Looking Over Allopolyploid Clover

The allotetraploid species white clover (Trifolium repens) resulted fromhybridization of two diploid European species whose extant relatives are found only in limited regions: Trifolium occidentale is a creeping clover found only in saline areas near the shores of Western Europe, and Trifolium pallescens is found only at restricted altitudes in alpine habitats (see figure). So, how did I come to be looking over a lovely patch of white clover in my lawn here in Chicago? Indeed, this legume serves as a valuable forage that grows nearly everywhere, with its native range extending across Western Asia, Europe, and Northern Africa and its introduced range extending around the world (see figure). When did the allopolyploidy event that produced T. repens occur, what were the genomic and transcriptomic consequences, and did this help white clover with its remarkable niche expansion? To examine the effects of allopolyploidy in clover, Griffiths et al. (2019) sequenced the genomes and transcriptomes (leaves, roots, shoots, and flowers) of T. repens, T. occidentale, and T. pallescens. Comparison of the full chloroplast genomes confirmed that T. pallescens represents the maternal parent and chloroplast donor for T. repens. Moreover, comparison of the rDNA in the nuclear genome confirmed that T. occidentale represents the other parent and the authors identified subgenome-specific polymorphisms in T. repens that corresponded to polymorphisms in the two diploids. Addressing the question of when, examination of the divergence of the three species, based on differences between pairwise alignments of the progenitor genomes themselves and the corresponding subgenomes, led to an estimated time of ;15 to 28,000 years ago, during the depths of the last glaciation. The authors speculate that the progenitors may have been growing together in glacial refugia and, indeed, the progenitors must have been together for some time because white clover appears to result from multiple hybridization events. Examination of re-sequencing data from four outbred individuals and genotyping-bysequencing in white clover populations showed that T. repens did not undergo a major genetic bottleneck, as would be expected if it resulted from a single hybridization and chromosome doubling or fusion of unreduced gametes that produced only one progenitor. Rather, the data suggest that multiple hybridization events occurred in the early history of white clover. The authors speculate that this allowed a wider sampling of the genetic diversity of the progenitors, which was carried over into the emerging new species, underpinning the variation found in modern T. repens. Furthermore, white clover appears to have undergone a substantial population increase, consistent with it expanding to different niches after the glaciation. Range of White Clover and the Extant Relatives of Its Diploid Progenitors.