Comparative Microsatellite Analysis Research Articles

Comparative microsatellite analysis of zeboid cattle with breeds of Bos taurus

Comparative genotyping of a population of zeboid cattle (Bos taurus × Bos indicus) and eight populations of B. taurus breeds, including six domestic (Нolmogorskaya, Yaroslavskaya, Red Gorbatovskaya, Kostromskaya, Tagil’skaya, Gray Ukrainian) and two transboundary European breeds (Holstein and Brown Swiss). A total of 562 individuals were examined. Based on the results of the STR analysis, it was found that all population samples of B. taurus were characterized by an average allelic diversity AR = 4.87–6.7 and a fairly high level of genetic variability HE = 0.68–0.76 with a slight predominance of random matings FIS = –0.1... 0.0. In zeboid cattle, the corresponding indicators were AR = 5.96, HE = 0.72 and FIS = –0.0278. At the same time, differences in the genetic structure of the B. taurus breeds under consideration were largely determined by population-demographic fluctuations, and the genetic and phenotypic heterogeneity detected in the population of zeboid cattle was determined by a decrease in the effect of artificial selection.

Comparative Microsatellite Analysis of Zeboid Cattle with Breeds of Bos taurus

Comparative Microsatellite Analysis of Zeboid Cattle with Breeds of Bos taurus

Comparative analysis of microsatellites in coding regions provides insights into the adaptability of the giant panda, polar bear and brown bear.

Short Tandem repeats (STRs) often occur within coding regions and adaptive selection could play a vital role in shaping the landscape of coding STRs. Here, we identified 849, 1282 and 1501 genes that contained 966, 1565 and 1921 STRs in the coding regions of the giant panda, polar bear and brown bear genomes, respectively. The results showed that coding STRs were subject to strong selection on STR type, motif, repetition and mode of evolution. Coding STRs were primarily found in regulatory genes. Of the three ursids studied, we found 585 differential genes in the giant panda. Gene Ontology analysis showed that the significant enrichment term (insulin-like growth factor receptor signaling pathway) exerted direct carbohydrate metabolic effects in vivo in this species. The enrichment of this pathway suggested that the giant panda's ability to absorb carbohydrates (starch) and adapt to a bamboo diet might be enhanced by variable coding STRs. We also identified 377 conserved coding STRs located in 377 genes across the three species. Kyoto Encyclopedia of Genes and Genomesenrichment analysis showed that these genes were significantly enriched in two pathway involved in key physiological processes, including cardiovascular function and energy metabolism regulation. This study provides an important resource for future studies on the regulation of rapid diet and environmental adaptation of species by coding STRs.

Maternal vs Fetal Origin of Placental Intervillous Thrombi.

ObjectivesTo determine maternal vs fetal origin for blood in placental intervillous thrombi (IVTs).MethodsWe used comparative analysis of microsatellites (short tandem repeats [STRs]), sex chromosome fluorescence in situ hybridization (FISH), and immunohistochemistry (IHC) for fetal (ɑ-fetoprotein [AFP]) and maternal (immunoglobulin M [IgM]) serum proteins to distinguish the origin of IVTs. Using an informatics approach, we tested the association between IVTs and fetomaternal hemorrhage (FMH).ResultsIn 9 of 10 cases, the preponderance of evidence showed that the thrombus was mostly or entirely maternal in origin. In 1 case, the thrombus was of mixed origins. STR testing was prone to contamination by entrapped fetal villi. FISH was useful but limited only to cases with male fetuses. IgM showed stronger staining than AFP in 9 cases, supporting maternal origin. By informatics, we found no association between IVTs and FMH.ConclusionsEvidence supports a maternal origin for blood in IVTs. IHC for IgM and AFP may be clinically useful in determining maternal vs fetal contribution to IVTs.

