Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits

Abstract

Background and Aims Lolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS). Methods BAC-based physical maps for L. perenne were constructed from ~212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map. Key Results Between ~3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with ~35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes. Conclusions Combining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.

Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

“…In most cases, a large part of the phenotypic variance remains unexplained by loci detected by GWAS (Maher, 2008), a problem that was notably encountered in perennial ryegrass (Harper et al., 2019). GWAS models control for false‐positive associations due to population structure or genetic relatedness and inference statistics are corrected for multiple tests (Yu et al., 2006).…”

A new genetic locus for self-compatibility in the outcrossing grass species perennial ryegrass (Lolium perenne)

“…Overall, it can be concluded that a range of SC genes, either associated directly with the SI loci or as unlinked modifier loci, exist within largely self-incompatible species and enable populations to retain genetic diversity and at the same time have the ability to colonize new habitats where mate choice might be restricted, potentially extending the natural range of the species. This flexible reproductive strategy may well be partly responsible for the success of L. perenne , which has a wide geographical distribution ( Beddows, 1967 ) that, although accelerated by agricultural use, has occurred through natural processes predating primitive agriculture ( Harper et al , 2019 ; Blanco-Pastor et al , 2019 ).…”

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)

“…The genotype under study is, in some ways, atypical in that it is an inbred and, as a consequence, largely homozygous genotype. This genotype was chosen as it was used for the published genome and physical map assemblies for perennial ryegrass [41, 67] and so brings direct advantages to the analysis in terms of the quality of the available gene annotations. Additionally, as this study directly references the published perennial ryegrass genome assembly, it is hoped that this will also contribute to the development of a genomic platform for the further genetic dissection of the drought response in a wider selection of perennial ryegrass germplasm reflecting both agricultural and landscape adaptations.…”