scholarly journals Microsatellites in the silkworm, Bombyx mori: Abundance, polymorphism, and strain characterization

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1057-1065 ◽  
Author(s):  
K Damodar Reddy ◽  
E G Abraham ◽  
J Nagaraju
Keyword(s):  
Microsatellite Markers ◽  
Bombyx Mori ◽  
Honey Bee ◽  
Genomic Library ◽  
Dominant Inheritance ◽  
Strain Characterization ◽  
Ssr Loci ◽  
Silkworm Genome ◽  
Partial Genomic Library ◽  
Simple Sequence

We have isolated and characterized microsatellites (simple sequence repeat (SSR) loci) from the silkworm genome. The screening of a partial genomic library by the conventional hybridization method led to the isolation of 28 microsatellites harbouring clones. The abundance of (CA)n repeats in the silkworm genome was akin to those reported in the other organisms such as honey bee, pig, and human, but the (CT)n repeat motif is less common compared to bumble bee and honey bee genomes. Detailed analysis of 13 diverse silkworm strains with a representative of 15 microsatellite loci revealed a number of alleles ranging from 3 to 17 with heterozygosity values of 0.66-0.90. Along with strain-specific microsatellite markers, diapause and non-diapause strain-specific alleles were also identified. The repeat length did not show any relationship with the degree of polymorphism in the present study. The co-dominant inheritance of microsatellite markers was demonstrated in F1 offspring. A list of primer sequences that tag each locus is provided. The availability of microsatellite markers can be expected to enhance the power and resolution of genome analysis in silkworm.Key words: microsatellites, simple sequence repeats, polymorphisms, silkworm strains, Bombyx mori.

scholarly journals Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Suping Feng ◽  
Helin Tong ◽  
You Chen ◽  
Jingyi Wang ◽  
Yeyuan Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genomic Library ◽  
Trinucleotide Repeats ◽  
The Other ◽  
Diversity Analysis ◽  
Dominant Type ◽  
Genetic Diversity Analysis ◽  
Ssr Loci ◽  
Ssr Development

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

Microsatellite marker analysis of an anther-derived potato family: skewed segregation and gene–centromere mapping

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 236-242 ◽  
Author(s):  
Eduard Chani ◽  
Varda Ashkenazi ◽  
Jossi Hillel ◽  
Richard E Veilleux
Keyword(s):  
Anther Culture ◽  
Segregation Distortion ◽  
Interspecific Hybrid ◽  
Genomic Library ◽  
Unreduced Gametes ◽  
Distorted Segregation ◽  
Backcross Population ◽  
Skewed Segregation ◽  
Ssr Loci ◽  
Simple Sequence

Segregation patterns of polymorphic simple sequence repeat (SSR) primer pairs were investigated in monoploid potato families derived from anther culture. A total of 14 primers developed from the sequences in the database, as well as from a genomic library of potato, was used. Distorted segregation was observed for seven (50%) polymorphic loci among monoploids derived from an interspecific hybrid. Similar distortion was observed for only one of five loci that could be contrasted between the two monoploid families. Segregation distortion was less common in the sexually derived backcross population between the interspecific hybrid and either of its parents. One locus could be putatively linked to a lethal allele because it showed distorted segregation in both monoploid families, a group of 70 heterozygous diploids derived from unreduced gametes through anther culture, and a backcross population. These diploids were used to map the polymorphic SSR markers with respect to the centromeres using half-tetrad analysis. The majority of the SSR loci mapped more than 33 cM from the centromere, suggesting the occurrence of a single crossover per chromosome arm.Key words: androgenesis, segregation distortion, simple sequence repeats (SSRs), Solanum phureja, unreduced gametes.

scholarly journals Microsatellite markers in analysis of resistance to coffee leaf miner in Arabica coffee

2011 ◽  
Vol 46 (12) ◽  
pp. 1650-1656 ◽  
Author(s):  
Gabriella Santos Pereira ◽  
Lilian Padilha ◽  
Edila Vilela Resende Von Pinho ◽  
Rita de Kássia Siqueira Teixeira ◽  
Carlos Henrique Siqueira de Carvalho ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Leaf Miner ◽  
Est Database ◽  
Ssr Loci ◽  
Leucoptera Coffeella ◽  
Coffee Leaf Miner ◽  
Expressed Sequence ◽  
Simple Sequence

