Linking porcine microsatellite markers to known genome regions by identifying their human orthologs

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 798-808 ◽  
Author(s):  
Zhihua Jiang ◽  
Jennifer J Michal
Keyword(s):  
Microsatellite Markers ◽  
Positional Cloning ◽  
Genome Mapping ◽  
Joint Analysis ◽  
Porcine Genome ◽  
Gene Markers ◽  
Human Orthologs ◽  
Human Genomic ◽  
Rh Panel ◽  
Simple Sequence

Microsatellites, or tandem simple sequence repeats (SSRs), have become one of the most popular molecular markers in genome mapping because of their abundance across genomes and because of their high levels of polymorphism. However, information on which genes surround or flank them has remained very limited for most SSRs, especially in livestock species. In this study, an in silico comparative mapping approach was developed to link porcine SSRs to known genome regions by identifying their human orthologs. From a total of 1321 porcine microsatellites used in this study, 228 were found to have blocks in alignment with human genomic sequences. These 228 SSRs span about 1459 cM of the porcine genome, but with uneven distributions, ranging from 2 on SSC12 to 24 on SSC14. Linking these porcine SSRs to the known genome regions in the human genome also revealed 16 new putative synteny groups between these two species. Fifteen SSRs on SSC3 with identified human orthologs were typed on a pig-hamster radiation hybrid (RH) panel and used in a joint analysis with 80 known gene markers previously mapped on SSC3 using the same panel. The analysis revealed that they were all highly linked to either one or both adjacent markers. These results indicated that assigning the porcine SSRs to known genome regions by identifying their human orthologs is a reliable approach. The process will provide a foundation for positional cloning of causative genes for economically important traits.Key words: pig, microsatellite markers, human orthologs, RH mapping.

scholarly journals Microsatellite Markers in Hazelnut: Isolation, Characterization, and Cross-species Amplification

2005 ◽  
Vol 130 (4) ◽  
pp. 543-549 ◽  
Author(s):  
Nahla V. Bassil ◽  
R. Botta ◽  
S.A. Mehlenbacher
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Geographical Origin ◽  
Genome Mapping ◽  
Polymorphic Information Content ◽  
Corylus Avellana ◽  
Expected Heterozygosity ◽  
Gaa Repeats ◽  
Microsatellite Alleles ◽  
Simple Sequence

Three microsatellite-enriched libraries of the european hazelnut (Corylus avellana L.) were constructed: library A for CA repeats, library B for GA repeats, and library C for GAA repeats. Twenty-five primer pairs amplified easy-to-score single loci and were used to investigate polymorphism among 20 C. avellana genotypes and to evaluate cross-species amplification in seven Corylus L. species. Microsatellite alleles were estimated by fluorescent capillary electrophoresis fragment sizing. The number of alleles per locus ranged from 2 to 12 (average = 7.16) in C. avellana and from 5 to 22 overall (average = 13.32). With the exception of CAC-B110, di-nucleotide SSRs were characterized by a relatively large number of alleles per locus (≥5), high average observed and expected heterozygosity (Ho and He > 0.6), and a high mean polymorphic information content (PIC ≥ 0.6) in C. avellana. In contrast, tri-nucleotide microsatellites were more homozygous (Ho = 0.4 on average) and less informative than di-nucleotide simple sequence repeats (SSRs) as indicated by a lower mean number of alleles per locus (4.5), He (0.59), and PIC (0.54). Cross-species amplification in Corylus was demonstrated. These microsatellite markers were highly heterozygous and polymorphic and differentiated among genotypes of C. avellana irrespective of geographical origin. They will aid in fingerprinting genotypes of the european hazelnut and other Corylus species, genome mapping, and genetic diversity assessments.

scholarly journals Inheritance and linkage analysis of co-dominant SSR markers on the Z chromosome of the silkworm (Bombyx mori L.)

