Genetic-geographic correlation revealed across a broad European ecotypic sample of perennial ryegrass (Lolium perenne) using array-based SNP genotyping

Theor Appl Genet. 2015 Oct;128(10):1917-32. doi: 10.1007/s00122-015-2556-3. Epub 2015 Jun 21.

Abstract

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. 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Plant / genetics
  • Ecotype*
  • Europe
  • Genetic Markers
  • Genetics, Population*
  • Genotype
  • Genotyping Techniques
  • Geography
  • Lolium / genetics*
  • Oligonucleotide Array Sequence Analysis
  • Polymorphism, Single Nucleotide*
  • Sequence Analysis, DNA

Substances

  • DNA, Plant
  • Genetic Markers