How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq

BackgroundFitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential to influence the success of management and conservation efforts, genetic similarity has been suggested to be used as a proxy to predict the outcome. Studies utilizing microsatellites (a neutral marker) to investigate associations between genetic distance and admixture effects show conflicting results. Marker types that yield information on genome-wide and/or adaptive variation might be more useful for predicting responses to inter-population hybridization. In this study we utilized published data for three populations of pike (Esox lucius) to investigate associations between offspring performance (hatching success) and parental genetic similarity in experimentally purebred and admixed families, based on neutral (microsatellites), genome-wide neutral (RADseq SNPs), and adaptive (SNPs under selection) markers.ResultsEstimated similarity varied among the markers, likely reflecting differences in their inherent properties, but was consistently higher in purebred than admixed families. A significant interaction between marker type and admixture treatment reflected that neutral SNPs yielded higher estimates than adaptive SNPs for admixed families whereas no difference was found for purebred families, which indicates that neutral similarity was not reflective of adaptive similarity. When all samples were pooled, no association between similarity and performance was found for any marker. For microsatellites, similarity was positively correlated with hatching success in purebred families, whereas no association was found in admixed families; however, the direction of the effect differed between the population combinations.ConclusionsThe results strengthen the notion that, as of today, there is no proxy that can reliably predicted the outcome of admixture. This emphasizes the need of further studies to advance knowledge that can shed light on how to safeguard against negative consequences of admixture, and thereby inform management and promote conservation of biological diversity.

Identification, distribution and comparative analysis of microsatellites in the chloroplast genome of Oryza species

Chloroplast genome is important because of its maternally inherited, conserved within species and stable in structure. This allows elucidation of inter-specific comparison, identification and establishment of evolutionary relationship among different species. Different classes of DNA elements were present in chloroplast genome of Oryza species, among them chloroplast microsatellites were supposed to be highly variable. In this study, a total of 102 sequences of chloroplast genome of 23 species of Oryza genus belonging to ten different genome types were downloaded from NCBI nucleotide database. The chloroplast DNA length varied from 134,401bp to 136,133bp. Microsatellite analysis revealed that total SSR number varied from 268 in O. coarctata to 281 in O. granulata. Comparative analysis of repeat type revealed that mononucleotide and trinucleotide were least present, while penta and hexa nucleotide motif were the most common type among all the Oryza species. Frequency analysis of the repeat revealed that T repeat among mono, AT among di, AAT among tri, AATA among tetra, AATTC among penta and AAAGAA among hexa nucleotide repeat was found to be common among most of the Oryza species. Total of five set of SSR markers flanking to penta and hexa nucleotide repeat types were developed which uniquely present among species, namely, O. barthi, O. sativa Japonica, O. cocarctata, O. rhizomatis and O. ridley. Phylogeny based on SSR markers indicate separate evolution of different SSR markers among individual species.

Chromosome specific microsatellite analysis of common wheat lines resistant to powdery mildew

Aim. Determine the chromosome localization of introgressions containing alien genes for resistance to powdery mildew transferred to the wheat genome from three Aegilops species: Ae. sharonensis, Ae. speltoides, and Ae. umbellulata. Methods. Comparative microsatellite analysis of amplicons’ spectra, derived from PCR with primers to SSR loci localized on seven chromosomes of wheat D subgenome. Results. Spectra of amplification of products with DNA of Aurora cultivar, genome substitution amphidiploids Aurosis, Aurodes and Aurolata, using primers to 44 microsatellite loci localized on seven chromosomes of common wheat D subgenome have been obtained. Absence of genome specificity has been determined for most of the analyzed loci. All the studied introgressive lines have been characterized by allele polymorphism for different number of microsatellite loci from all seven chromosomes of D subgenome. This polymorphism included new components in amplicons spectra, which have been different from components of Aurora and genome substituted amphidiploids. Heterozygous genotypes have been also observed. A part of polymorphic loci has been uninformative because the chromosome of genome substituted amphidiploid had null-allele for such loci. For specification of the information about homeological identity of alien chromatin in resistant lines, genes of morphological traits with known chromosome localization have been used. Conclusions. Screening of resistant to powdery mildew wheat introgressive lines for microsatellite loci does not allow an unambiguous identification of chromosome localization of resistance gene because of high polymorphism of microsatellite loci in the genomes of introgressive lines, and because many loci are non-informative. Assumptions have been made about possible connections of resistance genes with chromosomes of homeological groups 3 and 6 in lines derived from Aurodes; 1, 2, 3, and 6 – in lines derived from Aurolata; and homeological group 2 in lines derived from Aurosis.

