Plant Science & Landscape Architecture Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2797
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Item TYPE II MADS-BOX GENES ASSOCIATED WITH POPLAR APICAL BUD DEVELOPMENT AND DORMANCY(2008-04-25) Chen, Kuang-Yu; Coleman, Gary D; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)MADS-box transcription factors regulate the development of vegetative and reproductive organs in plants. Little is known about the role of MADS-box genes in tree development. Using phylogenetic analysis, 57 putative type II MADS-box genes representing 14 functional classes were identified in the Populus trichocarpa genome. cDNA sequencing of the poplar type II MADS-box genes indicates that 28.1% of the transcripts differed in the intron-exon structures predicted in the genome database and 19.3% of the transcripts appear to be alternatively spliced. The majority of the poplar type II MADS-box genes were expressed in a wide variety of tissues including shoot apices, leaves, bark, xylem, root, and floral tissues and in shoot apices during bud development and dormancy. These results indicate that poplar MADS-box genes have diverse regulatory roles in a broad range of tissues and developmental processes. Six poplar FLC-like genes, PtFLC1-PtFLC6, were identified in the poplar genome and expression of all six genes was detected in poplar shoot apices. The expression of one gene, PtFLC2, declined in apical buds during SD photoperiod and low temperature induced dormancy development suggesting a role in bud dormancy and may represent an analogous regulatory mechanism to the down-regulation of FLC during vernalization in Arabidopsis. In addition, several PtFLC2 splice isoforms (PtFLC2as1-9) were identified that were associated with the later stages of bud dormancy. Overexpression of the PtFLC2as1 isoform delayed photoperiod induced apical bud development and bud dormancy, growth cessation, and leaf senescence while overexpression of the PtFLC2as2 isoform appeared to accelerate bud development and dormancy and reduce the amount of chilling required to overcome dormancy. These findings suggest that PtFLC2, unlike Arabidopsis FLC, could be an integration point for both photoperiod and cold signals that regulate bud development and dormancy. These results also suggest that in addition to transcriptional regulation, that cold-mediated production of PtFLC2 splicing isoforms may have an important regulatory role in bud dormancy. The regulated production of splicing isoforms could regulate bud dormancy either by dominate negative interactions, by forming different protein complexes or regulating different pathways that regulate growth, dormancy, and dormancy release.Item GENETIC DIVERSITY AND LINKAGE DISEQUILIBRIUM IN WILD SOYBEAN, LANDRACES, ANCESTRAL, AND ELITE SOYBEAN POPULATIONS(2005-04-20) Hyten, Jr., David Lee; Costa, Jose M.; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Domestication, founder effects, and artificial selection can impact populations by reducing genome diversity and increasing the extent of linkage disequilibrium (LD). To understand the impact of these genetic bottlenecks and selection on sequence diversity and LD within soybean [Glycine max (L.) Merr.], 111 genes and three chromosomal regions located on linkage groups A2, G, and J were characterized in soybean. Four soybean populations were evaluated: 1) the wild ancestor of soybean (G. soja), 2) the population resulting from domestication (landraces), 3) Asian introductions from which North American cultivars were developed (ancestors), and 4) elite cultivars from the 1980's (elite). A total of 438 single nucleotide polymorphisms (SNPs) and 58 insertions-deletions were discovered within the 102 genes. Sequence diversity was lower than expected in G. soja with an overall theta equal to 0.00235, and was less than half that value (theta = 0.00115) in the landraces. Domestication eliminated most unique haplotypes with G. soja containing 240 unique haplotypes while the landraces only contained 42 unique haplotypes. The founder effect of the introduction of soybean to North America followed by intensive artificial selection, resulted in only a 30% decrease in nucleotide diversity. A total of 738 SNPs were discovered and genotyped in the four populations throughout three chromosomal regions. In G. soja LD did not extend past 100 kb while in the three cultivated soybean populations LD extended from 90 kb up to 600+ kb, most likely as a result of increased inbreeding and domestication. The three chromosomal regions varied in the extent of LD within the populations. G. soja is the greatest resource for unique alleles and may be best suited for fine mapping utilizing association analysis. The landraces do not contain much more variability than the elite cultivars but may have enough diversity to facilitate genetic improvement of elite cultivars. Finally, due to the extended levels of LD in the landraces and the elite cultivars, whole genome association analysis may be possible for the discovery of QTL.Item CHARACTERIZATION OF THE MYO-INOSITOL (3) PHOSPHATE SYNTHASE GENE (MIPS) AND MAPPING OF A LPA MUTANT IN SOYBEAN (GLYCINE MAX (L.) MERRILL).(2004-08-25) Salmon, Katherine Diane; Kenworthy, William J.; Costa, Jose M.; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Low phytic acid (LPA) is a mutation causing phosphorus to be stored as unbound phosphorus in the seed. LPA mutants show a high inorganic phosphorus (HIP) phenotype. Previous studies had indicated that LPA might be linked to the myo-inositol (3) phosphate synthase (MIPS) gene; this research attempted to associate a soybean HIP mutant with the MIPS gene. The parental and the F2 genotypes were tested in four ways: 1) SNP detection using the LCR protocol; 2) polymorphism detection with PCR; 3) high inorganic phosphorus (HIP) phenotype detection; and 4) oil and protein concentration. The two parental genotypes could not be differentiated in the LCR study. A PCR-based polymorphism was heritable in the F2 genotypes. HIP assay indicated multiple genes control the LPA mutant. A polymorphism was associated to the HIP phenotype. The three types of HIP phenotypes were not statistically different in oil and protein concentrations allowing implementation into a breeding program.Item Breeding Considerations for Improving Cadmium and Zinc Hyperaccumulation in Two Thlaspi caerulescens Populations(2004-05-05) Synkowski, Eva Claire Creighton; McIntosh, Marla S; Plant Science and Landscape Architecture (PSLA)Cadmium is the second most widespread soil metal contaminant in the world and it has been suggested that phytoremediation using hyperaccumulator plants could be used to effectively remove harmful levels of soil metals. This research was conducted to provide basic information necessary for developing a breeding program to improve the phytoremediation potential of Thlaspi caerulescens, a promising hyperaccumulator plant. By determining the genetic structure of the source populations and estimating the heritability of traits of interest, gain from selection was predicted. Bulk segregrant analysis of DNA polymorphisms was used to identify markers linked to cadmium hyperaccumulation. DNA markers would reduce time and expense of selecting superior genotypes. However, confounding effects from marker technology, experimental design, and sample size reduced the potential for implementing the detected markers in a breeding program. Future experiments may still detect markers for hyperaccumulation and the T. caerulescens populations studied are valuable for phytoremediation application.