Relevant bibliographies by topics / Microsatellite loci

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  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
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Academic literature on the topic 'Microsatellite loci'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 May 2024

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Journal articles on the topic "Microsatellite loci"

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England, Phillip R., David A. Briscoe, and Richard Frankham. "Microsatellite polymorphisms in a wild population of Drosophila melanogaster." Genetical Research 67, no. 3 (June 1996): 285–90. http://dx.doi.org/10.1017/s0016672300033760.

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SummaryHighly variable DNA polymorphisms called microsatellites are rapidly becoming the marker of choice in population genetic studies. Until now, microsatellites have not been utilized for Drosophila studies. We have identified eight polymorphic microsatellite loci in Drosophila melanogaster and used them to characterize the genetic variation in a wild population from the Tyrrell's winery in Australia. Microsatellites were isolated from a partial genomic DNA library. All microsatellites consist of (AC)n repeats ranging from n = 2 to n = 24. Six loci were assigned to chromosomal location by genetic mapping, with three loci on chromosome II, one locus on chromosome III and two loci on the X chromosome. Up to four microsatellite loci were multiplexed in the same reaction. Microsatellite variation is substantially greater than allozyme variation in the Tyrrell's Drosophila population. 80% of the microsatellite loci examined are polymorphic, compared with 28% of allozymes. The mean number of alleles per polymorphic locus is 5·2 in microsatellites compared with 30 in allozymes. The average observed heterozygosity of polymorphic microsatellites is 47% compared with 26% for allozymes. Microsatellite variation in Drosophila melanogaster is similar to that reported for other insects. Higher variability commends microsatellites over allozymes for genetic studies in Drosophila melanogaster.
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Yu, Kangfu, Soon J. Park, and Vaino Poysa. "Abundance and variation of microsatellite DNA sequences in beans (Phaseolus andVigna)." Genome 42, no. 1 (February 1, 1999): 27–34. http://dx.doi.org/10.1139/g98-100.

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Microsatellites or simple sequence repeats (SSRs) have been demonstrated to be abundant and hypervariable in some eukaryotic genomes. Although the presence of microsatellites is very well documented in many plant species, no information on microsatellites in beans (Phaseolus andVigna) is available. To assess the abundance and usefulness of bean microsatellites as genetic markers, 326 DNA sequences from the GenBank databases were searched. Sixty-one simple repetitive DNA sequences with 23 different types of repetitive DNA motifs were identified as potential microsatellites. Among these were 49 microsatellites from common bean (Phaseolus vulgaris) entries and 12 microsatellites from the genus Vigna. The most abundant type of microsatellite found in this search was that with di-nucleotide repeats of AT/TA. Microsatellites with tri- and tetra-nucleotide motifs were also identified. PCR analysis of 12 of the microsatellite-containing loci revealed that 11 of the 12 primer pairs could produce easily-scorable fragments, or groups of fragments. Allelic variation of the 11 loci was surveyed in 12 common bean inbred lines representing a diversity of germplasms. Seven of the 11 microsatellite loci were polymorphic and yielded 2-10 alleles. Analyses of the polymorphic loci in a common bean F6 recombinant inbred population showed that each segregated in a Mendelian fashion.Key words: microsatellite, simple sequence repeat, molecular marker, bean.
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Hale, M. L., A. M. Borland, and K. Wolff. "High degree of conservation of nuclear microsatellite loci in the genus Clusia." Genome 48, no. 5 (October 1, 2005): 946–50. http://dx.doi.org/10.1139/g05-048.

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In plants, microsatellites and their flanking DNA are rarely conserved across a whole genus, let alone other genera in the same family. Therefore, the possibility of using microsatellite primers developed for a species across a large number of plant species in the same genus is often limited. Remarkably, dinucleotide nuclear microsatellites developed for Clusia minor and for Clusia nemorosa amplified homologous microsatellites in species across the whole genus Clusia. In this present study, we report on the DNA sequence variation across the genus of 3 microsatellite loci with varying levels of variation. Compared over the species, there was a correlation between the lengths of the microsatellite loci. Interrupts occurred multiple times and did not seem to lead to the death of the microsatellite. These highly conserved markers will be useful for studying the variable reproductive systems in the genus Clusia.Key words: microsatellite, Clusia, cross-species amplification, microsatellite evolution.
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Colson, Isabelle, and David B. Goldstein. "Evidence for Complex Mutations at Microsatellite Loci in Drosophila." Genetics 152, no. 2 (June 1, 1999): 617–27. http://dx.doi.org/10.1093/genetics/152.2.617.

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Abstract Fifteen lines each of Drosophila melanogaster, D. simulans, and D. sechellia were scored for 19 microsatellite loci. One to four alleles of each locus in each species were sequenced, and microsatellite variability was compared with sequence structure. Only 7 loci had their size variation among species consistent with the occurrence of strictly stepwise mutations in the repeat array, the others showing extensive variability in the flanking region compared to that within the microsatellite itself. Polymorphisms apparently resulting from complex nonstepwise mutations involving the microsatellite were also observed, both within and between species. Maximum number of perfect repeats and variance of repeat count were found to be strongly correlated in microsatellites showing an apparently stepwise mutation pattern. These data indicate that many microsatellite mutation events are more complex than represented even by generalized stepwise mutation models. Care should therefore be taken in inferring population or phylogenetic relationships from microsatellite size data alone. The analysis also indicates, however, that evaluation of sequence structure may allow selection of microsatellites that more closely match the assumptions of stepwise models.
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Röder, Marion S., Victor Korzun, Bikram S. Gill, and Martin W. Ganal. "The physical mapping of microsatellite markers in wheat." Genome 41, no. 2 (April 1, 1998): 278–83. http://dx.doi.org/10.1139/g98-009.