Genome-wide mining and comparative analysis of microsatellites in three macaque species.

Microsatellites are found in taxonomically different organisms, and such repeats are related with genomic structure, function and certain diseases. To characterize microsatellites for macaques, we searched and compared SSRs with 1-6bp nucleotide motifs in rhesus, cynomolgus and pigtailed macaque. A total of 1395671, 1284929 and 1266348 perfect SSRs were mined, respectively. The most frequent perfect SSRs were mononucleotide SSRs. The most GC-content was in dinucleotide SSRs and the least was in the mononucleotide SSRs. Chromosome size was positively correlated with SSR number and negatively correlated with the relative frequency and density of SSRs. The GC content of chromosome SSRs were negatively correlated with relative frequency of SSRs and GC content of chromosome sequences. The features of microsatellite distribution in assembled genomes of the three species were greatly similar, which revealed that the distributional pattern of microsatellites is probably conservative in genus Macaca. The degenerated number of repeat motifs was found to be different in pentanucleotide and hexanucleotide repeats. Species-specific motifs for each macaque were significantly underrepresented. Overall, SSR frequencies of each chromosome in rhesus macaque were higher than in cynomolgus macaque. The maximum repeat times of mono- to pentanucleotide repeats in cynomolgus macaque was more than other two macaques. These results emphasize the genetic diversity and phylogenetic relationship of genus Macaca species. Our data will be beneficial for comparative genome mapping, understanding the distribution of SSRs and genome structure between these animal models, and provide a foundation for further development and identification of more macaque-specific SSRs.

Comparative analysis of microsatellites and compound microsatellites in T4-like viruses

Microsatellites or simple sequence repeats (SSRs) are known to present ubiquitously in genomes of eukaryotes and prokaryotes, as well as viruses. A comprehensive analysis of microsatellites and compound microsatellites (CM) was performed for 67 T4-like bacteriophage genomes. We found that the number of repeats was generally proportional to the size of the genome. CM were more abundant in genic regions, while their relative abundance was higher in intergenic regions. Meanwhile, the number of CM rapidly decreased with the increase of complexity but gradually increased with higher dMAX (maximum distance between any two adjacent microsatellites). (A)n/(T)n, (AT)n/(TA)n and (AAG)n were the most abundant repeats of mono-, di- and trinucleotide microsatellites, respectively. The number of microsatellites in reference sequences was significantly lower than that in corresponding random sequences. This result was mainly attributed to mono- and dinucleotide repeats which hardly exceeded 6bp in T4-like viruses. These observations may be helpful to understand the distribution of microsatellites and viral genetic diversity in T4-like viruses.

Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants

Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been shown to possess extensive variations in the length, number and distributionof SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR(2-6)(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR(2-6). However, GC content strongly showed negative correlation with relative density (R (2)=0.5, P<0.05) and relative abundance (R (2)=0.6, P<0.05) of cSSRs. In summary, our comparative studies of chloroplast genomes illustrate the variable distribution of microsatellites and revealed that chloroplast genome of smaller plants possesses relatively more genomic diversity compared to higher plants.

