Using Genome Wide Allele Frequency Fingerprints to Identify Allele Frequency Changes in Seeded Perennial Ryegrass Swards

Unlike varieties of many crops, in which all plants of a variety are identical, individual perennial ryegrass (PRG) cultivars are effectively genetically divergent populations of individuals that have been selected to have broadly similar characteristics. In addition, as opposed to annual crops, PRG cultivars are expected to remain in the field over a near decadal period before re-seeding. One consequence of these factors is that, once planted, the composition of perennial ryegrass swards can change over time in response to environmental variation and management practice. It was estimated that only 10% of the PRG plants sown in a sward survive after 10 years [1].

In order to gain a better insight into this phenomenon, we are using cutting edge genetic fingerprinting approach called “Genome Wide Allele Frequency Fingerprints” (GWAFFs), based on a genome-wide marker approach called genotyping by sequencing [2, 3] to monitor changes in the genetic composition of PRG swards over time. We are testing whether these changes are random, or whether they can be related to management practices causing some plants to be preferentially selected over others. The ultimate goal of the research is to identify regions of the genome that are responsible for determining the lifetime performance characteristics of grazed swards and to use this information in the future to develop better performing PRG cultivars using genomic selection-based strategies similar to those currently used in cattle breeding.

[1] New phytologist. 98(3): p. 503-513.

[2] PloS one. 8(3): p. e57438.

[3] PloS one. 6(5): p. e19379.