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

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-015-2556-3) contains supplementary material, which is available to authorized users

Collecting wild Miscanthus germplasm in Asia for crop improvement and conservation in Europe whilst adhering to the guidelines of the United Nations’ Convention on Biological Diversity

We would like to thank Dr Helen Ougham and Professor Howard Thomas for their valuable comments on this manuscript; Sarah Hawkins at IBERS for the leading of harvesting and phenotyping works; and Paul Barber at Plant Health and Seeds Inspectorate, Wales & West Midlands, Animal and Plant Health Agency (APHA) for advice on germplasm collection practice and quarantine management. This research was supported by the UK’s Department for Environment, Food and Rural Affairs (Defra) under a project entitled ‘Accession of CBD compliant Miscanthus and Triarrhena germplasm from China, Japan and Taiwan for incorporation in the UK Miscanthus breeding programme’ [grant no. NF0436]. The breeding and evaluation were conducted under ‘Genetic improvement of Miscanthus as a sustainable feedstock for bioenergy in the UK (GIANT)’ [supported by Defra and the Biotechnology and Biological Sciences Research Council (BBSRC http://dx.doi.org/10.13039/501100000690, ‘Research Councils UK’), UK, grant no. LK0863]. LH, ID and JCB were supported by BBSRC grant nos BBS/E/G/00003134 and BBS/E/W/0012843A.Peer reviewedPublisher PD

Exploiting the Brachypodium Tool Box in cereal and grass research

It is now a decade since Brachypodium distachyon (Brachypodium) was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) databases, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm collections and, recently, a complete genome sequence have been generated. In this review, we will describe the current status of the Brachypodium Tool Box and how it is beginning to be applied to study a range of biological traits. Further, as genomic analysis of larger cereals and forage grasses genomes are becoming easier, we will re-evaluate Brachypodium as a model species. We suggest that there remains an urgent need to employ reverse genetic and functional genomic approaches to identify the functionality of key genetic elements, which could be employed subsequently in plant breeding programmes; and a requirement for a Pooideae reference genome to aid assembling large pooid genomes. Brachypodium is an ideal system for functional genomic studies, because of its easy growth requirements, small physical stature, and rapid life cycle, coupled with the resources offered by the Brachypodium Tool Box. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust