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.

Aquaporins (AQPs) are channel proteins that facilitate the transport of water and various low molecular weight solutes including metalloids. Plant aquaporins have been divided into four major subfamilies: plasma membrane intrinsic proteins (PIPs), NOD26-like intrinsic proteins (NIPs), tonoplast intrinsic proteins (TIPs), and small basic intrinsic proteins (SIPs). Various studies have shown that the transport of metalloids including arsenite, antimonite, silicon and boron in plants is facilitated by members of NIP subfamily. In this study, we provided experimental evidences showing that members of rice PIP subfamily are involved in arsenite and boron permeability. RT-PCR analysis of seven OsPIPs; OsPIP1;2, OsPIP1;3, OsPIP2;4, OsPIP2;5, OsPIP2;6, OsPIP2;7, and OsPIP2;8 showed that these genes were downregulated under arsenite toxicity in shoots and roots. Whereas, these OsPIP genes were deferentially regulated in shoots and highly induced in roots by boron toxicity. Heterologous expression in Xenopus laevis oocytes showed that OsPIP2;4, OsPIP2;6, and OsPIP2;7 significantly increased the transport of arsenite. Expression of OsPIP candidate genes in HD9 yeast strain lacking the metalloids influx and efflux systems resulted in an increased boron sensitivity and accumulation. Overexpression of two OsPIP candidates; OsPIP1;3 and OsPIP2;6 in Arabidopsis yielded enhanced arsenite and boron tolerance with higher biomass and greater root length compared to wild type plants, however there was no difference in arsenic and boron accumulation in long-term uptake assays. Short duration exposure to AsIII resulted in both active influx and efflux of As in shoots and roots, suggesting a bidirectional transport activity of OsPIPs. Whereas, short-term uptake assay of tracer B (10B) in shoots and roots demonstrated increased 10 B influx in transgenic Arabidopsis lines indicating that these OsPIPs are also involved in mediating B transport in plants. We used RNAi approach to knockdown the expression of OsPIP1;3 and OsPIP2;6 in rice. We generated RNAi lines for both genes and qRT-PCR analysis showed a significant decrease in the transcript levels for OsPIP1;3 and OsPIP2;6. These RNAi lines will be the subject of future studies. These OsPIPs genes will be highly useful in developing arsenite and boron tolerant crops for enhanced yield in the areas affected by high As and B toxicity.