Sequencing approaches for estimating genetic diversity between ecotypes and populations in forage grasses
Stephen Byrne1 and Torben Asp1.
1Department of Molecular Biology and Genetics, Aarhus University, Denmark
Sequencing technology can now provide data in such throughput that it can directly be used to characterize genome wide variation, allowing the simultaneous discovery and typing of polymorphisms. Sequencing is also very suitable for characterizing genetic variation between populations, as we can directly count the number of reads supporting a variant to obtain estimates of allele frequencies. We have been applying a genotyping-by-sequencing (GBS) strategy to generate allele frequency fingerprints of populations. These allele frequency fingerprints can be used to estimate the structure of, and relationship between, populations that is based on variation throughout the genome. The GBS strategy has now been applied to ecotype populations collected and multiplied as part of the Public Private Partnership (PPP) pre-breeding project organized between the Nordic countries. This collection consists of 370 populations that were obtained from genebank collections to represent as wide a genetic diversity as possible. GBS has also been applied to a large collection of perennial ryegrass single genotypes obtained from ecotypes and varieties, with the aim of developing a population for genome-wide association studies (GWAS) in perennial ryegrass. The identified variants have been anchored onto scaffolds from an annotated draft sequence assembly of the perennial ryegrass genome, in order to estimate the extent of linkage disequilibrium, and to identify candidate genes for traits using GWAS.