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Microsatellite markers represent a new class of genetic markers in plants. Such markers reveal a high level of polymorphism even in species with a narrow genetic base, such as hexaploid wheat (Triticum aestivum L.). We used a large set of such markers and 25 deletion stocks of 'Chinese Spring' in a deletion-mapping experiment to study the physical distribution of dinucleotide microsatellite markers in homoeologous group 2 chromosomes of hexaploid wheat. Thirty-one microsatellite markers identified 14 loci in chromosome 2A, 9 loci in chromosome 2B, and 10 loci in chromosome 2D. The microsatellite loci were evenly distributed along the chromosome length, marking 18 of 27 defined physical intervals, including centromeric, interstitial, and telomeric regions. The apparent random distribution indicates that microsatellite markers provide excellent coverage of the wheat genome.Key words: deletion stocks, group 2 homoeologues, microsatellites, wheat.
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Kushny, James E. E., John W. Coffin, and Curtis Strobeck. "Genetic survey of caribou populations using microsatellite DNA." Rangifer 16, no. 4 (January 1, 1996): 351. http://dx.doi.org/10.7557/2.16.4.1277.

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Microsatellite loci are highly variable regions of eukaryotic DNA that consist of tandemly repeated sequences of one to six nucleotides in length. The use of microsatellites and the Polymerase Chain Reaction (PCR) are powerful tools for quantifying genetic variation within and among individual populations. Recently, we have developed primers for caribou that amplify 4 microsatellite loci. These microsatellite loci were used to survey the genetic variation in populations of Barren-ground caribou (Rangifer tarandus groenlandicus), Peary caribou (R.t. pearyi) and Woodland caribou (R.t. caribou) of Canada. The four loci examined were all polymorphic, revealing high levels of heterozygosity (> 0.74) in all of the study populations.
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Long, Dustin R., Adam Waalkes, Varun P. Panicker, Ronald J. Hause, and Stephen J. Salipante. "Identifying Optimal Loci for the Molecular Diagnosis of Microsatellite Instability." Clinical Chemistry 66, no. 10 (September 24, 2020): 1310–18. http://dx.doi.org/10.1093/clinchem/hvaa177.

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Abstract Background Microsatellite instability (MSI) predicts oncological response to checkpoint blockade immunotherapies. Although microsatellite mutation is pathognomonic for the condition, loci have unequal diagnostic value for predicting MSI within and across cancer types. Methods To better inform molecular diagnosis of MSI, we examined 9438 tumor-normal exome pairs and 901 whole genome sequence pairs from 32 different cancer types and cataloged genome-wide microsatellite instability events. Using a statistical framework, we identified microsatellite mutations that were predictive of MSI within and across cancer types. The diagnostic accuracy of different subsets of maximally informative markers was estimated computationally using a dedicated validation set. Results Twenty-five cancer types exhibited hypermutated states consistent with MSI. Recurrently mutated microsatellites associated with MSI were identifiable in 15 cancer types, but were largely specific to individual cancer types. Cancer-specific microsatellite panels of 1 to 7 loci were needed to attain ≥95% diagnostic sensitivity and specificity for 11 cancer types, and in 8 of the cancer types, 100% sensitivity and specificity were achieved. Breast cancer required 800 loci to achieve comparable performance. We were unable to identify recurrent microsatellite mutations supporting reliable MSI diagnosis in ovarian tumors. Features associated with informative microsatellites were cataloged. Conclusions Most microsatellites informative for MSI are specific to particular cancer types, requiring the use of tissue-specific loci for optimal diagnosis. Limited numbers of markers are needed to provide accurate MSI diagnosis in most tumor types, but it is challenging to diagnose breast and ovarian cancers using predefined microsatellite locus panels.
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Wang, Ying, Ming Kang, and Hongwen Huang. "Microsatellite Loci Transferability in Chestnut." Journal of the American Society for Horticultural Science 133, no. 5 (September 2008): 692–700. http://dx.doi.org/10.21273/jashs.133.5.692.

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Cross-species amplification of 55 microsatellite loci developed in european chestnut (Castanea sativa Mill.) and japanese chestnut (C. crenata Sieb & Zucc.) was tested in three chestnut species from China [C. mollissima Blume, C. seguinii Dode, and C. henryi (Skan.) Rehder & Wilson]. Among all the tested loci, 47 (85.5%), 47 (85.5%), and 44 (80%) were successfully amplified in each of the three Chinese species, respectively. All microsatellite loci tested from C. crenata successfully amplified in the Chinese species, while only 80.5%, 80.5%, and 73.2% of the loci originating from C. sativa amplified in the three Chinese species. The level of polymorphism and mean number of alleles was 58.2% and 4.12 for C. mollissima, 60% and 4.64 for C. seguinii, and 60% and 4.76 for C. henryi, with mean observed heterozygosity ranging from 0.440 to 0.549 and mean expected heterozygosity ranging from 0.506 to 0.615. Transferability of Castanea Mill. microsatellites provides a powerful tool for chestnut breeding programs and conservation genetic studies of Castanea species.
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McConnell, Stewart K., Patrick O'Reilly, Lorraine Hamilton, Jonathan M. Wright, and Paul Bentzen. "Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations." Canadian Journal of Fisheries and Aquatic Sciences 52, no. 9 (September 1, 1995): 1863–72. http://dx.doi.org/10.1139/f95-779.

