Relevant bibliographies by topics / Microsatellites analysi

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Academic literature on the topic 'Microsatellites analysi'

Author: Grafiati
Published: 11 March 2023

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Journal articles on the topic "Microsatellites analysi"

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Harr, Bettina, and Christian Schlötterer. "Long Microsatellite Alleles in Drosophila melanogaster Have a Downward Mutation Bias and Short Persistence Times, Which Cause Their Genome-Wide Underrepresentation." Genetics 155, no. 3 (July 1, 2000): 1213–20. http://dx.doi.org/10.1093/genetics/155.3.1213.

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Abstract Microsatellites are short tandemly repeated DNA sequence motifs that are highly variable in most organisms. In contrast to mammals, long microsatellites (>15 repeats) are extremely rare in the Drosophila melanogaster genome. To investigate this paucity of long microsatellites in Drosophila, we studied 19 loci with exceptionally long microsatellite alleles. Inter- and intraspecific analysis showed that long microsatellite alleles arose in D. melanogaster only very recently. This lack of old alleles with many repeats indicated that long microsatellite alleles have short persistence times. The size distribution of microsatellite mutations in mutation-accumulation lines suggests that long alleles have a mutation bias toward a reduction in the number of repeat units. This bias causes the short persistence times of long microsatellite alleles. We propose that species-specific, size-dependent mutation spectra of microsatellite alleles may provide a general mechanism to account for the observed differences in microsatellite length between species.
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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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Zhou, Wenchun, Frederic L. Kolb, Guihua Bai, Gregory Shaner, and Leslie L. Domier. "Genetic analysis of scab resistance QTL in wheat with microsatellite and AFLP markers." Genome 45, no. 4 (August 1, 2002): 719–27. http://dx.doi.org/10.1139/g02-034.

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Three chromosomal regions associated with scab resistance were detected in a common cultivar, Ning7840, by microsatellite and AFLP analysis. Six microsatellites on chromosome 3BS, Xgwm389, Xgwm533, Xbarc147, Xgwm493, Xbarc102, and Xbarc131, were integrated into an amplified fragment length polymorphism (AFLP) linkage group containing a major quantitative trait locus (QTL) for scab resistance in a mapping population of 133 recombinant inbred lines (RILs) derived from 'Ning7840' × 'Clark'. Based on single-factor analysis of variance of scab infection data from four experiments, Xgwm533 and Xbarc147 were the two microsatellite markers most tightly associated with the major scab resistance QTL. Interval analysis based on the integrated map of AFLP and microsatellite markers showed that the major QTL was located in a chromosome region about 8 cM in length around Xgwm533 and Xbarc147. Based on mapping of six microsatellite markers on eight 3BS deletion lines, the major QTL was located distal to breakage point 3BS-8. In total, 18 microsatellites were physically located on different subarm regions on 3BS. Two microsatellites, Xgwm120 and Xgwm614, were significantly associated with QTL for scab resistance on chromosome 2BL and 2AS, respectively. The resistance alleles on 3BS, 2BL, and 2AS were all derived from 'Ning7840'. Significant interaction between the major QTL on 3BS and the QTL on 2BL was detected based on microsatellite markers linked to them. Using these microsatellite markers would facilitate marker-assisted selection to improve scab resistance in wheat.Key words: Fusarium head blight, quantitative trait locus, physical mapping, Triticum aestivum L.
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Azmir, I. A., I. S. Md-Yasin, and Y. Esa. "Microsatellite Marker Mining Using PCR-Based Isolation of Microsatellite Arrays (PIMA) Method on Blue-Spotted Mudskipper, Boleophthalmus Boddarti." IOP Conference Series: Earth and Environmental Science 995, no. 1 (April 1, 2022): 012051. http://dx.doi.org/10.1088/1755-1315/995/1/012051.

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Abstract Microsatellites are small and are codominant markers that can be amplified with polymerase chain reaction. Both prokaryotic and eukaryotic organisms possess large amounts of the microsatellites repeat. Many microsatellites have high mutation rates that generate the high levels of allelic diversity necessary for genetic studies of processes acting on ecological time scales. The high variability of microsatellites provided the foundation for their successful application in a wide range of fundamental and applied fields of biology. However, de novo isolation is needed for most species hence in this study we tried to mine the microsatellite marker using PCR-based isolation of microsatellite arrays (PIMA) on Blue spotted mudskipper, Boleophthalmus boddarti a fish uniquely restricted to coastal and estuarine habitat was also commercially important. Out of three trials, seven microsatellite repeats were detected but only three repeat types (AAG)4, (TCAG)3 and (CT)4 can be useful as microsatellite marker following PHOBOS V3.3.12 analysis. Meanwhile, the detection of octa (AATACAT)2, penta (TGACA)2 and heptanucleotides (GGAGATA)2 were unable to be continued as functional microsatellite marker as there were missense variants and interruptions detected either on forward or reverse strand of the repeat. Thus, PIMA method could be considered as tedious and detected low yields of microsatellite markers. Nevertheless, the conventional method for generating microsatellite markers from PCR based methods could be done with in silico mining of microsatellite sequences from DNA sequence databases or next generation sequencing (NGS).
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White, E., R. Sahota, and S. Edes. "Rapid microsatellite analysis using discontinuous polyacrylamide gel electrophoresis." Genome 45, no. 6 (December 1, 2002): 1107–9. http://dx.doi.org/10.1139/g02-084.