Microsatellite analysis of chromosomes from the fifth homoeologous group in the introgressive Triticum aestivum/Amblyopyrum muticum wheat lines

Introgressive hybridization of common wheat has been and remains an efficient way for enriching its gene pool with resistance genes against environmental stress factors. In this aspect, T genome of the diploid species Amblyopyrum muticum (Boiss.) Eig. is believed to be prospective. The genome substitution amphidiploid Aurotica (AABBTT) with the A and B subgenomes from the common wheat cultivar Aurora and with the T subgenome from the indicated species is characterized by a high level of winter resistance. This trait is associated in wheat with the chromosomes of the fifth homoeologous group. Using a comparative microsatellite analysis of Aurora and Aurotica DNAs, we identified nine SSR loci specific for the wheat D genome, whose primers produced different amplicons from Aurotica DNA. The latter were used in screening F5 plants (Aurora × Aurotica) for the search of the specimens that carried the 5T chromosome or its fragments in their genomes. Among 234 plants, we detected 24 plants with disomic 5D/5T substitutions, which were the progeny of five F4 plants grown from two F2 plants. A significant number of plants contained the recombinant 5D/5T chromosome. The recombination event could occur in any generation starting with F2.

Comparative Microsatellite Analysis of Grass Carp Genomes of Two Gynogenetic Groups and the Xiangjiang River Group

The genomes of three groups of grass carp, namely the Xiangjiang River grass carp group (Xiangjiang group), a one-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-1 group), and a two-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-2 group), were comparatively analyzed with microsatellite markers. Genetic polymorphism had been observed in the Xiangjiang group and most of the examined loci had more than two alleles. But the degree of genetic diversity was not very high. Although all the examined genetic loci in the analyzed individuals were in homozygous state, the genotypes of different individuals of the group were not identical in the meio-gynogenetic-1 group. In the meio-gynogenetic-2 group, not only the examined genetic loci of each individual were homozygous but also the genotypes of all the analyzed individuals of the group were the same. These results suggested that the examined meio-gynogenetic-2 group is a homozygous group and homozygous clone could be produced by continuous artificial induction of gynogenesis for two generations. It was found that the polymorphism existed not only at the allele level but also at the locus level; many alleles of the microsatellite loci and some of the microsatellite loci had been lost during the process of artificial gynogenesis. Therefore, both protection of the diversity of natural grass carp resource and selection of homozygous traits with desired economic genotypes are very important aspects for grass carp breeding.

Genetic variation of melon (C. melo) compared to an extinct landrace from the Middle Ages (Hungary) I. rDNA, SSR and SNP analysis of 47 cultivars

Microsatellite profiles of 47 melon cultivars and landraces were analyzed and compared to the aDNA (ancient DNA) of seed remains from an extinct sample recovered from the 15th century (Budapest, Hungary). An aseptic incubation followed by ITS (internal transcribed spacer) analysis was used to exclude the exogenously and endogenously contaminated medieval seeds and to detect SNPs (single nucleotide polymorphism) in ITS1-5.8S-ITS2 region of rDNA (ribosomal DNA). SNPs were observed at the 94–95 bp (GC to either RC, RS or AG) of ITS1; and at 414 bp (A-to-T substitution), 470 bp (T to Y or C), 610 bp (A to R or G) and 633 bp (A-to-G transition) of ITS2. For comparative microsatellite analysis SSRs (simple sequence repeats) detected by ALF (automated laser fluorometer) was used. Eight of the 20 SSR primer pairs amplified 40 microsatellite alleles in identical fragment ranges. A total of 485 alleles were detected in the 47 melon cultivars. The number of alleles per marker ranged from 2 to 7 with an average of 5.7 including CMCT44 (2 alleles), CMAG59 (5 alleles), CMGA104 (5 alleles), CMCT134 (4 alleles), CMTA134 (6 alleles), CMCTT144 (7 alleles), CMTC168 (6 alleles) and CMCT170 (5 alleles). Sequence analysis of the microsatellite alleles showed different fragment lengths depending on changes in the number of unit of core sequences. Dendrogram produced by SPSS11 based on the presence versus absence of SSR alleles revealed that medieval melon had the closest genetic similarity to a registered melon cultivar Hogolyo selected from an old Hungarian melon landrace. These results also indicated that cloned DNA sequences recovered from aDNA of medieval melon can be of use for molecular breeding of modern melon cultivars via gene transfer.

