Evolution of Flowering Time in Native North American Grapevines
Type of Degreedissertation
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Native North American grapevines represent a significant portion of the biodiversity within the genus Vitis (Vitaceae). Previous studies of taxonomy and natural history suggested patterns of biogeography, phenology and reproductive isolations among wild species. Here specimen informatics and molecular approaches are used to test hypotheses on wild grapevine phylogeny, ecological niches, phenology and their genetic basis. RNA Polymerase II Subunit 2 (RPB2) genes were characterized to study angiosperm evolution and genus-wide phylogeny. Biogeography, ecology and phenology were studied using techniques from the emerging field of specimen informatics. Geographic ranges were estimated to investigate geographic modes of speciation. Ecological niche models built with geographic and environmental variables revealed ecological niche partitioning. Phenological information summarized from specimens suggested significant phenological separation among certain species. Grapevine genes controlling flowering time were characterized based on genomic analyses and molecular experimental approaches. Alternative transcription of grapevine FCA was discovered, indicating a conserved FCA auto-regulation mechanism between grapevine and Arabidopsis. Variation in microsatellite region discovered immediately upstream of TERMINAL FLOWER 1 (TFL1) was revealed with potential to affect species-specific TFL1 expression. Multi-locus phylogenetic analyses revealed congruence and conflicts among phylogenetic signals from flowering time genes and other nuclear markers for grapevine systematics. Molecular evolutionary analyses suggested lack of natural selection on flowering time genes within Vitis as a result of prevalent purifying selection. Molecular evolution of flowering time genes in Angiosperms revealed variations in evolutionary rates among different genes. CONSTANS (CO) showed an elevated nucleotide substitution rate while FLOWERING LOCUS C (FLC) showed an accelerated amino acid substitution rate compared with other genes. All genes showed spatial variations of selective constraints within coding regions. Most genes showed shifts of selective constraints accompanied with diversification of eudicots, suggesting possible connections between fast flowering gene evolution and the radiation of eudicots. Genomic analyses and annotation of FLC revealed an intron of unusually large size. Genome-wide survey of intron size in domesticated grapevine, Vitis vinifera, identified extensive intron size expansion compared with Arabidopsis and Populus. Large introns reduced gene expression levels but are evenly distributed among genes of different functions. Over 80% of the expanded intron space contain repetitive elements with an enrichment of recently inserted LTR-retrotransposons, suggesting an association between intron expansion and grapevine domestication and vegetative propagation.