Browsing by Subject "Microsatellites (Genetics)"
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Item Distribution and characterization of microsatellites in the emu genome (Dromaius novaehollandiae)(Texas Tech University, 1998-12) Roots, Ellen HFlightless birds, as compared to volant birds, have experienced a shift in evolutionary life-history strategy, and how this alteration is associated with C-value scores is a focus of this thesis. Examination of microsatellite probes representing four dinucleotides, nine trinucleotides and six tetranucleotides was used to estimate microsatellite frequencies in the emu (Dromaius novaehollandiae) genome in a library of 864 randomly-chosen recombinant cosmids. The average insert size was 26,774bp, with inserts ranging from 16,500 to 49,000bp. The primary cosmid library represents 1.46% percent of the emu haploid genome (estimated at 1.58xl09bp). The total number of microsatellite sites, interspersion rates and confidence intervals were calculated. The expected and observed frequencies of co-occurring microsatellites were calculated, and a chi-square test performed for significance. The distribution and characterization of the microsatellites were discussed within the comparative framework of other genomes from the literature. The cosmid library was probed with emu genomic DNA to determine the percent of single-copy DNA, which was estimated to be a minimum of 28.6%.Item Microsatellite evolution in mice (Apodemus): origin of alleles, multiple paternity, and mutation rate at Chernobyl(Texas Tech University, 1999-05) Makova, Kateryna D.The studies of fauna at Chemobyl are very complex. They involve obtaining permits to the restricted zone, intensive field work with exposure to radiation, precise cataloging of skins and tissues in the museum, laboratory molecular biology work and sophisticated data analysis. This requires a collaborative effort. Several papers were outlined as a function of my dissertation. Their status and correspondence to the chapters of the dissertation are outlined in Table 1.1. The author line reflects the complexity of work at Chernobyl and the need to have both field and laboratory analyses. The choice of mice of the genus Apodemus was dictated by their abundance in both control and zone locations (Baker et al. 1996). In addition, Apodemus is closely related to Mus and Rattus: all three genera belong to the same subfamily (Murinae). The original idea was to test microsatellite primer pairs that were shown to successfully amplify both Mus and Rattus DNA on DNA from Apodemus. Four primer pairs specific to both Mus and Rattus microsatellites in genes encoding tumor necrosis factor, nerve growth hormone, insulin-like growth factor II and c-myc oncogene (Moore ef al. 1991) were used for amplification of Apodemus DNA. Consistently clean amplification products could not be obtained. This is in agreement with Kondo etal. (1993), who used Rattus microsatellite primers to amplify mouse Mus DNA and vice versa. Less than 10% of primer pairs they tested amplified DNA from the other species and gave polymorphic PCR products. Thus, I was faced with the challenge of developing microsatellites specifically for Apodemus.Item The evaluation of seven microsatellite markers and real time ultrasound information as tools for selecting animals for improved carcass characteristics and beef tenderness(Texas Tech University, 2002-12) Barham, Brett LeeThis study evaluated seven published bovine microsatellite markers selected from the USDA-MARC database for their usefulness as a selection tool for beef tenderness. Data from steers from ten different sire breeds were sorted into the top (upper tail, n = 25) and bottom (lower tall, n = 25) steers for average daily gain, marbling score, rib eye area, and Warner-Bratzler shear force (WBS) following a 14 d aging treatment. The resulting 200 animals were genotyped by a commercial laboratory (Celera AgGen, Davis, CA) for microsatellite markers BMC1501 (Leptin), BMC9001 (Nebulin), BMS 1678 (Thyroglobulin), BY5 (Myostatin), URB011 (Calpain), CAST (Calpastatin), and BM2394 (WBS). For all but one marker, additional alleles were discovered in the study. Additionally, analysis revealed that several markers had significant effects on some carcass and tenderness traits. These results imply that it may be possible to select for unique alleles to help Improve beef tenderness. Moreover, the study analyzed the Impact of growth Implants, sire breed and sire on carcass value and profitability. Implanted animals showed an increased carcass value of over $40 per head over non-Implanted animals. There was a range of sire EPD's for carcass value of $67 (-$37 to $30) from all sires in the study, indicating that sire selection can be a very important aspect of profitability in a retained ownership program. The decision to retain ownership is often a financial risk, therefore it is important to consider all management options that have a potential to maximize profit. Realized profit from retaining ownership was higher for animals implanted (P < 0.05). Non-implanted animals had a negative LS means for realized profit (-$27 per animal), while both SS and SR implant treatments had positive realized profit ($32 and $15 per head, respectively). The study also evaluated a new real time ultrasound software package to determine accuracy of prediction of carcass traits and tenderness. Pearson correlation coefficients between carcass fat thickness and ultrasound fat thickness was highly correlated (r = 0.81). Similarly, Spearman's correlation coefficient was also highly correlated for ultrasound fat thickness and carcass fat thickness (r = 0.84). Analysis of variance results indicated that ultrasound fat thickness measurements accounted for a significant amount of carcass fat thickness variation (R^= 0.65, P< 0.0001). Pearson correlation coefficients between average percent chemical fat and marbling score with ultrasound percent intramuscular fat was 0.519 and 0.600, respectively. Pearson correlation coefficient between the carcass ribeye area and ultrasound ribeye area was insignificant at 0.063 (P = 0.6132) as was the Spearman's correlation coefficient (r = 0.086; P = 0.4938). Analysis of variance between ultrasound ribeye area revealed that it failed to account for a significant amount of variation in carcass ribeye measurements (R^ = 0.004, P = 0.613). Results indicated that the software does not accurately predict ribeye area. The unique aspect of the software utilized in the study is the ability to predict tendemess. However, the data revealed an Insignificant correlation between ultrasound tenderness score and WBS or any sensory panel tenderness ratings. Additionally, analysis of variance failed to detect an association between ultrasound tenderness scores and WBS and sensory panel scores.