Genetic analysis of domestication and carotenoid accumulation in carrot (Daucus carota L.) and the polyploidization of switchgrass (Panicum virgatum L.)

Carrot is among the richest sources of provitamin A β-carotene in the human diet. Despite progress in breeding for increased β-carotene content, relatively little is known about the origin of orange carrots and the genetics of carotenoid accumulation in carrot. The Y, Y₂ and Or genes are the three genes associated with the accumulation of various carotenoids in carrot. Y controls the accumulation of all carotenoids, and Y₂ controls the accumulation of β-carotene. Or also controls the accumulation of β-carotene, yet knowledge about its role in this process is limited. The motivation behind this work was to better understand the role of Or in promoting the accumulation of β-carotene in carrot as well as identify the origin of orange carrots using genetic data. In addition to carrot, this work also investigates the polyploidization of Switchgrass, a potential biofuel crop, by characterizing a retrotransposon family enriched in one of the two subgenomes. In order to address these research questions, an experimental mapping population was generated in which y and y₂ were fixed in their homozygous recessive states and Or was segregating. Next, transcriptomes of carrots fixed for the two Or alleles were analyzed across three developmental timepoints. Finally, nearly 400 diverse resequenced carrots were surveyed for signatures of selection. Additionally, in order to characterize the polyploidization of switchgrass and improve the genome assembly, chromosomes were classified into their correct subgenome based on repeat content as well as the abundance of a novel retrotransposon family named Switch and time of polyploidization was estimated based on insertion times of intact retrotransposons. These findings lay the foundation for additional research in carrot and switchgrass, as well as the development of markers for marker-assisted selection in breeding programs.