Large Scale SNP Analysis Reveals Genomic Diversity within European and Asian Red Clover (Trifolium pratense L.) Germplasm

Red clover is an important cool temperate forage legume. It is native to Europe, South and Central Asia, and Northwest Africa, where it is adapted to many environments. Selective breeding has resulted in elite lines of red clover being tall with few branches and large leaves, making it an ideal silage crop. To expand the use of red clover, there is a need for varieties with better grazing tolerance and persistency. These properties have been linked to a more prostrate growth habit. Ecotypes vary considerably in morphology, flowering time, and leaf size, and are potential sources of novel variation, that could be incorporated into improved varieties. We have assessed the genetic diversity in a large ecotype panel and elite varieties of red clover using single nucleotide polymorphisms. A PCA of the SNP data revealed a strong east west split to the ecotype accessions. Fst values indicated moderate differentiation; with higher levels of variation within rather than between the accessions. Using BayeScan and other methods, we identified potential regions of the genome under selection. An assessment of linkage disequilibrium showed a slower decay in the ecotypes compared to synthetic populations. A preliminary genome wide association study based on one years’ phenotypic data, identified one SNP which was significantly associated with flowering time. The minor allele reduced the overall time to flowering by 11 days. Ecotypes from this work are being used in a pre-breeding crossing program, to incorporate some of their phenotypic traits and to further study their genetic control.