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Weedy rice is a persistent weed of cultivated rice (Oryza sativa) fields worldwide, which competes with the crop and drastically reduces yields. Within the US, two main populations of genetically differentiated weedy rice exist, the straw-hulled (SH) group and the black-hulled awned (BHA) group. Current research suggests that both groups are derived from Asian cultivated rice. However, the weeds differ from the cultivated groups in various morphological traits. My research focus is on the genetic basis of two such traits: seed shattering ability and differences in flowering time. The persistence of weedy rice has been partly attributed to its ability to shatter (disperse) seed prior to crop harvesting. I have investigated the shattering phenotype in a collection of US weedy rice accessions and find that all US weedy rice groups shatter seeds easily. Additionally, I characterized the morphology of the abscission layer at the site where seed release occurs and find that weeds begin to degrade their abscission layers at least five days prior to wild plants. I also assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice and find that all cultivated and weedy rice share similar haplotypes at sh4. These haplotypes contain a single derived mutation associated with decreased seed shattering during domestication. The combination of a shared cultivar sh4 allele and a highly shattering phenotype suggests that US weedy rice have re-acquired the shattering trait after divergence from their crop progenitors through alternative genetic mechanisms. Additionally, my investigation into flowering time in weedy rice shows that weed populations differ in their flowering times. I also assessed allelic identity and diversity at two genes involved in the transition to flowering, Hd1 and Hd3a, and again found haplotype sharing between weeds and cultivars with Hd1 only accounting for some of the flowering time differences between weeds. In order to locate genomic regions containing additional candidate genes I conducted a QTL mapping study on two F2 populations derived from crosses of weedy rice with cultivated rice. My results show sharing of QTL for flowering time between populations, yet lack of sharing of QTL for shattering.

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