2008 ◽  
Vol 90 (2) ◽  
pp. 151-156 ◽  
Author(s):  
XUE-XIA MIAO ◽  
WEI-HUA LI ◽  
MU-WANG LI ◽  
YUN-PO ZHAO ◽  
XIAN-RU GUO ◽  
...  
Keyword(s):  
Linkage Map ◽  
Bombyx Mori ◽  
Ssr Markers ◽  
Positional Cloning ◽  
Z Chromosome ◽  
Pcr Marker ◽  
Backcross Population ◽  
In The Beginning ◽  
Simple Sequence ◽  
Visible Mutation

SummaryMicrosatellites or simple sequence repeats (SSRs) are co-dominant molecular markers. When we used fluorescent SSR markers to construct a linkage map for the female heterogametic silkworm (Bombyx mori, ZW), we found that some loci did not segregate in a Mendelian ratio of 1:1 in a backcross population. These loci segregated in a 3:1 ratio of single bands compared with double bands. Further examination of band patterns indicated that three types of SSR bands were present: two homozygotes and one heterozygote. In the beginning, we considered to discard these markers. By scoring male and female F1 individuals, we confirmed that these loci were located on the Z chromosome. Using the sex-linked visible mutation sch (K05) and its wild-type (C108), we constructed an F1 male backcross (BC1M) mapping population. The combination of sch backcross and SSR data enabled us to map the SSR markers to the Z chromosome. By adjusting input parameters based on these data, we were able to use Mapmaker software to construct a linkage map. This strategy takes advantage of co-dominant markers for positional cloning of genes on the Z chromosome. We localized sch to the Z chromosome relative to six SSR markers and one PCR marker, covering a total of 76·1 cM. The sch mutation is an important sex-linked visible mutation widely used in breeding of commercial silkworms (e.g. male silkworm selection rearing). Localization of the sch gene may prove helpful in cloning the gene and developing strains for marker-assisted selection in silkworm breeding.

scholarly journals  Genetic diversity of Czech apple cultivars inferred from microsatellite markers analysis

2012 ◽  
Vol 39 (No. 4) ◽  
pp. 149-157 ◽  
Author(s):  
J. Patzak ◽  
F. Paprštein ◽  
A. Henychová ◽  
J. Sedlák
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Simple Sequence Repeat ◽  
Cultivar Identification ◽  
Genetic Relationships ◽  
Similarity Coefficient ◽  
Collection Management ◽  
Apple Cultivars ◽  
Repeat Primer ◽  
Simple Sequence

Genetic diversity and genetic relationships of Czech apple cultivars were evaluated. Trees of 33 Czech apple cultivars and 97 reference foreign cultivars were analysed using the set of 10 SSR (simple sequence repeat) primer pairs. The total of 89 polymorphic alleles were amplified, while the number of alleles per locus ranged from 4 to 14. The SSR dendrogram, based on the Jaccard’s similarity coefficient, divided apple cultivars into three major groups: Cox’s Orange Pippin, McIntosh and Golden Delicious ancestries. The clustering highly depended on pedigree and origin of apple cultivars. Spontaneous mutated cultivars were identical with their progenitors. We proved that microsatellite markers were useful for evaluation of genetic resources, collection management and cultivar identification.  

scholarly journals Identifying Pollen Donors and Success Rate of Individual Pollinizers in European Plum (Prunus domestica L.) Using Microsatellite Markers

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 264
Author(s):  
Meland ◽  
Frøynes ◽  
Fotiric Akšić ◽  
Pojskić ◽  
Kalamujić Stroil ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Success Rate ◽  
Genetic Characterization ◽  
Prunus Domestica ◽  
Tissue Samples ◽  
Self Pollination ◽  
Self Fertilization ◽  
High Level ◽  
Very High ◽  
Simple Sequence