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Atlantic salmon populations show low levels of genetic differentiation relative to other salmonid species, when surveyed by allozymes, and with mitochondrial DNA and nuclear ribosomal DNA markers. Here we report the application of three novel microsatellite VNTR loci to population differentiation in Atlantic salmon. A total of 232 microsatellites, cloned from Atlantic salmon, were classified as perfect, imperfect, and compound repeats. Microsatellite length, as in other teleosts, was significantly larger than published mammalian microsatellites. Primers for PCR amplification of three salmon microsatellites were designed. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for five populations from Nova Scotia, Canada, and from Europe. Nei's genetic distances of 0.02–0.9 were observed among populations. There was a clear discrimination between Canadian and European fish based on unique alleles present at two loci. These Atlantic salmon primers also amplify presumably homologous loci in nine other salmonid species. The polymorphic microsatellites loci reported here demonstrate great potential as genetic markers in population, breeding, and evolutionary studies.
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Ling, Chen, Wu Lixia, Hou Rong, Shen Fujun, Zhang Wenping, Tang Yao, Yuan Yaohua, Zhao Bo, and Zhang Liang. "Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey (Rhinopithecus roxellana)." Conservation Genetics Resources 12, no. 4 (April 3, 2020): 611–20. http://dx.doi.org/10.1007/s12686-020-01147-7.

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Abstract Microsatellite markers are popular for assigning parentage, but single-nucleotide polymorphisms (SNPs) have only been applied in this area recently. To evaluate these two markers which have been previously studied in golden snub-nosed monkeys, we genotyped 12 individuals using 37 microsatellite loci and 37 SNP markers. The data showed that 32 of 37 microsatellite loci were polymorphic, and most microsatellite loci were high informative (mean PIC = 0.599). Meanwhile, 24 of 37 SNP markers were polymorphic and most were low informative (mean PIC = 0.244). For microsatellites, the combined exclusion probability with one-parent-unknown/known (CE-1P/CE-2P) nearly reached 1, while for the SNP markers, CE-2P only reached 0.9582. Under the condition of one parent known/unknown, the CE-2P and CE-1P could meet the international human parental standard (0.9973) by using five or nine microsatellite loci respectively. For SNP markers, we doubled the loci (n = 48) and simulated parentage testing, and the data showed that the CE-2P was 0.998 while the CE-1P was still low. This result indicated that the SNP loci which we used here had low polymorphism and that more loci need to be developed in the future. In addition, we corrected one case of failed identification by excluding siblings and reducing the range of candidate paternities.
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Dissertations / Theses on the topic "Microsatellite loci"

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Chilakamarri, Sunita R. "Genetic differentiation in Alewife populations using microsatellite loci." Link to electronic thesis, 2005. http://www.wpi.edu/Pubs/ETD/Available/etd-053105-164623/.

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Hey, Grace Valasi, University of Western Sydney, of Science Technology and Environment College, and of Science Food and Horticulture School. "Identification of individual koalas: microsatellite analysis of faecal DNA." THESIS_CSTE_SFH_Hey_G.xml, 2003. http://handle.uws.edu.au:8081/1959.7/451.

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Current studies of koalas in the wild mainly rely on information gathered by traditional field methods, such as community sightings, spotlighting, radiotracking, animal trappings, ear tagging and faecal pellet incidence. Collection of faeces is potentially the most reliable source of non-invasively obtaining DNA samples, which can be used to identify specific individuals. This thesis demonstrated a simple, rapid and reproducible method of extracting DNA from Koala faecal pellets using a commercially available DNA extraction kit, shows the maximum age of pellets from which DNA can be reliably extracted and defines the conditions required for the long term storage of pellets before DNA extraction is carried out. Mitochondrial DNA PCR analysis provided a simple and rapid indication of the success of both the faecal DNA extraction and pellet collection process. The faecal DNA was successfully used for microsatellite analysis and the subsequent genetic profiling of individuals from within the Campbelltown Koala population. The study paves the way for the analysis of microsatellite loci in koala faecal pellet DAN to study populations, which are too sparsely distributed to allow the capture of individual koalas
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Field, Dawn. "Mutation, selection & the evolution of microsatellite loci in microbial genomes /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1998. http://wwwlib.umi.com/cr/ucsd/fullcit?p9911848.

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Dimsoski, Pero. "Variation in microsatellite loci and trait differences in Yorkshire and Large White /." The Ohio State University, 1996. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487935958845124.

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Henderson, Matt. "The effect of habitat fragmentation on the population genetic structure of the Western European hedgehog (Erinaceus europaeus)." Thesis, University of Southampton, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342656.

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Vishakha, FNU. "CHARACTERIZATION OF MICROSATELLITE LOCI AND PILOT POPULATION GENETIC ANALYSIS IN HICKORY SHAD, ALOSA MEDIOCRIS." VCU Scholars Compass, 2012. http://scholarscompass.vcu.edu/etd/422.

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The hickory shad (Alosa mediocris) is a relatively understudied species of the anadromous fish sub-family Alosinae. This study, the first population genetic analysis of this species, employed 12 neutral microsatellite loci to estimate genetic diversity and population structure in tributaries of lower Chesapeake Bay, Virginia including James River and its tributaries (Appomattox and Chickahominy Rivers), Rappahannock River, and Pamunkey River. Genetic variation was extremely low. Estimates of observed heterozygosity were lower than expected heterozygosity. Significant population structure was detected among the six samples (FST = 0.093, p = 0.01). Effective population sizes were low (Ne ranged from 2 to 134). The lack of genetic diversity, especially compared to that of the American shad, was striking and could be the result of a bottleneck that took place more than thirty years ago which may plausibly account for the low genetic variation observed across all populations.
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Cunningham, Christopher. "Colerectal cancer genetics : a study of chromosome 8p tumour suppressor loci and microsatellite instability." Thesis, University of Edinburgh, 1997. http://hdl.handle.net/1842/21177.

