Browsing by Subject "SNP"
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Item Comparative Genomics of Gossypium spp. through GBS and Candidate Genes ? Delving into the Controlling Factors behind Photoperiodic Flowering(2013-08-09) Young, Carla Jo LoganCotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photoperiodism. Traditionally, due to differing floral times, wild and cultivated cotton species were unable to be bred together in many commercial production areas world-wide. This worldwide breeding problem has inhibited new trait incorporation. Before favorable traits from undomesticated cotton could be integrated into cultivated elite lines using marker-assisted selection breeding, the markers associated with photoperiod independence needed to be discovered. In order to increase information about this debilitating trait, we set out to identify informative markers associated with photoperiodism. This study was segmented into four areas. First, we reviewed the history of cotton to highlight current problems in production. Next, we explored cotton?s floral development through a study of floral transition candidate genes. The third area was an in-depth analysis of Phytochrome C (previously linked to photoperiod independence in other crops). In the final area of study, we used Genotype-By-Sequencing (GBS), in a segregating population, was used to determine photoperiod independence associated with single nucleotide polymorphisms (SNPs). In short, this research reported SNP differences in thirty-eight candidate gene homologs within the flowering time network, including photoreceptors, light dependent transcripts, circadian clock regulators, and floral integrators. Also, our research linked other discrete SNP differences, in addition to those contained within candidate genes, to photoperiodicity within cotton. In conclusion, the SNP markers that our study found may be used in future marker assisted selection (MAS) breeding schemas to incorporate desirable traits into elite lines without the introgression of photoperiod sensitivity.Item Environmental and genetic strategies to improve carotenoids and quality in watermelon(Texas A&M University, 2007-04-25) Bang, Hae JeenThe evaluation of environmental and genotypic effects on fruit physical and chemical characteristics enables assessment of the feasibility of selecting diploid and/or triploid cultivars for either specific or more diverse locations. Isolation and characterization of genes encoding enzymes in the carotenoid biosynthetic pathway provides fundamental genetic information which can facilitate breeding of watermelon cultivars having desirable flesh colors and enhanced beneficial carotenoids. For the environmental studies, the effects of deficit irrigation on lycopene content, total soluble solids, firmness, and yield of diploid and triploid watermelon were evaluated in different locations and growing seasons. Irrigation regimes were 1.0 evapotranspiration (ET), 0.75 ET, and 0.5 ET. To investigate if there is a consistent response in cultivars across diverse locations, studies were conducted in three distinct Texas regions. Deficit irrigation reduced total marketable yield, and increased the yield of small fruits. Location and irrigation regimes had major influences on yield. Soluble solids content increased with deficit irrigation at 0.5 ET in triploids, but not in diploids. Flesh firmness also increased in triploids compared to diploids. Lycopene content increased with maturity at all irrigation regimes and cultivars. This work confirms that deficit irrigation directly reduces yield, but does not reduce lycopene and fruit quality of the triploids used in this study. From the genetic studies, a total of eight genes encoding enzymes in the carotenoid biosynthetic pathway were isolated and characterized. Two members of the phytoene synthase (PSY) gene family were identified; PSY-A was expressed in all type of tissues, but PSY-B transcript was detected only in ovary, leaf, and root tissues. Gene expression of carotenoid isomerase (CRTISO) was not detected in salmon yellow. A color inheritance study of watermelon flesh indicated that a single gene might determine color difference between canary yellow and red without an inhibitory effect. A cleaved amplified polymorphic sequence (CAPS) marker developed from the SNP marker tagging two different lycopene ????-cyclase (LCYB) alleles cosegregated perfectly with color phenotypes. It was concluded that color determination may be due to a reduced activity of LCYB enzyme in red, whereby a phenylalanine is conserved among canary yellow and valine is conserved among red watermelon.Item Estimating population histories using single-nucleotide polymorphisms sampled throughout genomes(2013-05) McTavish, Emily Jane Bell; Hillis, David M., 1958-Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We used 47,506 single-nucleotide polymorphisms (SNPs) to investigate cattle population history. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. We found that New World cattle breeds, as well as many related breeds of cattle in southern Europe, exhibit ancestry from both the taurine and indicine lineages. Although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. We extended these analyses to compare timing of admixture in several breeds of taurine-indicine hybrid origin. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture. By comparing test individuals to standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed individuals using the SBS metric. We genotyped SNP loci using the bovine 50K SNP panel. The selection of sites to include in SNP analyses can influence inferences from the data, especially when particular populations are used to select the array of polymorphic sites. To test the impact of this bias on the inference of population genetic parameters, we used empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We compared the inference of population histories for simulated data sets across different ascertainment conditions using F[subscript ST] and principal components analysis (PCA). Ascertainment bias that results in an over-representation of within-group polymorphism decreases estimates of F[subscript ST] between groups. Geographically biased selection of polymorphic SNPs changes the weighting of principal component axes and can bias inferences about