Amdahl, H. | Search bioRxiv

bioRxiv2025

Genomic prediction of agronomic traits in perennial ryegrass (Lolium perenne L.) and genotype x environment interactions at the limit of the species distribution

BackgroundIn breeding the aim is to identify and accumulate beneficial variants. However, detection of these variants may be challenging in the presence of extensive genotype x environment interactions (GxE), as variant effects will be conditional on environment. MethodsThe study assesses the performance of 264 diploid perennial ryegrass accessions in a multi-environment field trial. We investigate the extent of GxE, for yield (total dry matter) and persistence traits, i.e. winter kill and spring cover, under environmental conditions experienced in Nordic and Baltic regions at the limit of the species distribution. Two different approaches to modelling GxE were tested: reaction norm and envirotyping, and the models were validated under three different breeding scenarios. ResultsOur analysis documented the presence of significant GxE interaction for all traits investigated in the study. Validation showed improvements in prediction accuracy when accounting for GxE: up to 4% for yield when predicting in unobserved environments, and up to 22% and 9% for spring cover and winter kill, respectively when predicting unobserved germplasm. Genome-wide-association-studies (GWAS) were utilized to detect genetic variants with marginal effects (environment-independent effect) and conditional effects (environment-dependent effects). Results showed the presence of large-effect genetic variants with marginal effects, in addition to few QTL whose effects were adaptive under specific environmental conditions while neutral or deleterious under different environmental conditions. ConclusionThis study demonstrates the usefulness and limitations of genomic prediction models for predicting GxE in highly diverse samples, and describes the extent of GxE interactions at the limit of species distribution for perennial ryegrass. Finally, our study points toward adaptive variation, which may enhance persistence of perennial ryegrass populations in Nordic and Baltic growing conditions.

genetics↗

bioRxiv2022

Multi-location trials and population-based genotyping reveal high diversity and adaptation to breeding environments in a large collection of red clover

Red clover (Trifolium pratense L.) is an outcrossing forage legume that has adapted to a wide range of climatic and growing conditions across Europe. Red clover is valued for its high yield potential and forage quality. The high amount of genetic diversity present in red clover provides an invaluable, but often poorly characterized resource to improve key traits such as yield, quality, and resistance to biotic and abiotic stresses. In this study, we examined the genetic and phenotypic diversity within a diverse set of 395 diploid red clover accessions via genome wide allele frequency fingerprinting and multi-location field trials across Europe. We found that the genetic structure of accessions mostly reflected their geographic origin and only few cases were detected, where breeders integrated foreign genetic resources into their local breeding pools. Phenotypic performance of accessions in the multi-location field trials revealed a very strong accession x location interaction. Notably, breeding material and cultivars generally performed well at the location where they were developed. Local adaptation was especially prominent in Nordic red clover accessions that showed a distinct adaptation to the growing conditions and cutting regime of the North. Our results confirmed that red clover cultivars were bred from regional ecotypes and show a narrow adaptation to regional conditions. Our study can serve as a valuable basis for identifying interesting material that express the desired characteristics and contribute to the adaptation of red clover to future climatic conditions.

genetics↗