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Fourteen chromosome 8 polymorphic loci were analysed for loss of heterozygosity in 119 colorectal cancers selected at random. Loss of heterozygosity was detected in 59.6% (59/99) of informative cases. Markers were of sufficient density to allow the construction of a deletion map which delineated two discrete regions likely to contain tumour suppressor loci. A 4cM region at 8p22-21.3 between markers D8S133 and LPL and a further locus at 8p21-11.2, between markers D8S137 and D8S136, estimated to span some 17cM. Loss of heterozygosity on chromosome 8p was found to be independent of tumour site, Duke's stage, patient age, sex and survival. Analysis of 50 sporadic colorectal adenomas revealed a low frequency of chromosome 8p loss of heterozygosity, suggesting that the tumour suppressor loci are preferentially involved in the later stages of colorectal carcinogenesis. The role of defective DNA mismatch repair in colorectal cancer predisposition has been reported recently. These defects are manifested by microsatellite instability. Such instability was noted in tumour DNA during chromosome 8p loss of heterozygosity studies and the project was extended to investigate this phenomenon. The prevalence of microsatellite instability was determined in 245 colorectal cancers. 16.7% (41/245) displayed replication errors at one or more microsatellite loci, suggesting underlying errors in mismatch repair. Cancers displaying microsatellite instability tended to arise in the proximal colon, maintained nuclear diploidy and were associated with a significantly improved survival. The presence of replication errors was independent of patient age and sex, loss of heterozygosity at chromosomes 5q and 17p and immunohistochemistry for p53 protein. Loss of heterozygosity affecting chromosome 8p and defective DNA mismatch repair are frequent genetic abnormalities in colorectal cancers. This project provides important data localising the putative tumour suppressor genes to two discrete regions on chromosome 8p. This will aid future efforts towards cloning and identifying the genes involved. In addition, the prevalence and clinicopathological features of microsatellite instability have been established, in a large population of unselected colorectal cancers, allowing insight into the involvement of this mechanism in sporadic colorectal carcinogenesis.
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Cloutier, Alison. "Assessment of size homoplasy at three microsatellite loci in the California market squid Loligo opalescens." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/MQ61542.pdf.

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Paz-García, David A., Adrián Munguía-Vega, Tomas Plomozo-Lugo, and Amy Hudson Weaver. "Characterization of 32 microsatellite loci for the Pacific red snapper, Lutjanus peru, through next generation sequencing." SPRINGER, 2017. http://hdl.handle.net/10150/626030.

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We developed a set of hypervariable microsatellite markers for the Pacific red snapper (Lutjanus peru), an economically important marine fish for small-scale fisheries in the west coast of Mexico. We performed shotgun genome sequencing with the 454 XL titanium chemistry and used bioinformatic tools to search for perfect microsatellite loci. We selected 66 primer pairs that were synthesized and genotyped in an ABI PRISM 3730XL DNA sequencer in 32 individuals from the Gulf of California. We estimated levels of genetic diversity, deviations from linkage and Hardy-Weinberg equilibrium, estimated the frequency of null alleles and the probability of individual identity for the new markers. We reanalyzed 16 loci in 16 individuals to estimate genotyping error rates. Eighteen loci failed to amplify, 16 loci were discarded due to unspecific amplifications and 32 loci (14 tetranucleotide and 18 dinucleotide) were successfully scored. The average number of alleles per locus was 21 (+/- 6.87, SD) and ranged from 8 to 34. The average observed and expected heterozygosities were 0.787 (+/- 0.144 SD, range 0.250-0.935) and 0.909 (+/- 0.122 SD, range 0.381-0.965), respectively. No significant linkage was detected. Eight loci showed deviations from Hardy-Weinberg equilibrium, and from these, four loci showed moderate null allele frequencies (0.104-0.220). The probability of individual identity for the new loci was 1.46(-62). Genotyping error rates averaged 9.58%. The new markers will be useful to investigate patterns of larval dispersal, metapopulation dynamics, fine-scale genetic structure and diversity aimed to inform the implementation of spatially explicit fisheries management strategies in the Gulf of California.
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Castilho, da Costa A. Rita C. F. "Genetic analysis of European seabass (Dicentrarchus Labrax L.) from Portuguese waters using allozyme and microsatellite loci." Thesis, University of Stirling, 1998. http://hdl.handle.net/1893/21585.

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Genetic differentiation among juvenile samples of the European seabass (Dicentrarchus labrax) from the coast of Portugal is reported by means of two types of genetic markers: allozymes and microsatellites. Repeat samples were taken from 5 different nursery grounds (Aveiro, Foz, Obidos, Milfontes and Faro) along the coast of Portugal between November 1992 and February 1994. Starch-gel electrophoresis was used to assess the level and distribution of genetic variability of 38 loci. Six of these were found to be polymorphic at the 99% level and were used in population surveys: AAT-3*, ADA *, GPI-I *, GPI-2*, G3PDH-2*, SOD*. Statistical analysis revealed low but statistically significant multilocus F.'I (0.0108, p
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Book chapters on the topic "Microsatellite loci"

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Flores-Rentería, Lluvia, and Andrew Krohn. "Scoring Microsatellite Loci." In Methods in Molecular Biology, 319–36. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-389-3_21.