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A method for screening large numbers of samples for microsatellites using discontinuous, non-denaturing polyacrylamide gels and rapid fluorescent gel staining is described. Disc electrophoresis on slab gels provides high-resolution of PCR products. It is useful for collecting population data once microsatellite loci have been characterized.Key words: microsatellite, discontinuous polyacrylamide gel electrophoresis, non-denaturing
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Buschiazzo, E., and N. J. Gemmell. "Evolutionary and phylogenetic significance of platypus microsatellites conserved in mammalian and other vertebrate genomes." Australian Journal of Zoology 57, no. 4 (2009): 175. http://dx.doi.org/10.1071/zo09038.

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Building on the recent publication of the first monotreme genome, that of the platypus, and the discovery that many platypus microsatellites are found in the genomes of three mammals (opossum, human, mouse) and two non-mammalian vertebrates (chicken, lizard), we investigated further the evolutionary conservation of microsatellites identified in the monotreme lineage and tested whether the conservation of microsatellites we observe in vertebrates has phylogenetic signal. Most conserved platypus microsatellites (75%) were found in one species, with the platypus sharing many more microsatellites with mammals than with reptiles (83% versus 30%). Within mammals, unexpectedly, many more platypus microsatellites had orthologues in the opossum genome than in that of either human or mouse, which was at odds with the very well supported view that monotremes diverged from a lineage containing both eutherians and marsupials (Theria hypothesis). We investigated the phylogenetic significance of microsatellite conservation through Bayesian and maximum parsimony tree reconstruction using presence/absence data of microsatellite loci conserved in a total of 18 species, including the platypus. Although models of evolution implemented in current phylogenetic reconstruction algorithms are not tailor-made for microsatellite data, we were able to construct vertebrate phylogenies that correspond well to the accepted mammalian phylogeny, with two of our three reconstructions supporting the Theria hypothesis. Our analysis provides ground for new theoretical development in phylogeny-based analyses of conserved microsatellite data.
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Tanck, M. WT, A. P. Palstra, M. van de Weerd, C. P. Leffering, JJ van der Poel, H. Bovenhuis, and J. Komen. "Segregation of microsatellite alleles and residual heterozygosity at single loci in homozygous androgenetic common carp (Cyprinus carpio L.)." Genome 44, no. 5 (October 1, 2001): 743–51. http://dx.doi.org/10.1139/g01-072.

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Thirty-three androgenetic progeny groups of common carp were analysed using 11 microsatellite markers to (i) verify the homozygous status of the 566 androgenetic individuals, (ii) analyse the microsatellite allele segregation, and (iii) study the possible association of microsatellite alleles with phenotypic traits. In total, 92% of the androgenetic individuals proved to be homozygous at all 11 loci. Forty-three of the 47 heterozygous individuals were heterozygous at a single locus only. This heterozygosity was probably due to DNA fragments caused by UV irradiation of the eggs, although the maternal origin of the fragments could not be proved beyond doubt. Screening with 11 microsatellites also revealed two linkage groups, a segregation distortion at two microsatellite loci, and the possible association of some microsatellites with mass, length, stress-related plasma cortisol levels, and basal plasma glucose levels. The success of the linkage and association study could be explained by a low recombination frequency due to high chiasma interference. This would imply a relatively short genetic map for common carp.Key words: doubled haploids, residual heterozygosity, microsatellite allele segregation, linkage analysis, common carp.
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Wang, Ying, Mingjie Chen, Hong Wang, Jing-Fang Wang, and Dapeng Bao. "Microsatellites in the Genome of the Edible Mushroom,Volvariella volvacea." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/281912.

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Using bioinformatics software and database, we have characterized the microsatellite pattern in theV. volvaceagenome and compared it with microsatellite patterns found in the genomes of four other edible fungi:Coprinopsis cinerea,Schizophyllum commune,Agaricus bisporus,andPleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in theV. volvaceagene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides) outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes.
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Feng, Xiaochuan, Stephen M. Rich, Donna Akiyoshi, James K. Tumwine, Addy Kekitiinwa, Nicolette Nabukeera, Saul Tzipori, and Giovanni Widmer. "Extensive Polymorphism in Cryptosporidium parvumIdentified by Multilocus Microsatellite Analysis." Applied and Environmental Microbiology 66, no. 8 (August 1, 2000): 3344–49. http://dx.doi.org/10.1128/aem.66.8.3344-3349.2000.

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ABSTRACT Restriction fragment length polymorphism and DNA sequence analysis discern two main types of Cryptosporidium parvum. We present a survey of length polymorphism at several microsatellite loci for type 1 and type 2 isolates. A total of 14 microsatellite loci were identified from C. parvum DNA sequences deposited in public databases. All repeats were mono-, di-, and trinucleotide repeats of A, AT, and AAT, reflecting the high AT content of the C. parvum genome. Several of these loci showed significant length polymorphism, with as many as seven alleles identified for a single locus. Differences between alleles ranged from 1 to 27 bp. Karyotype analysis using probes flanking three microsatellites localized each marker to an individual chromosomal band, suggesting that these markers are single copy. In a sample of 19 isolates for which at least three microsatellites were typed, a majority of isolates displayed a unique multilocus fingerprint. Microsatellite analysis of isolates passaged between different host species identified genotypic changes consistent with changes in parasite populations.
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Kaundun, Shiv Shankhar, and Satoru Matsumoto. "Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis." Genome 45, no. 6 (December 1, 2002): 1041–48. http://dx.doi.org/10.1139/g02-070.

