Genotyping-by-Sequencing of a set of diverse spring barley (Hordeum vulgare) accessions
Poster Jul 08, 2014
Tina Lüders (1), Jens Keilwagen (2), Neele Wendler (3), Axel Himmelbach (3), Rajiv Sharma (3), Benjamin Kilian (3,4), Nils Stein (3), Frank Ordon (1)
Next-generation sequencing technologies have become affordable to use sequencing for standard genotyping in genetic mapping studies. The aim of the work presented was the saturation of a set of 192 spring barley accessions with a high density of SNP markers in a Genotyping-by-Sequencing (GBS) approach. The set of barley accessions from different origins represents a broad spectrum of the genetic diversity and exhibits low linkage disequilibrium making it useful for high-resolution association mapping studies. Indeed, the set of barley accessions has previously been genotyped with 45 SSR markers, 1536 Illumina GoldenGate markers, 1935 DArT markers and the 9k iSelect chip. However, a higher number of SNP markers is needed at a density that reflects genome-wide linkage disequilibrium structure and haplotype diversity. The GBS experiment comprised the construction of a reduced-representation 192-plex library and its sequencing on one Illumina HiSeq 2000 lane (1 x 100 cycles). A reference-based computational pipeline was applied to analyze 20 GB of sequencing data. Using GBS, 7,439 bi-allelic, high-quality SNP markers could be generated. A high proportion (about 82%) of the SNPs was anchored to the integrated physical and genetic map of barley. It is expected that the saturation of the set of diverse barley accessions with a high density of GBS markers will improve whole-genome association mapping in terms of locating candidate genes. Furthermore, association mapping will provide markers linked to genes of interest that are targeted in barley breeding.
Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes. The majority of these are located in the intergenic or intragenic regions suggesting that the implicated variants may alter chromatin conformation. This, in turn, is likely to influence the expression of nearby or more remotely located genes to alter beta cell function. At present, however, detailed molecular and functional analyses are still lacking for most of these variants. We recently analysed one of these loci and mapped five causal variants in an islet-specific enhancer cluster within the STARD10 gene locus. Here, we aimed to understand how these causal variants influence b-cell function by alteration of the chromatin structure of enhancer clusterREAD MORE
Early life stress (ELS) is highly associated with development of psychopathology
and mood disorders in adulthood. Genetic studies have identified variation in the gene calcium voltage-gated channel subunit alpha1C (CACNA1C) to increase risk for several psychiatric disorders. This poster assessed the expression of Cacna1c following prepubertal stress.