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Andrés, José A., and Steven M. Bogdanowicz. "Isolating Microsatellite Loci: Looking Back, Looking Ahead." In Methods in Molecular Biology, 211–32. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-228-1_12.

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Rajora, O. P., and M. H. Rahman. "Microsatellite DNA markers and their usefulness in poplars, and conservation of microsatellite DNA loci in Salicaceae." In Genetic Response of Forest Systems to Changing Environmental Conditions, 105–15. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-015-9839-2_9.

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Stefanini, F. M., and M. W. Feldman. "Microsatellite Loci and the Origin of Modern Humans: A Bayesian Analysis." In Evolutionary Theory and Processes: Modern Perspectives, 249–69. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4830-6_15.

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Chakraborty, Ranajit. "Statistical Issues Regarding the Use of Microsatellite Loci for Molecular Anthropological Studies." In Genomic Diversity, 223–35. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-4263-6_16.

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Fernandez-Silva, Iria, and Robert J. Toonen. "Optimizing Selection of Microsatellite Loci from 454 Pyrosequencing via Post-sequencing Bioinformatic Analyses." In Methods in Molecular Biology, 101–20. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-389-3_7.

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Eisen, Jonathan A. "Mechanistic basis for microsatellite instability." In Microsatellites: Evolution and Applications, 34–48. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780198504085.003.0004.

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Abstract The inherent instability of microsatellite loci makes them exceptionally useful for evolutionary and genetic studies. This instability is predominantly due to changes in the number of copies of the microsatellite repeat. Most copy number changes at microsatellites are caused by slip-strand mispairing errors during DNA replication. Some of these errors are corrected by exonucleolytic proofreading and mismatch repair, but many escape repair and become mutations. Thus microsatellite instability can be considered to be a balance between the generation of replication errors by slip-strand mispairing and the correction of some of these errors by exonucleolytic proofreading and mismatch repair. The factors that cause this process to occur much more frequently in microsatellites that in non-repeat containing DNA are discussed. However, not all microsatellites are equally unstable because not all are equally prone to this mutation process. The mechanisms by which a variety of factors cause this variation in stability among microsatellites are discussed.
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Schloitterer, Christian, and Thomas Wiehe. "Microsatellites, a neutral marker to infer selective sweeps." In Microsatellites: Evolution and Applications, 238–48. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780198504085.003.0018.

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Abstract In recent years microsatellites have become popular as a highly variable neutral marker. In natural populations, microsatellite variability is determined by new mutations, genetic drift, and selection at linked chromosomal regions. In this chapter. we focus on the consequences of directional selection on observed microsatellite variability in natural populations. A test statistic is introduced that permits the identification of such 'selective sweeps'. The test is designed to detect reduced genetic variation in a specific locus-population combination from a data set of several microsatellite loci in multiple populations. Theoretical considerations, however, predict that selective sweeps may only be detected where microsatellites have a mutation rate which is below a certain threshold.
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Glenn, Travis C., and Nancy A. Schable. "Isolating Microsatellite DNA Loci." In Methods in Enzymology, 202–22. Elsevier, 2005. http://dx.doi.org/10.1016/s0076-6879(05)95013-1.

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Hall, John. "Hidden Variation in Microsatellite Loci." In Forensic DNA Analysis, 199–220. CRC Press, 2013. http://dx.doi.org/10.1201/b15361-14.

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Conference papers on the topic "Microsatellite loci"

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Savichenko, Violetta, Svetlana Ramazanova, and Saida Guchetl. "Fragment analysis of microsatellite DNA loci for genotyping soybean varieties." In INTERNATIONAL SCIENTIFIC AND PRACTICAL CONFERENCE “CURRENT ISSUES OF BIOLOGY, BREEDING, TECHNOLOGY AND PROCESSING OF AGRICULTURAL CROPS” (CIBTA2022) (To the 110th anniversary of V.S. Pustovoit All-Russian Research Institute of Oil Crops). AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0140280.

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Рамазанова, С. A., and В. Г. Савиченко. "THE ANALYSIS OF POLYMORPHISM OF DNA MICROSATELLITE LOCI FOR SOYBEAN GENOTYPING." In Материалы I Всероссийской научно-практической конференции с международным участием «Геномика и современные биотехнологии в размножении, селекции и сохранении растений». Crossref, 2020. http://dx.doi.org/10.47882/genbio.2020.93.48.023.

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Strange, James P. "Sixteen novel microsatellite loci forMegachile rotundata(Hymenoptera: Megachilidae) and related taxa." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.115455.

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Savichenko, V. G., and S. A. Ramazanova. "THE IDENTIFICATION OF SOYBEAN VARIETIES OF THE BREEDING OF V.S. PUSTOVOIT ALL-RUSSIAN RESEARCH INSTITUTE OF OIL CROPS BY MICROSATELLITE ANALYSIS." In 11-я Всероссийская конференция молодых учёных и специалистов «Актуальные вопросы биологии, селекции, технологии возделывания и переработки сельскохозяйственных культур». V.S. Pustovoit All-Russian Research Institute of Oil Crops, 2021. http://dx.doi.org/10.25230/conf11-2021-97-101.