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The advantage of the cross transferability of heterologous chloroplast and nuclear microsatellite primers was taken to detect polymorphism among 24 tea (Camellia sinensis (L.) O. Kuntze) genotypes, including both the assamica and the sinensis varieties. Primer information was obtained from the closely related Camellia japonica species for four nuclear microsatellites, and from Nicotiana tabaccum for seven universal chloroplast microsatellites. All of the nuclear microsatellite loci tested generated an expected DNA fragment in tea, revealing between three and five alleles per locus. Four out of the seven chloroplast microsatellites primers amplified positively, and of these only one was polymorphic with three alleles, which is in agreement with the conserved nature of chloroplast microsatellites at the intraspecific level. A factorial correspondence analysis carried out on all genotypes and nuclear microsatellite alleles separated the assamica and sinensis genotypes into two groups, thus demonstrating the value of these markers in establishing the genetic relationship between tea varieties. Genetic diversity measured with nuclear microsatellites was higher than that measured with other types of molecular markers, offering prospects for their use in fingerprinting, mapping, and population genetic studies, whereas polymorphisms detected at a cpSSR locus will allow the determination of plastid inheritance in the species. Key words: tea, Camellia sinensis, SSR, microsatellites, genetic diversity.
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Dissertations / Theses on the topic "Microsatellites analysi"

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Jentzsch, Iris Miriam Vargas. "Comparative genomics of microsatellite abundance: a critical analysis of methods and definitions." Thesis, University of Canterbury. Biological Sciences, 2009. http://hdl.handle.net/10092/4282.

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This PhD dissertation is focused on short tandemly repeated nucleotide patterns which occur extremely often across DNA sequences, called microsatellites. The main characteristic of microsatellites, and probably the reason why they are so abundant across genomes, is the extremely high frequency of specific replication errors occurring within their sequences, which usually cause addition or deletion of one or more complete tandem repeat units. Due to these errors, frequent fluctuations in the number of repetitive units can be observed among cellular and organismal generations. The molecular mechanisms as well as the consequences of these microsatellite mutations, both, on a generational as well as on an evolutionary scale, have sparked debate and controversy among the scientific community. Furthermore, the bioinformatic approaches used to study microsatellites and the ways microsatellites are referred to in the general literature are often not rigurous, leading to misinterpretations and inconsistencies among studies. As an introduction to this complex topic, in Chapter I I present a review of the knowledge accumulated on microsatellites during the past two decades. A major part of this chapter has been published in the Encyclopedia of Life Sciences in a Chapter about microsatellite evolution (see Publication 1 in Appendix II). The ongoing controversy about the rates and patterns of microsatellite mutation was evident to me since before starting this PhD thesis. However, the subtler problems inherent to the computational analyses of microsatellites within genomes only became apparent when retrieving information on microsatellite distribution and abundance for the design of comparative genomic analyses. There are numerous publications analyzing the microsatellite content of genomes but, in most cases, the results presented can neither be reliably compared nor reproduced, mainly due to the lack of details on the microsatellite search process (particularly the program’s algorithm and the search parameters used) and because the results are expressed in terms that are relative to the search process (i.e. measures based on the absolute number of microsatellites). Therefore, in Chapter II I present a critical review of all available software tools designed to scan DNA sequences for microsatellites. My aim in undertaking this review was to assess the comparability of search results among microsatellite programs, and to identify the programs most suitable for the generation of microsatellite datasets for a thorough and reproducible comparative analysis of microsatellite content among genomic sequences. Using sequence data where the number and types of microsatellites were empirical know I compared the ability of 19 programs to accurately identify and report microsatellites. I then chose the two programs which, based on the algorithm and its parameters as well as the output informativity, offered the information most suitable for biological interpretation, while also reflecting as close as possible the microsatellite content of the test files. From the analysis of microsatellite search results generated by the various programs available, it became apparent that the program’s search parameters, which are specified by the user in order to define the microsatellite characteristics to the program, influence dramatically the resulting datasets. This is especially true for programs suited to allow imperfections within tandem repeats, because imperfect repetitions can not be defined accurately as is the case for perfect ones, and because several different algorithms have been proposed to address this problem. The detection of approximate microsatellites is, however, essential for the study of microsatellite evolution and for comparative analyses based on microsatellites. It is now well accepted that small deviations from perfect tandem repeat structure are common within microsatellites and larger repeats, and a number of different algorithms have been developed to confront the challenge of finding and registering microsatellites with all expectable kinds of imperfection. However, biologists have still to apply these tools to their full potential. In biological analyses single tandem repeat hits are consistently interpreted as isolated and independent repeats. This interpretation also depends on the search strategy used to report the microsatellites in DNA sequences and, therefore, I was particularly interested in the capacity of repeat finding programs to report imperfect microsatellites allowing interpretations that are useful in a biological sense. After analzying a series of tandem repeat finding programs I optimized my microsatellite searches to yield the best possible datasets for assessing and comparing the degree of imperfection of microsatellites among different genomes (Chapter III) During the program comparisons performed in Chapter II, I show that the most critical search parameter influencing microsatellite search results is the minimum length threshold. Biologically speaking, there is no consensus with respect to the minimum length, beyond which a short tandem repeat is expected to become prone to microsatellite-like mutations. Usually, a single absolute value of ~12 nucleotides is assigned irrespective of motif length.. In other cases thresholds are assigned in terms of number of repeat units (i.e. 3 to 5 repeats or more), which are better applied individually for each motif. The variation in these thresholds is considerable and not always justifiable. In addition, any current minimum length measures are likely naïve because it is clear that different microsatellite motifs undergo replication slippage at different length thresholds. Therefore, in Chapter III, I apply two probabilistic models to predict the minimum length at which microsatellites of varying motif types become overrepresented in different genomes based on the individual oligonucleotide frequency data of these genomes. Finally, after a range of optimizations and critical analyses, I performed a preliminary analysis of microsatellite abundance among 24 high quality complete eukaryotic genomes, including also 8 prokaryotic and 5 archaeal genomes for contrast. The availability of the methodologies and the microsatellite datasets generated in this project will allow informed formulation of questions for more specific genome research, either about microsatellites, or about other genomic features microsatellites could influence. These datasets are what I would have needed at the beginning of my PhD to support my experimental design, and are essential for the adequate data interpretation of microsatellite data in the context of the major evolutionary units; chromosomes and genomes.
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Zhang, Peizhi. "Bovine microsatellite analysis using digoxigenin labelling /." [S.l : s.n.], 1994. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.

