College of Agriculture & Natural Resources
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The collections in this community comprise faculty research works, as well as graduate theses and dissertations.
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Item Genetic Variation in Nitrogen and Phosphorus Levels in Broiler Excreta: Opportunity for Improving both Birds and the Environment(2010) sasikala appukuttan, arun kirshna; Siewerdt, Frank; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The increase in poultry meat consumption has resulted in intensified poultry farming operations with consequent concentration of excreta in major production areas. The nutrient content in the soil surrounding the poultry farms has increased as a result of the high content of nitrogen (N) and phosphorus (P) in the poultry excreta. The current study aimed to propose a strategy to reduce the N and P content in excreta through genetic selection of broilers for efficient nutrient utilization. The traits measured (on a dry matter basis) were the percentage of N in the excreta (PNE) and the percentage of P in the excreta (PPE). Individual 24-hr excreta samples were collected from 6 wk old birds. Excreta samples were collected from a commercial breeding farm at two different time periods from line A and line B birds respectively, and analyzed for PNE and PPE. Analysis of excreta samples collected during the first period (197 bird samples belonging to 15 sire families) and second period (278 birds belonging to 25 sire families) suggested a heritability of 0.08, 0.16 for PNE and 0, 0.20 for PPE, respectively. Phenotypic and genetic correlations between the measured traits from the two lines were very low; however, phenotypic correlation analysis of PNE and PPE with other traits of commercial interest showed some favorable as well as neutral associations. Blood samples collected from the birds were used for an association study of the excreta traits with four candidate genes. The candidate genes were selected based on the results of previous research. Some of the SNPs from the candidate genes were found to have additive and dominance effect on the excreta and production traits and were usually favorably associated with mutations in higher frequency in the populations. The results suggest that genetic selection of birds for PNE and PPE could improve the environment and the market value of the birds.Item DELINEATING THE ROLES OF C. ELEGANS HEME RESPONSIVE GENES HRG-2 AND HRG-3 IN HEME HOMEOSTASIS(2009) Chen, Caiyong; Hamza, Iqbal; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Heme is an essential cofactor for diverse biological processes such as oxygen transport, xenobiotic detoxification, and circadian clock control. Since free heme is hydrophobic and cytotoxic, we hypothesize that within eukaryotic cells, specific trafficking pathways exist for the delivery of heme to different subcellular destinations where hemoproteins reside. To identify molecules that may be involved in heme homeostasis, we conducted a C. elegans microarray experiment on RNA extracted from worms grown at different concentrations of heme in axenic liquid medium. Analysis of the microarrays revealed that the mRNA levels of heme-responsive gene-2 (hrg-2) and hrg-3 increased more than 70 fold when worms were grown at 4 µM compared to 20 µM heme. hrg-2 is expressed in hypodermal tissues in the worm, and the protein localizes to the endoplasmic reticulum and the apical plasma membrane. In vitro hemin agarose pull-down experiments indicate that HRG-2 binds heme. Deletion of hrg-2 in C. elegans leads to reduced growth rate at low heme. Moreover, expression of HRG-2 in hem1δ, a heme-deficient yeast strain, results in growth rescue at submicromolar concentrations of exogenous heme. These results indicate that HRG-2 may either directly participate in heme uptake or facilitate heme delivery to another protein. Unlike hrg-2, hrg-3 is exclusively expressed in the worm intestine under heme deficiency. Following its synthesis, HRG-3 is secreted into the body cavity pseudocoelom. Deletion of hrg-3 results in increased heme levels in the worm intestine, suggesting that HRG-3 may function in intercellular heme transport in C. elegans. To identify the functional network or pathways for HRG-2 and HRG-3, we performed a genome-wide microarray analysis using RNA samples prepared from the worms grown at different concentrations of heme and oxygen. The results showed that a total of 446 genes were transcriptionally altered by heme and/or oxygen. Among them, 41 and 29 genes exhibited similar expression profiles to hrg-2 and hrg-3, respectively. We postulate that these genes may function in conjunction with hrg-2 and hrg-3. Taken together, we have identified two novel heme-responsive genes in metazoa that may play critical roles in modulating organismal heme homeostasis in C. elegans.Item THE FUNCTION OF MRN (MRE11-RAD50-NBS1) COMPLEX DURING WRN (WERNER) FACILITATED ATM (ATAXIA-TELANGIECTASIA MUTATED) ACTIVATION(2009) Ma, Junhao; Cheng, Wen-Hsing; Nutrition; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)WRN (Werner) protein is a member of the RecQ family showing helicase and exonuclease activity. WRN protein may lose function upon mutation and causes Werner syndrome (WS) which is an autosomal recessive, cancer-prone and premature aging disease. ATM (Ataxia-Telangiectasia mutated) protein initiates a signaling pathway in response