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The identification of breeding material and certification of varieties is of great importance for the protection of the copyright of breeders. Microsatellite DNA loci are effectively used for these purposes. The aim of the research was to identify the soybean varieties of the breeding of V.S. Pustovoit All-Russian Research Institute of Oil Crops using the previously tested 12 microsatellite markers. As a result of research, we obtained the unique sets of alleles for eight varieties; two varieties had identical alleles. We divided all soybean genotypes into two large clusters. We observed the closest genetic relation between the varieties Duar and Kora (the Armavir experimental station of V.S. Pustovoit All-Russian Research Institute of Oil Crops. The resulting sets of alleles can be used to develop molecular genetic passports.
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Ilyasov, R. A., A. G. Nikolenko, and H. W. Kwon. "GENETIC IMPROVEMENT OF HONEY BEES FOR KEEPING IN EXTREMAL CLIMATIC CONDITIONS." In V International Scientific Conference CONCEPTUAL AND APPLIED ASPECTS OF INVERTEBRATE SCIENTIFIC RESEARCH AND BIOLOGICAL EDUCATION. Tomsk State University Press, 2020. http://dx.doi.org/10.17223/978-5-94621-931-0-2020-55.

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Genetic improvement of honey bee populations based on molecular genetics features is faster and precision in comparison with morphometry and behavior-based methods. We developed the method based on nine nuclear microsatellite loci that allow a selection of most adaptive honey bee colonies by genetically defined features. Our study the heterozygosity of the dark European bee A. m. mellifera inhabiting the extremely cold region of the Ural Mountains to provide a marker-assisted selection for revealing the high adapted to extremely cold climate honey bee population can be applied for markerassisted selection of honey bees adapted to beekeeping in extremal climatic conditions.
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A.V., Vorobieva, Golovinov I.V., Alimova A.Sh, Gaidamachenko V.N., and Nebesikhina N.A. "ASSESSMENT OF THE GENETIC DIVERSITY OF THE RUSSIAN STURGEON BROOD STOCK OF THE DONSKOY STURGEON PLANT BY MICROSATELLITE NUCLEAR MARKERS." In II INTERNATIONAL SCIENTIFIC AND PRACTICAL CONFERENCE "DEVELOPMENT AND MODERN PROBLEMS OF AQUACULTURE" ("AQUACULTURE 2022" CONFERENCE). DSTU-Print, 2022. http://dx.doi.org/10.23947/aquaculture.2022.41-43.

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The article presents a study of the genetic diversity of the Russian sturgeon (Acipenser gueldenstaedtii) of the brood stock (RMS) of the Donskoy sturgeon hatchery (DOZ) using the analysis of microsatellite nuclear markers. In the course of the study, a general decrease in the heterozygosity of the population for four of the five loci studied was established, and in the study of the RMS population over the past two years, rare groups of alleles were identified that were not found in the sample for 2014. The data obtained can be used by the plant when drawing up crossbreeding schemes to preserve the overall allelic (genetic) diversity of the population.
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Zhongbao Li, Zhanlin Wang, Yuanyu Cao, Guiling Zhang, Ning Wu, Xiaoyun Lin, Zhihong Zhang, and Xinjiang Tian. "Notice of Retraction: Isolation and characterization of five new polymorphic microsatellite loci of coelomactra antiquata (Spengler)." In 2010 2nd Conference on Environmental Science and Information Application Technology (ESIAT 2010). IEEE, 2010. http://dx.doi.org/10.1109/esiat.2010.5568534.

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Ramazanova, Svetlana, Evgeny Badyanov, and Saida Guchetl. "Identification and validation of microsatellite DNA loci of the downy mildew (Plarg) resistance gene in sunflower." In INTERNATIONAL SCIENTIFIC AND PRACTICAL CONFERENCE “CURRENT ISSUES OF BIOLOGY, BREEDING, TECHNOLOGY AND PROCESSING OF AGRICULTURAL CROPS” (CIBTA2022) (To the 110th anniversary of V.S. Pustovoit All-Russian Research Institute of Oil Crops). AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0140282.

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Li, Jian, Zhenghang Wang, Bo Yang, Bin Li, Yunjie Song, Bei Zhang, Xiaochen Zhao, et al. "Abstract 5477: A novel loci-selected method for microsatellite instability detection validated on a large Chinese cohort." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-5477.

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Xiaoyun Lin, Yuanyu Cao, Zhongbao Li, Wenjing Li, Guiling Zhang, Zhanlin Wang, Ning Wu, Zhihong Zhang, and Xinjiang Tian. "Notice of Retraction: Isolation and characterization of ten new polymorphic microsatellite loci of the mud crab, Scylla paramamosain." In 2010 2nd Conference on Environmental Science and Information Application Technology (ESIAT 2010). IEEE, 2010. http://dx.doi.org/10.1109/esiat.2010.5568726.

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Reports on the topic "Microsatellite loci"

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Soller, Moshe (Morris), Hans Cheng, and Lyman Crittenden. Mapping the Chicken Genome, Including Loci Affecting Traits of Economic Importance. United States Department of Agriculture, September 1994. http://dx.doi.org/10.32747/1994.7568779.bard.