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MELIS, RICCARDO. "Analisi del differenziamento genetico tra popolazioni di Octopus vulgaris Cuvier, 1797 mediante marcatori nucleari e mitocondriali." Doctoral thesis, Università degli Studi di Cagliari, 2014. http://hdl.handle.net/11584/266514.

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The common octopus, Octopus vulgaris Cuvier, 1797, represents an important commercial fishery marine resource all over the world, characterized by increasing requests from the markets. In the Mediterranean Sea, especially for the Italian fishery, this species constitutes an important portion of trawling and artisanal landings. In Italy, despite the great socio-economic interest, specific management measures do not exist at the national level for this resource. The common octopus is a very interesting topic both for applied studies and for the basic research, especially at the taxonomic level, because of the uncertainties regarding the occurrence of a single species, with cosmopolitan distribution, or the existence of multiple species forming a ‘species complex’. The principal aim of this work is the genetic characterization of seven populations of O. vulgaris along the coasts of Sardinia in order to obtain useful indications for the selection of correct management units. The genetic analyses have been realized using three different genetic markers, two mitochondrial (the Cytochrome Oxidase I (COI) and III (COIII) genes), and one nuclear marker (five microsatellites loci). All markers proved to be useful in investigating the genetic structure of the populations. In particular, the mitochondrial sequences were useful in comparisons with homologous ones from the GenBank database to evaluate the species’ taxonomy. The results of AMOVA show a substantial homogeneity in Sardinian populations that display low levels of differentiation, both with the nuclear marker (FST=0.004 ns), and the mitochondrial ones (ΦSTCOI=0.003 ns; ΦSTCOIII=0.0002 ns). The pairwise analyses show low levels of differentiation and not significant values for all the genetic markers. The lack of significant genetic differentiation in the Sardinian samples is further confirmed by DAPC, PCA analyses and the Bayesian clustering of the software STRUCTURE. The demography was investigated using all the genetic markers, which pointed out the lack of demographic changes in recent time. The multimodal mismatch distributions reaffirm the occurrence of populations demographically stable. The stability of the populations was confirmed by the haplotype network analyses with the two mitochondrial markers, highlighting a common situation in stationary populations: several principal haplotypes, shared by all the locations, and an increasing number of new secondary haplotypes arising from mutational events. The COI and COIII sequences permitted the comparison of the Sardinian haplotypes with the O. vulgaris sequences available in GenBank. Both markers highlight a genetic affinity among Sardinian specimens and the sequences from the Mediterranean Sea (France, Spain, Central Mediterranean and Turkey), the Eastern Atlantic Ocean (Morocco, Senegal and Galicia), the Southern Atlantic Ocean (South Africa and Tristan da Cunha) and the Southern Indian Ocean (Amsterdam and Saint Paul Islands). This substantial genetic homogeneity contrasts with some sequences (from specimens collected in Turkey, Japan, China, Brazil and Venezuela) that resulted to be highly divergent from all the others. This finding reaffirms the potential existence of several O. vulgaris populations, just partially interconnected, or the even occurrence of distinct species, and emphasizes the need for more detailed phylogeographic and taxonomic studies of the Octopus genus to confirm or exclude the presence of cryptic species within the taxon, as suggested by several authors.
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Bodur, Cagri. "Genetic Structure Analysis Of Honeybee Populations Based On Microsatellites." Phd thesis, METU, 2005. http://etd.lib.metu.edu.tr/upload/12606592/index.pdf.