European plum cultivars (Prunus domestica L.) are hexaploid and partially self-fertile or self-sterile requiring compatible pollinizers with overlapping bloom times. Therefore, inter-planting of different pollinizer cultivars is recommended. In order to identify successful pollinizers of the plum cultivars ‘Edda’, ‘Opal’ (self-fertile), ‘Jubileum’, ‘Reeves’, ‘Mallard’, ‘Avalon’, ‘Cacanska Lepotica’ (self-fertile), and ‘Valor’, 60 fruits per cultivar were collected from nine orchards in 2017 and 2018, all of which were located in Ullensvang, western Norway. DNA extraction was subsequently conducted from the obtained embryos, followed by genetic characterization using seven microsatellite markers. Tissue samples from all possible pollinizers were collected during the summer of 2017 and the same DNA approach was conducted. Results showed that ‘Opal’ was the most successful pollinizer among the investigated plum cultivars. The main exception was ‘Cacanska Lepotica’, which consistently displayed very high level of self-pollination. The most successful foreign pollinizer of ‘Opal’ was ‘Mallard’. However, in more than two thirds of embryos extracted from ‘Opal’ fruits self-fertilization was determined. ‘Reeves’ was identified as the most successful pollinizer among embryos collected from ‘Valor’. Among the five cultivars (‘Edda’, ‘Jubileum’, ‘Reeves’, ‘Mallard’, and ‘Avalon’) that did not display self-pollination, the pollinizer success rate of ‘Opal’, ranged from 36.5% (‘Mallard’) to 93.5% (‘Edda’) in 2017, while in 2018 this rate ranged from 43.5% (‘Jubileum’ and ‘Reeves’) up to 96.5% (‘Edda’). Overall, genotyping embryos using SSRs (simple sequence repeats) proved an effective method in determining the success rate of individual pollinizers among European plum cultivars.

Genetic diversity among a founder parent and widely grown wheat cultivars derived from the same origin based on morphological traits and microsatellite markers

2012 ◽  
Vol 63 (4) ◽  
pp. 303 ◽  
Author(s):  
X. J. Li ◽  
X. Xu ◽  
X. M. Yang ◽  
X. Q. Li ◽  
W. H. Liu ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Simple Sequence Repeat ◽  
Morphological Traits ◽  
Sequence Repeat ◽  
Repeat Analysis ◽  
Simple Sequence Repeat Analysis ◽  
Close Proximity ◽  
Genome Information ◽  
Simple Sequence ◽  
Founder Parent

Founder parents have contributed significantly to the improvement of wheat. Beijing 8 has been used as a founder parent in developing many outstanding improved cultivars in China. The widely grown cultivars Beijing 8 and 6 additional derivatives both derived from the cross ‘Bima 4 × Early Premium’ in China, were characterised using seven morphological traits and 537 microsatellite markers. Phenotypic comparisons revealed that Beijing 8 was similar for certain characteristics to the widely grown cultivars Shijiazhuang 54 and Jinan 2, hinting that acceptable performance for yield components may be the basis for Beijing 8 serving as a founder parent. Simple sequence repeat analysis indicated that Bima 4 contributed more genome information to the derivatives than Early Premium. Fifty-nine unique simple sequence repeat alleles, present in Beijing 8 and absent in other cultivars, were observed. Nearly all loci were in close proximity to the positions of known genes conferring important traits. Furthermore, pedigree tracking found that the frequencies of alleles unique to Beijing 8 varied from 0 to 0.96 in its 51 descendants, suggesting that some of them underwent rigorous selection during breeding.

Data Mining for Simple Sequence Repeats in Expressed Sequence Tags from Japanese Flounder (Paralichthys olivaceus)

2013 ◽  
Vol 765-767 ◽  
pp. 274-277
Author(s):  
Song Bo Chen ◽  
Xin Lu Xie ◽  
Gong Li ◽  
Hai Jin Liu
Keyword(s):  
Genome Mapping ◽  
Average Distance ◽  
Paralichthys Olivaceus ◽  
Japanese Flounder ◽  
Genetic Studies ◽  
Dominant Type ◽  
The Public ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