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A total of 195 microsatellites were added to the chicken genome map. Mapping of fifty known genes revealed a high degree of conserved linkage order between human and chicken genomes. A new, statistically powerful mapping design, the full-sib intercross line (produced by mating two parents, and intercrossing their progeny over a number of generations), was developed for use in species with high reproductive capacity. The Jerusalem Resource Population (JRP), now at the F12 generation, was established to implement this design i chickens. The biometrical picutre in the JRP is similar to that generally found in chicken populations; inbreeding effects were not observed. The F2 and F3 generations of the JRP were genotyped with respect to twelve production traits, using a battery of 23 microsatellites markers. The number of significant effects was twice that expected on chance alone, validating the high statistical power of the JRP with respect to QTL differentiating the parental lines. Selective DNA pooling, based on estimation of marker allele frequencies in pooled DNA samples, has been proposed to reduce high genotyping costs of QTL mapping. A method to correct for overlapping shadow bands of dinucleotide microsatellite markers in pooled DNA samples was developed and validated. In a retrospective study using this procedure, previously mapped loci affecting Marek's disease were successfully identified.
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Gall, Graham A. E., Gideon Hulata, Eric M. Hallerman, Bernard May, and Umiel Nakdimon. Creating and Characterizing Genetic Variation in Tilapia through the Creation of an Artificial Center of Origin. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7574344.bard.

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Five stocks of tilapia [oreochromis niloticus (on), red O. niloticus (ROn), O. aureus (Oa), O. mossambicus (Om), and Sarotherodon galilaeus (Sg)] were used to produce two-way (F1), three-way (3WC) and four-way crosses (4WC). Three 4WC groups, containing equal representation of all four species, formed the base population for a new synthetic stock, called an "artificial center of origin" (ACO). Four genomic maps were created using microsatellite and AFLP markers, two from a 3WC family [Om female and (Oa x ROn) male] and two from a 4WC family [(Om x Oas) females and (Sg x On) male]. Sixty-two loci segregating from the female parent of the 3WC mapped to 14 linkage groups while 214 loci from the male parent mapped to 24 linkage groups. Similarly, 131 loci segregating from the female parent of the 4WC mapped to 26 linkage groups and 118 loci from the male parent mapped to 25 linkage groups. Preliminary screening of an F2 and a 4WC family identified a number of loci associated with cold tolerance and body weight. These loci were clustered in a few linkage groups, suggesting they may be indicative of quantitative trait loci.
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Veilleux, Richard E., Jossi Hillel, A. Raymond Miller, and David Levy. Molecular Analysis by SSR of Genes Associated with Alkaloid Synthesis in a Segregating Monoploid Potato Family. United States Department of Agriculture, May 1994. http://dx.doi.org/10.32747/1994.7570550.bard.

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More than 15,000 anthers of an interspecific hybrid (CP2) between two diploid (2n=2x=24) potato species, Solanum chacoense (weedy) and S. phureja (cultivated), were cultured to generate a family of monoploid (haploid, 2n-1x=12) plants. Of 260 regenerated plants, 34 were monoploid, 210 diploid and 16 tetraploid. SSR analysis revealed that six monoploids were genetically identical and 14 diploids were homozygous, thus limiting the population to 42 (28 monoploids and 14 homozygous diploids). New microsatellite loci were developed for potato from database sequences (15), a conventional genomic library (6), an enriched library (18) and tomato (11). Of these, 13 were polymorphic in the CP2 family and 11 were used to study genetic segregatin. Four of 11 exhibited skewed segregation in the monoploid family. Seven of 18 microsatellite markers were polymorphic and informative on a set of 12 tetraploid potato cultivars. Acetylleptinidine (ALD) is the aglycone of leptines, a natural defense against insects, especially the highly destructuve Colorado potato beetle. ALD is absend in S. phureja but highly expressed in the S. chacoense parent of CP2. A backcross population between CP2 and tis S. phureja parent was used to examine segregation for ALD. Bulks of 10 backcross individuals that expressed ALD and 10 that did not were used to identify putative RAPD markers associatd with the trait. Of 80 primers tested, one putative marker amplified by OPQ02 was present in eight of ten individuals comprising the high bulk and absent in all 10 individuals comprising the low bulk. This is a putative marker for ALD expression in potato.
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Hulata, Gideon, and Graham A. E. Gall. Breed Improvement of Tilapia: Selective Breeding for Cold Tolerance and for Growth Rate in Fresh and Saline Water. United States Department of Agriculture, November 2003. http://dx.doi.org/10.32747/2003.7586478.bard.

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The main objective of this project was to initiate a breeding program to produce cold-tolerant and salinity-tolerant synthetic breeds of tilapia, from a base population consisting of a four-species hybrid population created under an earlier BARD project. A secondary objective was to estimate genetic parameters for the traits growth rate under fresh- and salt-water and for cold tolerance. A third objective was to place quantitative trait loci that affect these traits of interest (e.g., growth rate in fresh-water, salt-water and cold tolerance) on the growing linkage map of primarily microsatellite loci. We have encountered fertility problems that were apparently the result of the complex genetic structure of this base population. The failure in producing the first generation of the breeding program has forced us to stop the intended breeding program. Thus, upon approval of BARD office, this objective was dropped and during the last year we have focused on the secondary objective of the original project during the third year of the project, but failed to perform the intended analysis to estimate genetic parameters for the traits of interest. We have succeeded, however, to strengthen the earlier identification of a QTL for cold tolerance by analyzing further segregating families. The results support the existence of a QTL for cold tolerance on linkage group 15, corresponding to UNH linkage group 23. The results also indicate a QTL for the same trait on linkage group 12, corresponding to UNH linkage group 4.
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Weller, Joel I., Harris A. Lewin, and Micha Ron. Determination of Allele Frequencies for Quantitative Trait Loci in Commercial Animal Populations. United States Department of Agriculture, February 2005. http://dx.doi.org/10.32747/2005.7586473.bard.