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We analyzed the genetic structures of 11 honeybee (Apis mellifera) populations from Tü
rkiye and one population from Cyprus using 9 microsatellite loci. Average gene diversity levels were found to change between 0,542 and 0,681. Heterozygosity levels, mean number of alleles per population, presence of diagnostic alleles and pairwise FST values confirmed the mitochondrial DNA finding that Anatolian honeybees belong to north Mediterranean (C) lineage. We detected a very high level of genetic divergence among populations of Tü
rkiye and Cyprus based on pairwise FST levels (between 0,0 and 0,2). Out of 66 population pairs 52 were found to be genetically different significantly. This level of significant differentiation has not been reported yet in any other study conducted on European and African honeybee populations. High allelic ranges, and high divergence indicate that Anatolia is a genetic centre for C lineage honeybees. We suggest that certain precautions should be taken to limit or forbid introduction and trade of Italian and Carniolan honeybees to Tü
rkiye and Cyprus in order to preserve genetic resources formed in these territories in thousands of years. Effectivity at previously isolated regions in Artvin, Ardahan and Kirklareli was confirmed by the high genetic differentiation in honeybees of these regions. Genetically differentiated Karaburun and Cyprus honeybees v and geographical positions of the regions make these zones first candidates as new isolation areas.
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Bond, Joanna Margaret. "Genetic analysis of the sperm whale (Physeter macrocephalus) using microsatellites." Thesis, University of Cambridge, 1999. https://www.repository.cam.ac.uk/handle/1810/265611.

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The sperm whale is the largest of the toothed whales (Odontoceti), and inhabits deep waters from equatorial to Polar Regions. Sperm whales are social and commonly l r . found in small groups. However, sociality varies according to sex and age. Immature males form bachelor groups that disperse as they mature, mature males are frequently encountered alone. Sperm whales are renowned for their diving capabilities. Therefore, surface observations are only possible for 10 to 15 minutes every hour. Consequently, the sperm whale is an ideal candidate for investigation using genetic markers. Genetic variation can reveal information on geographical structuring of populations and, on a finer scale, the social organisation within these groups. The focus of this thesis is an investigation into the structure of populations around the Azores. To date, this work represents the most comprehensive molecular investigation into North Atlantic sperm whales. Since 1988 sloughed skin samples have been collected from the Azores but, to facilitate the comparison between local and global structuring, samples were also obtained from a number of geographically distinct regions. Twelve microsatellite loci and a marker to indicate sex were selected for screening. Genetic variation was sufficient to allow identification of individuals with a high degree of accuracy. A system of scoring the amplification quality was found to be both a simple and accurate method of determining the reliability of a genotype. Errors were found to arise infrequently, hence their influence in the final dataset was considered negligible. Of the 467 sloughed skin samples collected from the Azores, 102 individuals were identified. The majority of these samples had been collected from groups. As groups are presumed to be matrilineal, the identification of mother calf pairs was anticipated. However the samples revealed few parent offspring combinations. Within a group the majority of whales were related at the level of half )siblings. This indicates that I I Azorean groups comprise of individuals related through either the maternal or paternal lineage. Full siblings were also identified, which suggests that a degree of mate choice can occur. The first insight into the relationships within bachelor groups arose when two such groups, stranded off the coast of Scotland, were examined. Individuals within the groups were predominantly unrelated to each other. However, potential half/sibling relationships within the groups were identified. A mother offspring pair was identified between an Azorean whale and one of the stranded whales. Microsatellite data from Atlantic (n=I32) and Pacific (n=I59) sperm whales revealed low, but significant, inter-ocean variation. However, examinations of populations structuring on a finer scale (geographic regions) failed to reveal any consistent pattern of differentiation. This lack of differentiation is surprising when compared with other cetaceans, all of which show increased genetic differentiation with distance.
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Valsecchi, Elena. "Genetic analysis of the humpback whale (Megaptera novaeangliae) using microsatellites." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242544.

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Santani, Avni Bhawan. "Genomic analysis of the horse Y chromosome." Texas A&M University, 2004. http://hdl.handle.net/1969.1/1494.

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Stallion fertility is of significant economic importance in the multibillion dollar equine industry. Presently, the underlying genetic causes of infertility in stallions are unknown. Analysis of the human genome has shown that in more than 25% of cases, male infertility is associated with deletions/rearrangements in the Y chromosome. Presently there is no gene map for the Y chromosome in the horse. Therefore, the primary aim of this study is to build a detailed physical map of the chromosome with a long-term aim to identify and analyze Y-specific factors affecting fertility in stallions. To materialize this, we constructed the first radiation hybrid and FISH map of the euchromatic region of the horse Y chromosome. This basic map was used to obtain Y-specific BAC clones that provided new STS markers from the end sequences. Chromosome walking provided 73 BACs comprising 7 contigs that were built across the euchromatic region using 124 markers for content mapping. The results were validated by restriction fingerprinting and Fiber FISH. The map is presently the most informative among the domestic species and second to only human and mouse Y chromosome maps. The construction of this map will pave the way for isolation and functional characterization of genes critical for normal male fertility and reproduction and will in the future lead to the development of a diagnostic test to facilitate early identification of deletions/rearrangements on the Y chromosome of potentially affected foals/stallions. The second part of the study comprised the first extended investigation to assess genetic variation in the horse Y chromosome. Approximately 4.5Mb of the euchromatic region was screened for polymorphic microsatellite markers. Of the 27 markers that were characterized and screened for polymorphism in 14 breeds of the domestic horse and eight extant equids, only one was polymorphic in the domestic horse, suggesting a low level of genetic variation on the chromosome. However, 21 of the markers showed noteworthy variation (on average four alleles/marker) among the eight equids. These markers will be vital in future studies aimed at elucidating the genetic relationships between the various equids through phylogenetic analysis.
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Rouger, Romuald. "Restoration genetics of north-west European saltmarshes : a multi-scale analysis of population genetic structure in Puccinellia maritima and Triglochin maritima." Thesis, University of Stirling, 2014. http://hdl.handle.net/1893/21634.

