genetic mapping by reducing the time, labor, and cost per genotyping marker. In addition, the ability to perform genotyping-by-sequencing (GBS) has facilitated large-scale population genetic analyses by providing a simpler way to survey segregating genetic variation in natural populations. Here we present two protocols for GBS, using the Illumina platform, that can be applied to a wide range of genotyping projects in different species. The first protocol is for genotyping a subset of marker positions genome-wide using restriction digestion, and the second is for preparing inexpensive paired-end whole-genome libraries. We discuss the suitability of each approach for different genotyping applications and provide notes for adapting these protocols for use with a liquid-handling robot.

Farewell to Claude

Posted on November 29, 2016

We’re saying farewell to Claude; read more

after a very successful time in Weigelworld, he will move South and establish his own group at the GMI in Vienna

We wish you all the best! 

With VIB colleagues: Variation in Gibberellin Responses

Posted on November 28, 2016

Natural Variation of Molecular and Morphological Gibberellin Responses read more

Nam, Y. J., Herman, D., Blomme, J., Chae, E., Kojima, M., Coppens, F., Storme, V., Van Daele, T., Dhondt, S., Sakakibara, H., Weigel, D., Inzé, D., Gonzalez, N.

Although phytohormones such as gibberellins are essential for many conserved aspects of plant physiology and development, plants vary greatly in their responses to these regulatory compounds. Here, we use genetic perturbation of endogenous gibberellin levels to probe the extent of intraspecific variation in gibberellin responses in natural accessions of Arabidopsis thaliana (Arabidopsis). We find that these accessions vary greatly in their ability to buffer the effects of overexpression of GA20ox1, encoding a rate-limiting enzyme for gibberellin biosynthesis, with substantial differences in bioactive gibberellin concentrations as well as transcriptomes and growth trajectories. These findings demonstrate a surprising level of flexibility in the wiring of regulatory networks underlying hormone metabolism and signalling.

Farewell to Wanyan

Posted on November 17, 2016

We're saying goodbye to Wanyan and wish her all the very best for her future. read more

Thank you for a wonderful three years in the lab, and we hope you find the time to visit us soon!

Detlef tells us why he loves Genetics

Posted on November 11, 2016

Essay on Occasion of having Been Awarded the GSA Medal 2016 read more

The Genetics Society of America (GSA) Medal is awarded to an individual for outstanding contributions to the field of genetics in the last 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics, and exemplify the ingenuity of GSA membership. This year’s recipient was Detlef, and in this personal essay he writes about how he fell in love with Genetics, and continues to think of himself first and foremost as a geneticist.

To the article

AraPheno is online

Posted on November 09, 2016

AraPheno: a public database for Arabidopsis thaliana phenotypes read more

Seren, Ü., Grimm, D. G., Fitz, J., Weigel, D., Nordborg, M., Borgwardt, K. M., and Korte, A.

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. 

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