to DNA double strand breaks (DSBs). Genomic disorder ataxia-telangiectasia (A-T) is associated with defective ATM. WRN protein is involved in ATM pathway activation when cells are exposed to DSBs associated with replication fork collapse. Because the Mre11-Rad50-Nbs1 (MRN) complex, a sensor of DSBs, is known to interact with WRN and ATM, we investigated whether the MRN complex mediates the WRN-dependent ATM pathway activation. In this study, we employed short-hairpin RNA to generate WRN- and Nbs1-deficient U-2 OS (osteosarcoma) cells. Cells were treated with clastogens which induce collapsed replication forks, thus provided proof for whether WRN facilitates ATM activation via MRN complex. This study serves as a basis for future investigation on the correlation between ATM, MRN complex and WRN, which will ultimately help understand the mechanism of aging and cancer.Item ASSOCIATION OF SINGLE NUCLEOTIDE POLYMORPHISMS WITH PHENOTYPIC PRODUCTION TRAITS IN BROILER CHICKENS(2009) Liu, Xuan; Porter, Tom E; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This research investigated the association between SNPs and phenotypic production traits in fat and lean chicken broiler lines. In previous research, eleven SNPs in the promoter regions of four candidate genes were selected. In this study, significant associations were detected between AKR1B10 SNP1 and SDC1 SNP1 and fat yield. SDC1 SNP1 was significantly associated with fat weight. SOD3 SNP2 was associated with breast yield. Five sire-SNP interactions and one sex-SNP interaction were significant. There was a significant interaction between sex and SDC1 SNP3 on muscle-related factor. GPC3 SNP1 interacted with time period on body weight from week 1 to week 9. QTLs on chromosomes 1, 3 and 4 for body fat were refined by incorporating these SNPs into QTL analysis. These genetic markers may be of great value for marker-assisted selection (MAS) for chickens with less abdominal fat as well as genetic markers for body fat accumulation in humans.Item Post-bottleneck inbreeding accumulation reduces fitness in laboratory populations of Tribolium castaneum under environmental stress(2008) Choiniere, Ashley Danielle; Siewerdt, Frank; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Populations are often driven to extinction due to low genetic diversity. One major cause for loss of genetic diversity in a population is a demographic bottleneck. A demographic bottleneck was imposed on twenty-one populations of Tribolium castaneum using multiple strategies. After recovering to original census numbers, the populations were subjected to stressful environments, and fitness was quantified. There was a significant decrease in additive genetic variance in all populations as a result of the bottleneck event (P<0.05). As estimated inbreeding accumulation increased, there was a decrease in the mean of fitness related traits, such as adult weight, total progeny, fecundity and survivorship. This relationship was best explained using quadratic models and became even more significant when the populations were under stress. This suggests that both dominance and epistatic gene effects are playing a role in phenotypic expression of traits and that expression may be flexible, supporting survival and fitness.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.Item Quantitative Trait Loci and Promoter Analysis of the Bovine Butyrophilin Gene(2004-01-27) Zegeye, Abiy; Mather, Ian H; Animal SciencesThe butyrophilin gene (BTN1A1) has been described in all mammalian species so far investigated. BTN1A1 is a likely QTL candidate that affects an economically important trait in dairy animals because it is specifically expressed in lactating mammary tissue and the gene product BTN1A1 may function in the secretion of milk lipid. Five PCR-RFLP intragenic markers were identified. Three of the five markers are bi-allelic, however, the two 5'-most markers may be multiallelic loci. The markers were further used to conduct a QTL analysis to examine any allelic substitution effects on economically important milk production traits, namely, total protein, percent protein, total fat, percent fat, somatic cell score, herd life, and milk yield. One significant effect was detected for percent protein. Other effects were not significant, but this could possibly be due to the skewed allelic frequency distribution, or because the variable nucleotides were either intronic or coded for a conservative amino acid substitution. The 5' flanking region of bBTN was cloned and sequenced. Computational and transient transfection assays were conducted to identify regions of bBTN that are important for its expression. A computational analysis was conducted to compare and analyze the 5' flanking region of cow, goat, human and mouse sequences. Several regions of homology were identified that code for shared binding motifs. However, neither the transcription start site (TSS) nor the other segments of similarity in the proximal promoter region were analogous to other 'milk protein genes' such as the caseins and α-lactalbumin, and other widely studied non-mammary-specific genes. Transient transfection assays in HC11 cells indicate the region from -1kb to -0.45 kb is sufficient to drive the expression of a reporter gene. bBTN appears to contain a novel set of elements that define the (TSS) and proximal promoter modules. A more incisive examination will circumscribe the major cis-acting elements.