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Increasing human pressure combined with sea level rise and increased storminess is threatening coastal ecosystems around the world. Among these ecosystems, saltmarshes are particularly endangered due to their position in temperate areas with low wave action where human density is often high (e.g. estuaries). Around the UK, centuries of land reclamation have led to a substantial decrease of the area of saltmarsh. Over the past decades, restoration schemes have been implemented in numerous coastal locations in an attempt to counteract this loss. Such schemes involve allowing sea water to inundate a previously embanked area and letting the vegetation develop naturally, thereby reverting to saltmarsh through natural colonisation. However, surveys of restored areas that have looked at the recovery of plant species diversity or functional characteristics often show that restored saltmarshes do not reach the state of a natural saltmarsh ecosystem. While there is much data at the species level, recovery of plant intra-specific diversity (genetic diversity) has not been assessed in restored saltmarsh although this component of biodiversity is receiving increasing attention for its effect on ecosystem function. This thesis represents the first attempt to (1) characterize the nation-wide genetic structure of two important north-west European saltmarsh plant species, the common saltmarsh grass (Puccinellia maritima) and the sea arrowgrass (Triglochin maritima) and (2) compare levels of genetic diversity and structure between restored and natural ecosystems. Microsatellite molecular markers were developed for both species. Using innovative methods to analyse the genetic data obtained for these two polyploid species, this thesis highlights that genetic diversity at the national scale is organised regionally for both species, although gene-flow is still restricted between populations within the same region. Gene-flow between populations is determined by different processes depending on the species. While coastal processes mainly influence gene dispersal in P. maritima, overland routes of dispersal are involved for T. maritima. These differences are believed to be due to differences in dispersal ecology between the two species. Although gene-flow exists between distant saltmarshes, the genetic analysis of P. maritima and T. maritima colonists arriving on restored sites highlighted their local origin and reaffirmed that it is preferable to restore saltmarsh where a nearby natural saltmarsh can act as a source of colonists. A multiple paired-site comparison identified similar genetic diversity between restored and natural saltmarshes indicating that restoration of local genetic diversity is rapid for both species. A single site comparison at Skinflats in the Forth estuary compared fine-scale spatial genetic structure between the restored and natural saltmarsh. Interestingly, no structure was detected for T. maritima either in restored or natural saltmarsh. In contrast, a strong genetic structure organised along the elevation gradient was observed in the natural saltmarsh for P. maritima but was absent in the restored saltmarsh. The origin of this structure is not clear but could be due to restricted gene-flow between individuals from different elevations due to strong post-zygotic selection, as suggested in previous work. In any case, this lack of structure in the restored saltmarsh indicates that genetic recovery is incomplete in this respect for P. maritima. This thesis introduces the growing field of restoration genetics to saltmarsh ecology and identifies the principal population genetic trends in two of the species dominating the vegetation of north-west European saltmarshes community. The information given here will be useful for restoration practitioners and provides a strong foundation for future work characterizing the importance of genetic diversity for saltmarsh function.
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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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Takahashi, Takeshi. "Clonal Analysis of Multifocal Urothelial Cancers using Microsatellite Markers." Kyoto University, 2001. http://hdl.handle.net/2433/150512.

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Books on the topic "Microsatellites analysi"

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Ellegren, Hans. Genome analysis with microsatellite markers. Uppsala: Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 1993.

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1962-, Hajeer Ali, Worthington Jane 1961-, and John Sally 1964-, eds. SNP and microsatellite genotyping: Markers for genetic analysis. Natick, MA: Eaton Pub., 2000.

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Nowakowska, Justyna. Analysis of microsatellite sequences in Scots pine: [proceedings of Workshop WP 5.4, forest tree genetics : Sekocin, Poland, 24-27 August 2004]. Edited by Instytut Badawczy Leśnictwa (Warsaw, Poland). Warsaw: Forest Research Institute, 2005.

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Shaklee, James B. Microsatellite DNA analysis and run timing of chinook salmon in the White River, Puyallup Basin. Olympia, WA: Washington Dept. of Fish and Wildlife, Fish Program, Science Division, 2003.

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Grewe, Peter M. An assessment of bigeye (Thunnus obesus) population structure in the Pacific Ocean, based on mitochondrial DNA and DNA microsatellite analysis. [Honolulu, Hawaii: University of Hawaii, Joint Institute for Marine and Atmospheric Research, 1998.

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Umar, A. Lynch Syndrome (HNPCC) and Microsatellite Instability Analysis Guidelines, Part 2. IOS Press, 2006.

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Hajeer, Ali. Snp And Microsatellite Genotyping: Markers For Genetic Analysis (MOLECULAR LABORATORY METHODS (BIOTECHNIQUES BOOKS)). EATON PUBLISHING, 2000.

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Systems-Level Feasibility Analysis of a Microsatellite Rendezvous with Non-Cooperative Targets. Storming Media, 2004.