proportions of admixture and population histories using PCA. By combining empirical and simulated data, we were able to both test methods for inferring population histories from genomic SNP data and apply these methods to practical problems.Item Genetic Analysis of Bread Making Quality Stability in Wheat using a Halberd X Len Recombinant Inbred Line Population(2012-07-16) Poudel, AshimaWheat grain quality has a complex genetic architecture heavily influenced by the growing environment. Consistency in wheat quality not only affects the efficiency of milling and baking but also the quality of end-use products. The objectives of this study were to 1) analyze the different wheat quality parameters in Recombinant Inbred Lines (RILs) grown under different environments, and 2) to identify Quantitative Trait Loci (QTLs) associated with quality stability in RILs grown under different environments. A set of 180 RILs derived from two spring wheat lines 'Halberd' and 'Len' were grown at Uvalde and College Station TX, in the 2009/2010 growing season and at Chillicothe and College Station TX, in 2010/2011 growing seasons. The experiment was laid out in Randomized Complete Block Design (RCBD) with four replications within each location. Each line was tested for multiple quality traits that included grain hardness, protein content, dough mixing properties and bread baking quality using Single Kernel Characterization System (SKCS), Near-Infrared Reflectance Spectrometry (NIRS) analysis, mixograph and the Sodium Dodecyl Sulfate Sedimentation (SDSS) test. Genetic linkage map construction was carried out with 116 single nucleotide polymorphism (SNP) markers in the RILs. Then composite interval mapping was carried out to identify QTLs associated with quality traits. The SDSS column height was positively correlated across four environments. Similarly, it was found to have significant positive correlation with mixing tolerance and peak time within and also across locations. However, the SDSS was negatively correlated with the hardness index. The protein percent was not significant with any of the quality traits within and across environments. We were able to detect many QTLs for different quality traits but most of them were site specific. Only a few QTLs were consistent across environments. Most of the QTLs for quality traits i.e., SDSS, peak time, mixing tolerance and hardness index were identified on chromosome 1B. We were able to detect overlapped QTLs for SDSS column height and mixing tolerance on chromosome 1B. Furthermore, overlapping QTLs for mixing tolerance and peak time were detected on an unknown chromosome. We also detected overlapping QTLs for hardness index on chromosome 1B. We identified one stable QTL for SDSS column height on chromosome 4B. This QTL was detected based on the coefficient of variation (CV) for SDSS in four different environments.Item Genomic Differences Between Highly Fertile and Sub-Fertile Holstein Dairy Heifers(2012-07-16) Navarrette, Ashley ElizabethInfertility in dairy cattle remains a major economic loss to dairy producers. Identifying dairy cattle with superior genetic potential for improved fertility would increase dairy farm profitability. Dairy heifers were classified into two groups based upon services per conception (SPC); those animals with a single SPC were determined to be highly fertile and animals with greater than or equal to 4 SPC were classified as sub-fertile. Whole genome association analysis was performed on 20 individual heifers from each group utilizing a 777K highly density (HD) single nucleotide polymorphism (SNP) chip. Genomic data were evaluated utilizing PLINK, a whole genome association analysis toolset, and 570,620 SNP were available for analysis with a total of 39 samples being analyzed. Forty-four SNP were determined to be associated with fertility classification (P <= 0.00001) and were located on Bos taurus chromosome (BTA) 2, 4, 9, 19, and 26. The SNP and ranges between SNP were analyzed using BLAST-Like Alignment Tool (BLAT); SNP were associated with 5 candidate genes for reproduction. The SNP on BTA 2 were located within the region coding for the non-imprinted Prader-Willi/Angelman syndrome 2 (NIPA2) gene, which is involved in gestational magnesium transport. Also on BTA 2, SNP were identified within the region encoding for cytoplasmic fragile X mental retardation 1 (FMR1) interaction protein 1 (CYFIP1). The CYFIP1 gene is involved with the functionality of FMR1 and has been linked to premature ovarian failure in humans. Additionally, 3 SNP on BTA 9 were located near monofunctional C1-tetrahydrofolate synthase (MTHFD1L), which has been linked to neural tube defects during gestation in humans A difference in allele frequency was observed between the two groups for SNP located on BTA19 in proximity to two genes, zinc finger 18 (ZNF18) and mitogen activated protein kinase 4 (MAP2K4). The ZNF18 motif and MAP2K4 were found to be involved in heart development of the early embryo and associated with toll-like receptors (TLR) involved in gonadotropin releasing hormone (GnRH) signaling, respectively. The involvement of one or all of these genes may further explain reduced fertility in dairy cattle.Item Identification of Signatures of Selection in Bos Taurus Beef and Dairy Cattle Using Genome-wide SNP Genotypes(2010-10-12) Choi, Jung WooThe objectives of this study were to identify signatures of selection in Bos taurus beef and dairy cattle populations and to annotate regions of selection with gene, function and QTL information. Differences in minor allele frequencies, population-average FST, population-specific FST, and integrated extended haplotype homozygosity scores were applied to a subset of the bovine HapMap data to characterize signatures of selection in 7 Bos taurus beef and 5 Bos taurus dairy cattle populations. Numerous single nucleotide polymorphisms (SNP) exhibited evidence of selection across the genome and regions of BTA2 and BTA14 that are considered to be under positive selection in beef and dairy cattle, respectively, were highlighted. The current density of SNP limited our ability to annotate regions putatively under selection because most SNP in the assay were intergenic. This is likely because of the betweenbreed SNP discovery method that was used, which typically identifies SNP with higher allele frequencies.