The evolution of sex-determining chromosomes from autosomes is a universal feature of dioecious organisms, and remarkably, the same evolutionary steps seem to occur in animals, fungi and plants. Despite studies in a wide range of organisms, the very earliest stages in this chromosomal transition remain nearly unexplored. Through the use of two closely related species of wild strawberry, and a merger of approaches including genetics, genomics, bioinformatics, ecology and systematics, this research will offer transformative insight into the steps fundamental to this transition. In particular, the genomic fingerprint and selective forces responsible for recombination suppression will be examined in detail. This work will also provide taxonomic diversity and much needed data for comparative genomic studies of sex-determining genomic regions across the flowering plants.
This work will contribute to the promotion of undergraduate, graduate student and postdoc training in genomics, bioinformatics, genetic and ecological experimental design, as well as the development of a middle school curriculum that will focus on genetics in strawberry. It will contribute to society by expanding our specific knowledge of genes for sex-determination, and general knowledge of genetic and genomic diversity in important wild relatives of the cultivated strawberry, as well as provide plant and genomic resources to the wider scientific community via national databases and germplasm repositories. This work will also shed first light on the genomic changes that accompany the co-occurrence of genome merger and separate sexes that is a feature of many plant lineages.
A key outcome of this research is the first complete resolution of the genome composition of the progenitors of the cultivated strawberry. This has been a longstanding, difficult question, due to the complex octoploidy (four diploid genomes) of the cultivated strawberry and its direct ancestors. The woodland strawberry, Fragaria vesca, contributed one of the four genomes to the cultivated strawberry. The other three came from a Japanese species, Fragaria iinumae. It has been suspected for about 20 years that these two species were involved, and the predominant hypothesis was that each contributed two of the four genomes. Our unexpected result was that there were ancestrally three Japanese strawberry genomes, and only one of the woodland strawberry. However, we also found 48 distinct locations where one of the Japanese strawberry genomes has been replaced by sequence from the woodland strawberry. Remarkably, this process is unidirectional, with no cases of the woodland strawberry genome replaced by sequence from a Japanese strawberry genome. This biased replacement has not been previously observed, and it will be of interest to discover if it occurs in other polyploid plants. The practical value of this information is that it will allow scientists evaluating particular gene sequences within the cultivated strawberry to classify them by their genome of origin. For example, we determined that the genes responsible for sex expression (male and female plants) in the direct ancestors of the cultivated strawberries are on two different subgenomes. Plant breeders and geneticists working to improve the cultivated strawberry, as well as anyone working on other crops with polyploid (multiple) genomes (wheat, cotton, potato, to name a few) can make use of the POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes) method developed as part of this research project. POLiMAPS greatly simplifies the analysis of genetic variation in these plants. In addition, it is anticipated that this approach will be applied to resolve the unknown genomic ancestry of other polyploids, including oats, sweet potato and sugarcane. For more details on this research, visit the Wild Strawberry website.