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Duquette, Rémi. MOST (Micro-variability of Oscillations of STars) microsatellite structural analysis and design. 2000.

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Book chapters on the topic "Microsatellites analysi"

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Ibbotson, Rachel E., and Anton E. Parker. "Microsatellite Analysis." In Medical Biomethods Handbook, 463–69. Totowa, NJ: Humana Press, 2005. http://dx.doi.org/10.1385/1-59259-870-6:463.

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Winter, Peter, Bruno Hüttel, Kurt Weising, and Günter Kahl. "Microsatellites and Molecular Breeding: Exploitation of Microsatellite Variability for the Analysis of a Monotonous Genome." In Molecular Techniques in Crop Improvement, 85–137. Dordrecht: Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-017-2356-5_4.

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Orjuela-Sánchez, Pamela, Michelle C. Brandi, and Marcelo U. Ferreira. "Microsatellite Analysis of Malaria Parasites." In Methods in Molecular Biology, 247–58. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-389-3_17.

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Birnbaum, Kenneth D., and Howard C. Rosenbaum. "A Practical Guide for Microsatellite Analysis." In Techniques in Molecular Systematics and Evolution, 351–64. Basel: Birkhäuser Basel, 2002. http://dx.doi.org/10.1007/978-3-0348-8125-8_16.

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Kim, Kyung Seok, and Thomas W. Sappington. "Microsatellite Data Analysis for Population Genetics." In Methods in Molecular Biology, 271–95. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-389-3_19.

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Mellersh, Cathryn. "Microsatellite-Based Candidate Gene Linkage Analysis Studies." In Methods in Molecular Biology, 75–86. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-188-8_5.

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Rithidech, Kanokporn, and John J. Dunn. "Combining Multiplex and Touchdown PCR for Microsatellite Analysis." In PCR Protocols, 295–99. Totowa, NJ: Humana Press, 2003. http://dx.doi.org/10.1007/978-1-4612-0055-0_42.

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Khierallah, Hussam S. M., Saleh M. Bader, Alladin Hamwieh, and Michael Baum. "Date Palm Genetic Diversity Analysis Using Microsatellite Polymorphism." In Methods in Molecular Biology, 113–24. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7159-6_11.

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Elfimova, Natalia, Wafa Amer, and Margarete Odenthal. "Analysis of Microsatellite Instability by Microfluidic-Based Electrophoresis." In Methods in Molecular Biology, 287–96. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-029-8_25.

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Zhang, Yipeng, Hai Huang, and Shenyan Chen. "Structure analysis and optimisation of SSS-1 microsatellite." In Aerospace and Associated Technology, 351–56. London: Routledge, 2022. http://dx.doi.org/10.1201/9781003324539-64.

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Conference papers on the topic "Microsatellites analysi"

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Dastoom Laatleyli, Hassan, Ali Abedian, and Hessamodin Teimouri. "Investigating Optimum Procedures Needed to Maintain a Model Satellite’s CG Stable About Design Point, Under Subsystem Configuration Changes." In ASME 2010 10th Biennial Conference on Engineering Systems Design and Analysis. ASMEDC, 2010. http://dx.doi.org/10.1115/esda2010-25271.

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During design, microsatellites are subject to different changes like the changes in weight, location and dimension of parts and elements of subsystems and the payload. These changes should be accumulated by the structure subsystem in a way that some key structural parameters like the center of gravity (CG) and inertia moments remain unchanged. This subject is also important regarding the design of a modular structure of a satellite. In the present study it is tried to accommodate any changes in weight and location of any part(s) and element(s) of a microsatellite by optimum (minimum) rearrangement of other parts on their plane of rest in order to keep the CG and inertia moments unchanged. This is performed by a special mathematics modeling considering the existing constraints. Of course, no addition or subtractions of weight from the remaining parts are assumed. Also, in order to keep the original structural design intact, no movement of the parts except in the close neighborhood of their original location is allowed. At the end, this study shows that it is possible to move other subsystems on some suitable paths as a result of changing one subsystem mass from −100% (omitting that element) to 100% (doubling the weight of that element) to maintain the overall CG position in its previous position.
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Gainullina, K. P. "SSR analysis of pea (Pisum sativum L.) cultivars and lines." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.079.

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The analysis of molecular genetic diversity of pea cultivars by microsatellites was conducted. A high level of polymorphism of SSR loci which allows using them for identification of the studied cultivars and lines was revealed.
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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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Savenko, E. G., Zh M. Mukhina, and V. A. Glazyrina. "Use of experimental biotechnology for accelerated development of breeding material." In CURRENT STATE, PROBLEMS AND PROSPECTS OF THE DEVELOPMENT OF AGRARIAN SCIENCE. Federal State Budget Scientific Institution “Research Institute of Agriculture of Crimea”, 2020. http://dx.doi.org/10.33952/2542-0720-2020-5-9-10-93.

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The combination of such biotechnological techniques as experimental haploidy and molecular marking allows developing breeding material with simultaneous DNA analysis of its genetic homogeneity (obtaining microsatellite profiles). According to the results of SSR genotyping, DNA passports were obtained for androgenic cultivars ‘Sonnet’ and ‘Sonata’.
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Mudunuri, Suresh B., Allam Appa Rao, S. Pallamsetty, and H. A. Nagarajaram. "Comparative analysis of microsatellite detecting software." In the International Symposium. New York, New York, USA: ACM Press, 2010. http://dx.doi.org/10.1145/1722024.1722068.

