ABSTRACT: SNP matrix of barley collection from german ex-situ genbank IPK and ICARDA (International Center for Agricultural Research in the Dry Areas) wheat genebank accessions
Project description:Genome-wide prediction approaches are promising for pre-breeding: predicting the performance of plant genetic resources can unlock their hidden potential and fill the information gap in genebanks across the world and, hence, fuel the pipeline of pre-breeding programs. As a proof-of-concept, we evaluated the power of across-genebank prediction for extensive germplasm collections relying on historical data on flowering/heading date, plant height, and thousand kernel weight of 9,344 barley (Hordeum vulgare L.) plant genetic resources from the German Federal ex situ Genebank for Agricultural and Horticultural Crops (IPK) and of 1,089 accessions from the International Center of Agricultural Research in Dry Areas (ICARDA) genebank.
Project description:Genotyping-by-sequencing (GBS) raw data of 319 plants from 32 barley accessions of the German Federal ex situ genebank hosted at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben.
Project description:These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content.