Genotyping by sequencing and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)

The important worldwide forage crop red clover ( Trifolium pratense L.) is widely cultivated as cattle feed and for soil improvement. Wild populations landraces have great natural diversity that could be used to improve clover. However, date, there still insufficient knowledge about the genetic phenotypic of species. Here, we developed a low-cost complexity reduced mRNA analysis (mRNA-GBS) compared results with population (GBS) previously published mRNA-Seq data, assess whether intraspecific variation within between transcriptome responses possible simultaneously. mRNA-GBS approach was successful. SNP analyses from revealed comparable patterns GBS results, but due site-specific multifactorial influences environmental well conceptual methodological limitations mRNA-GBS, it not link sequencing depth greenhouse field expression studies. Nevertheless, use short sequences upstream poly(A) tail reduce are promising approaches combine genetics profiling analyze many individuals trait differences simultaneously cost-effectively, even in non-model our study design across different regions Germany also challenging. differential most likely overlays highly complex plant under conditions.