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"University microsatellites for the Seismic-Magnetosphere Phenomena analysis." In 55th International Astronautical Congress of the International Astronautical Federation, the International Academy of Astronautics, and the International Institute of Space Law. Reston, Virigina: American Institute of Aeronautics and Astronautics, 2004. http://dx.doi.org/10.2514/6.iac-04-w.2.03.

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Boudier, Guillaume, and N. Merat. "Propulsion Analysis of Demeter Microsatellite Fluidic Passivation." In 48th AIAA/ASME/SAE/ASEE Joint Propulsion Conference & Exhibit. Reston, Virigina: American Institute of Aeronautics and Astronautics, 2012. http://dx.doi.org/10.2514/6.2012-4286.

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Scarì, Ettore, Matteo Ceriotti, Camilla Colombo, and Massimiliano Vasile. "Mission Analysis of Hevelius - Lunar Microsatellit..." In 56th International Astronautical Congress of the International Astronautical Federation, the International Academy of Astronautics, and the International Institute of Space Law. Reston, Virigina: American Institute of Aeronautics and Astronautics, 2005. http://dx.doi.org/10.2514/6.iac-05-b5.2.09.

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Jian Song. "Genome-wide in silico analysis of microsatellites in Sorghum bicolor." In 2009 International Conference on Future BioMedical Information Engineering (FBIE). IEEE, 2009. http://dx.doi.org/10.1109/fbie.2009.5405801.

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Chen, Tao, Ping-Xiang Li, and Liang-pei Zhang. "Retrieving vegetation cover by using BP neural network based on Beijing-1 microsatellite data." In International Conference on Earth Observation Data Processing and Analysis, edited by Deren Li, Jianya Gong, and Huayi Wu. SPIE, 2008. http://dx.doi.org/10.1117/12.812495.

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Reports on the topic "Microsatellites analysi"

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Jin, Yuanyang, and Zhimin Suo. Immunocheckpoint inhibitors for advanced gastric cancer or gastroesophageal junction cancer with different microsatellite stability: a systematic review and meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, October 2022. http://dx.doi.org/10.37766/inplasy2022.10.0106.

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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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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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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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Michelmore, Richard, Eviatar Nevo, Abraham Korol, and Tzion Fahima. Genetic Diversity at Resistance Gene Clusters in Wild Populations of Lactuca. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7573075.bard.

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Genetic resistance is often the least expensive, most effective, and ecologically-sound method of disease control. It is becoming apparent that plant genomes contain large numbers of disease resistance genes. However, the numbers of different resistance specificities within a genepool and the genetic mechanisms generating diversity are poorly understood. Our objectives were to characterize diversity in clusters of resistance genes in wild progenitors of cultivated lettuce in Israel and California in comparison to diversity within cultivated lettuce, and to determine the extent of gene flow, recombination, and genetic instability in generating variation within clusters of resistance genes. Genetic diversity of resistance genes was analyzed in wild and cultivated germplasm using molecular markers derived from lettuce resistance gene sequences of the NBS-LRR type that mapped to the major cluster if resistance genes in lettuce (Sicard et al. 1999). Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR- encoding regions, were developed from sequences of resistance gene homologs at the Dm3 cluster (RGC2s) in lettuce. Variation for these markers was assessed in germplasm including 74 genotypes of cultivated lettuce, L. saliva and 71 accessions of the three wild Lactuca spp., L. serriola, L. saligna and L. virosa that represent the major species in the sexually accessible genepool for lettuce. Diversity was also studied within and between natural populations of L. serriola from Israel and California. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. We documented a variety of genetic events occurring at clusters of resistance genes for the second objective (Sicard et al., 1999; Woo el al., in prep; Kuang et al., in prepb). The diversity of resistance genes in haplotypes provided evidence for gene duplication and unequal crossing over during the evolution of this cluster of resistance genes. Comparison of nine resistance genes in cv. Diana identified 22 gene conversion and five intergenic recombinations. We cloned and sequenced a 700 bp region from the middle of RGC2 genes from six genotypes, two each from L. saliva, L. serriola, and L. saligna . We have identified over 60 unique RGC2 sequences. Phylogenetic analysis surprisingly demonstrated much greater similarity between than within genotypes. This led to the realization that resistance genes are evolving much slower than had previously been assumed and to a new model as to how resistance genes are evolving (Michelmore and Meyers, 1998). The genetic structure of L. serriola was studied using 319 AFLP markers (Kuang et al., in prepa). Forty-one populations from Turkey, Armenia, Israel, and California as well as seven European countries were examined. AFLP marker data showed that the Turkish and Armenian populations were the most polymorphic populations and the European populations were the least. The Davis, CA population, a recent post-Columbian colonization, showed medium genetic diversity and was genetically close to the Turkish populations. Our results suggest that Turkey - Armenia may be the center of origin and diversity of L. serriola and may therefore have the greatest diversity of resistance genes. Our characterization of the diversity of resistance genes and the genetic mechanisms generating it will allow informed exploration, in situ and ex situ conservation, and utilization of germplasm resources for disease control. The results of this project provide the basis for our future research work, which will lead to a detailed understanding of the evolution of resistance genes in plants.
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