A comparative microsatellite analysis of colorectal cancer in patients 50 years of age

OBJECTIVE: This study was undertaken to investigate microsatellite instability and allelic imbalance in a cohort of young patients (<35 yr) and older patients (>50 yr) with sporadic colorectal carcinomas in the Kwa-Zulu Natal region of South Africa. METHODS: Normal and tumor DNA was isolated from formalin-fixed, paraffin-embedded tissue from 32 patients <35 yr and from 50 patients >50 yr of age. Tumors were staged using the modified Astler-Coller classification. Fluorescent-based DNA technology using an automated DNA sequencer (Alf Express Automated DNA Sequencer) was employed. CY5 labeled primers for microsatellite markers in chromosomes 18, 3, and 2 (DCC, D18S34, D18S58, D3S659, D3S1255, and D2S123) were used. The data were captured and analyzed using the Fragment Manager Software. RESULTS: The informativity of the microsatellite markers ranged from 50% to 71.8%. Microsatellite instability was seen in 44 of 82 cases (53.7%) for at least one of the six markers. Low frequency MSI (MSI-L) was seen in 28 of 82 cases (34.2%) and high frequency MSI (MSI-H) in 16 of 82 cases (19.5%). In the <35-yr age group, MSI-L was seen in six cases (18.8%) and MSI-H in 10 cases (31.3%). In the >50 yr age group, MSI-L was seen in 22 cases (44%) and MSI-H in six cases (12%). Twelve cases showed AI for DCC, seven showed AI for D18S34, and four showed AI for D18S58. MSI was found in 13, 10, and 16 cases for each of these markers, respectively. Allelic imbalance for the D3S659, D2S123, and D3S1255 loci was 3 of 82 cases (3.7%), 10 of 82 cases (12.2%), and 13 of 80 cases (16.3%), respectively. MSI was 14.6% for both D3S659 and D2S123 and was 6.3% for the D3S1255 marker. CONCLUSIONS: Loss of heterozygosity in the region of the DCC locus ranged from 9.3% to 26.7%, and MSI ranged from 12.2% to 19.5% of cases. Allelic imbalance in the region of the repair genes ranged from 6.8% to 27% in the informative cases. MSI, however, ranged from 5% to 12%. These figures are similar to those of other studies done in other parts of the world. Further, no correlation was found between the genetic results and clinicopathological parameters: i.e., tumor stage, grade and clinical parameters of age and gender. However, genetic abnormalities were more common in the younger cohort of patients, and this may translate into the earlier age of presentation. This opens the potential for genetic screening.

Comparative microsatellite analysis in discerning origin of disseminated tumor: The case of a patient with malignant ascites and a history of multiple tumors

The origin of metastatic carcinoma is now always easily resolved on the basis of conventional clinical and pathological parameters, particularly in patients with more than 1 primary tumor. When 1 of the tumors is a renal cell carcinoma, the clinical picture is further confounded by the tendency of these tumors to be locally silent, to metastasize to unusual sites, and to disseminate long after removal of the primary tumor. We compared tumors for loss (ie, deletion) of loci on chromosomal arms 3p, 5q, 11q, and 18q in a patient with a malignant ascites fluid, a remote history of renal and colonic neoplasms, and a strong clinical suspicion of disseminated gastrointestinal adenocarcinoma. DNA from microdissected tumors and normal tissues was subjected to polymerase chain reaction-based microsatellite analysis. Even though the clinical picture suggested a gastrointestinal origin, comparison of genetic alterations clearly showed that the malignant ascites represented recurrence of the renal cell carcinoma. The malignant ascites and the primary renal cell carcinoma showed identical patterns of allelic loss at all loci tested. In contrast, the malignant ascites and colonic adenoma showed discordant patterns of allelic loss. Comparative microsatellite analysis provides a rapid genetic approach for discerning the origin of metastatic tumor spread. This may be a useful diagnostic adjunct when tumor origin is not clear on clinical or morphological grounds. In some instances, it may even provide a reasonable alternative to an extensive and costly conventional work-up.