Based on ESTs of Japanese flounder (Paralichthys olivaceus) in the public database, EST-SSR makers were developed after mining and evaluating SSRs in them by bioinformatics methods. 5 927 non-redundant ESTs of Japanese flounder were screened and 390 SSRs were mined out. The frequency of these EST-SSRs was 7.95% and the average distance of distribution was 7.9 kb in non-redundant ESTs. The dinucleotide repest motif was dominant type (59.02%) with repeat motif AC being the most common (16.91%). The distribution of trinucleotide, tetranucleotide and hexanucleotide repeats were dispersive. 30 primer pairs for EST-SSRs were designed, 27 primer pairs showed the amplification, and 17 primer pairs showed polymorphisms, the rates of polymorphic EST-SSRs were 62.96% with the alleles per locus ranging from 2 to 6 (mean 3.5). The observed (HO) and expected (HE) heterozygosities of these EST-SSRs were 0.280.92 and 0.31550.8033, respectively. Two EST-SSR loci significantly deviated from the HardyWeinberg equilibrium (HWE) expectation, and theremaining 15 loci were in HWE. These new EST-SSR markers would provide sufficient polymorphism for population genetic studies and genome mapping of Japanese flounder.

Genetic analysis and molecular markers associated with multi-gynoecia (Mg) gene in Trigrain whea

2009 ◽  
Vol 89 (5) ◽  
pp. 845-850 ◽  
Author(s):  
Z Wang ◽  
D Xu ◽  
J Ji ◽  
J Wang ◽  
M Wang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Simple Sequence Repeats ◽  
Segregation Analysis ◽  
Dominant Gene ◽  
Distal Region ◽  
Allelism Test ◽  
Single Dominant Gene ◽  
Gene Segregation ◽  
Genetic Patterns ◽  
Simple Sequence

Trigrain wheat normally produces up to three gynoecia in a single floret and forms three close-set grains. The gene conferring the multi grain phenotype was earlier designated Mg, the multiple gynoecia gene. Different genetic patterns controlling this trait have been reported. In the present work we studied the inheritance of the three grains trait and identified simple sequence repeats (SSR) markers linked to the Mg gene. Segregation analysis in the cross IGDB-TW (trigrain wheat)/Chinese Spring confirmed that a single dominant gene controlled the three grains trait. An allelism test showed that the same gene controlled the trigrain trait in line Trigrain-Yin 1. A total of 339 microsatellite markers were tested for polymorphism by bulked segregation analysis (BSA) in an F2 population. Six microsatellite markers, Xcfd233, Xgdm6, Xgdm87, Xgwm311, Xgwm349 and Xgwm539, on chromosome 2DL, were linked to Mg. Using the CS 2D deletion lines, Mg gene was localized to the distal region of chromosome 2DL. The microsatellite markers identified in this study have the potential for further mapping and map-based cloning of the gene.Key words: Simple sequence repeats, physical mapping, trigrain wheat

Microsatellite markers for common lilac (Syringa vulgaris L.)

2013 ◽  
Vol 11 (3) ◽  
pp. 279-282 ◽  
Author(s):  
Inka Juntheikki-Palovaara ◽  
Kristiina Antonius ◽  
Leena Lindén ◽  
Helena Korpelainen
Keyword(s):  
Microsatellite Markers ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Pedigree Information ◽  
The Novel ◽  
Landscape Plant ◽  
Common Lilac ◽  
Genome Screening ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Common lilac is a popular landscape plant with nearly 2000 cultivars. In the present study, nine novel polymorphic microsatellite markers were developed for common lilac using genome screening with inter-simple sequence repeat primers. Each of the nine markers revealed two to five alleles. The markers were used for genotyping of 75 common lilac shrubs, including 17 accessions that represented named cultivars. A dendrogram, based on the allele profiles of the shrubs, was generally in agreement with the grouping made on the basis of morphological traits, as well as with the pedigree information available. The novel markers appear valuable for differentiation between common lilac cultivars.

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