T. Blackmore, I. Thomas, R. McMahon, W. Powell, M Hegarty

Theoretical and Applied Genetics; October 2015, Volume 128, Issue 10, pp 1917-1932

Abstract

Key message

Publically available SNP array increases the marker density for genotyping of forage crop, Lolium perenne . Applied to 90 European ecotypes composed of 716 individuals identifies a significant genetic–geographic correlation.

Abstract

Grassland ecosystems are ubiquitous across temperate and tropical regions, totalling 37 % of the terrestrial land cover of the planet, and thus represent a global resource for understanding local adaptations to environment. However, genomic resources for grass species (outside cereals) are relatively poor. The advent of next-generation DNA sequencing and high-density SNP genotyping platforms enables the development of dense marker assays for population genetics analyses and genome-wide association studies. A high-density SNP marker resource (Illumina Infinium assay) for perennial ryegrass (Lolium perenne) was created and validated in a broad ecotype collection of 716 individuals sampled from 90 sites across Europe. Genetic diversity within and between populations was assessed. A strong correlation of geographic origin to genetic structure was found using principal component analysis, with significant correlation to longitude and latitude (P < 0.001). The potential of this array as a resource for studies of germplasm diversity and identifying traits underpinning adaptive variation is highlighted.

See: http://link.springer.com/article/10.1007/s00122-015-2556-3/fulltext.html

Fig. 2

STRUCTURE analysis of ecotypes based on 2185 SNPs for K = 2, with probability of membership to group 1 shown against longitude of sample site. Optimal value of K determined using STRUCTURE Harvester. The consensus probability of group membership, as determined using CLUMPP, is plotted against the longitude of the sample site for each individual. Correlation of longitude to group 1 membership; R ² = −0.7815