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Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From these analyses it is not possible to determine allelic frequencies in the population at large, or whether the same alleles are segregating in different families. We proposed to answer this question by application of the "modified granddaughter design", in which granddaughters with a common maternal grandsire are both genotyped and analyzed for the economic traits. The objectives of the proposal were: 1) to fine map three segregating ETL previously detected by a daughter design analysis of the Israeli dairy cattle population; 2) to determine the effects of ETL alleles in different families relative to the population mean; 3) for each ETL, to determine the number of alleles and allele frequencies. The ETL on Bostaurusautosome (BT A) 6 chiefly affecting protein concentration was localized to a 4 cM chromosomal segment centered on the microsatellite BM143 by the daughter design. The modified granddaughter design was applied to a single family. The frequency of the allele increasing protein percent was estimated at 0.63+0.06. The hypothesis of equal allelic frequencies was rejected at p<0.05. Segregation of this ETL in the Israeli population was confirmed. The genes IBSP, SPP1, and LAP3 located adjacent to BM143 in the whole genome cattle- human comparative map were used as anchors for the human genome sequence and bovine BAC clones. Fifteen genes within 2 cM upstream of BM143 were located in the orthologous syntenic groups on HSA4q22 and HSA4p15. Only a single gene, SLIT2, was located within 2 cM downstream of BM143 in the orthologous HSA4p15 region. The order of these genes, as derived from physical mapping of BAC end sequences, was identical to the order within the orthologous syntenic groups on HSA4: FAM13A1, HERC3. CEB1, FLJ20637, PP2C-like, ABCG2, PKD2. SPP, MEP, IBSP, LAP3, EG1. KIAA1276, HCAPG, MLR1, BM143, and SLIT2. Four hundred and twenty AI bulls with genetic evaluations were genotyped for 12 SNPs identified in 10 of these genes, and for BM143. Seven SNPs displayed highly significant linkage disequilibrium effects on protein percentage (P<0.000l) with the greatest effect for SPP1. None of SNP genotypes for two sires heterozygous for the ETL, and six sires homozygous for the ETL completely corresponded to the causative mutation. The expression of SPP 1 and ABCG2 in the mammary gland corresponded to the lactation curve, as determined by microarray and QPCR assays, but not in the liver. Anti-sense SPP1 transgenic mice displayed abnormal mammary gland differentiation and milk secretion. Thus SPP 1 is a prime candidate gene for this ETL. We confirmed that DGAT1 is the ETL segregating on BTA 14 that chiefly effects fat concentration, and that the polymorphism is due to a missense mutation in an exon. Four hundred Israeli Holstein bulls were genotyped for this polymorphism, and the change in allelic frequency over the last 20 years was monitored.
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Weller, Joel, Harris Lewin, Micha Ron, and George Wiggans. Detection and Mapping of Genes Affecting Traits of Economic Importance in Dairy Cattle with the Aid of Molecular Genetic Markers. United States Department of Agriculture, December 1995. http://dx.doi.org/10.32747/1995.7613024.bard.

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Forty-seven poly-TG microsatellites were developed at the U of IL, and 11 genetic markers were developed at ARO, nine of which were poly-AGC microsatellites. Markers were typed on the reference families of CSIRO, Australia; GRANADA, Texas; and IRRF, Illinois, for chromosome assignment and linkage mapping. Nine North American al organizations contributed semen to the Dairy Bull DNA Repository (DBDR), which currently has 65,743 units from 3366 bulls. Semen was obtained for 31 out of 35 grandsires. Semen of 28 and 23 sons of two Israeli bulls was also collected. Eighteen grandsires were genotyped for 75 microsatellites. One thousand, three hundred and sixty-two sons with evaluation from 17 families were genotyped for 24 markers. Eleven thousand, six hundred and twenty sons genotypes were determined, of which 8,802 were informative. The genotype data was matched to the bulls' daughter yield deviations (DYD) for seven traits; milk, fat, and protein production; fat and protein percent; somatic cell concentration (SCS); and productive herd life. Seven loci had significant effects at p<0.05, but only two loci, TGLA263 and MGTG7, had significant effects at p<0.01, and the effect of TGLA263 on fat percentage was significant at p<0.0001. There was at least one significant effect for each of the seven traits analyzed.
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Weller, Joel, Harris Lewin, Micha Ron, George Wiggans, and Paul VanRaden. A Systematic Genome Search for Genes Affecting Economic Traits Dairy Cattle with the Aid of Genetic Markers. United States Department of Agriculture, April 1999. http://dx.doi.org/10.32747/1999.7695836.bard.

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The objectives were to continue collection of semen for the US dairy bull DNA repository, to conduct a systematic search of the Holstein genome for economically significant economic trait loci (ETL), to develop and refine statistical techniques for the analysis of the data generated, and to confirm significant effects by genotyping daughters i Israel and additional US sons. One-thousand-seventy-six sons of eight US grandsires were genotyped for 174 microsatellites located on all 29 autosomes. ETL were detected for milk production traits on seven chromosomes. ETL for milk and fat yield and fat and protein percentage on BTA3 was mapped to between the markers BL41 and TGLA263. The 95% confidence interval for the ETL affecting fat percentage on BTA14 localized this ETL between the contromere and chromosome position 11 cM. This ETL was verified in the Israeli cattle population by genotyping an independent sample of cows from seven families. The radiation hybrid data for the centromeric region of BTA14 is defined by a single linkage group. Order of Type I genes within this region, CYC-FADK-TG-SQLE, is conserved between human and cattle. Thus, HSA8, the human homologue of BTA14, can be used to identify candidate genes for the ETL.
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