The objective of this work was to analyze coffee (Coffea arabica) genotypes resistant to the coffee leaf miner (Leucoptera coffeella) using microsatellite markers. Sixty-six loci were evaluated, of which 63 were obtained from the Brazilian Coffee Expressed Sequence Tag (EST) database. These loci were amplified in bulks of individuals from F5 progenies of 'Siriema' (C. arabica x C. racemosa) resistant and susceptible to the insect, in eight samples of C. racemosa, and in a F6 population of 'Siriema' with 91 individuals segregating for resistance to the leaf miner. Polymorphisms were verified for two simple sequence repeat (SSR) loci in bulks of the susceptible progenies. The two polymorphic alleles were present in around 70% of the susceptible genotypes in F5 and in approximately 90% of the susceptible individuals in F6. However, the polymorphic EST-SSR markers among populations contrasting for resistance to leaf miner were not correlated to the evaluated characteristics. SSR markers show inter- and intraspecific polymorphism in C. arabica and C. racemosa.

scholarly journals Microsatellite Marker Development in Rose and its Application in Tetraploid Mapping

2006 ◽  
Vol 131 (3) ◽  
pp. 380-387 ◽  
Author(s):  
L.H. Zhang ◽  
D.H. Byrne ◽  
R.E. Ballard ◽  
S. Rajapakse
Keyword(s):  
Ssr Markers ◽  
Genomic Library ◽  
Cultivar Identification ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Specific Primers ◽  
Pcr Products ◽  
Ssr Loci ◽  
Tetraploid Parent ◽  
Simple Sequence

Microsatellite or simple sequence repeat (SSR) markers were developed from Rosa wichurana Crépin to combine two previously constructed tetraploid rose (Rosa hybrida L.) genetic maps. To isolate SSR-containing sequences from rose a small-insert genomic library was constructed from diploid Rosa wichurana and screened with several SSR probes. Specific primers were designed for 43 unique SSR regions, of which 30 primer pairs gave rise to clear PCR products. Seventeen SSR primer pairs (57%) produced polymorphism in the tetraploid rose 90-69 mapping family. These markers were incorporated into existing maps of the parents 86-7 and 82-1134, which were constructed primarily with AFLP markers. The current map of the male parent, amphidiploid 86-7, consists of 286 markers assigned to 14 linkage groups and covering 770 cm. The map of the female tetraploid parent, 82-1134, consists of 256 markers assigned to 20 linkage groups and covering 920 cm. Nineteen rose SSR loci were mapped on the 86-7 map and 11 on the 82-1134 map. Several homeologous linkage groups within maps were identified based on SSR markers. In addition, some of the SSR markers provided anchoring points between the two parental maps. SSR markers were also useful for joining small linkage groups. Based on shared SSR markers, consensus orders for four rose linkage groups between parental maps were generated. Microsatellite markers developed in this study will provide valuable tools for many aspects of rose research including future consolidation of diploid and tetraploid rose genetic linkage maps, genetic, phylogenetic and population analyses, cultivar identification, and marker-assisted selection.

scholarly journals Development of Simple Sequence Repeat Markers in Chinese Chestnut and Their Characterization in Diverse Chestnut Cultivars

2009 ◽  
Vol 134 (6) ◽  
pp. 610-617 ◽  
Author(s):  
Eiichi Inoue ◽  
Lin Ning ◽  
Hiromichi Hara ◽  
Shuan Ruan ◽  
Hiroyuki Anzai
Keyword(s):  
Simple Sequence Repeat ◽  
Genomic Library ◽  
Genetic Distances ◽  
The Other ◽  
Group Method ◽  
Enriched Library ◽  
Sequence Repeat ◽  
Chinese Chestnut ◽  
Ssr Loci ◽  
Simple Sequence

To develop and characterize valid simple sequence repeat (SSR) markers in chestnut (Castanea spp.), we used a selective hybridization method to perform SSR sequence enrichment in the genomic library of chinese chestnut (Castanea mollissima). From 47 sequences of the enriched library, we designed 24 primer pairs for SSR polymerase chain reaction (PCR). SSR PCR was performed for 23 chinese chestnut cultivars. Among the 24 primers, 22 primers amplified their respective SSR loci; 21 primer pairs yielded polymorphic fragments across the cultivars. Among these 21 primer pairs, 17 primer pairs amplified single SSR loci with polymorphisms. Multilocus amplification patterns were observed in the other four primers. For the corresponding 17 SSR loci, the number of alleles per locus was two to 13, and the average number of alleles was 7.19. The observed heterozygosity (number of genotypes of the heterozygote/total number of genotypes scored at that locus) ranged from 0.00 to 0.87 (average = 0.68), and the expected heterozygosity ranged from 0.00 to 0.87 (average = 0.68). One of the SSR loci—ICMA014—was a unique locus, because the primer pair for this locus did not amplify any fragment in any of the cultivars, except in Qianchi, which was used to construct the SSR-enriched genomic library. Cross-species amplifications using the 17 primer pairs were also successful in the other species of genus Castanea. A dendrogram depicting the relationships among the genotypes on the basis of genetic distances was generated using the unweighted pair group method with arithmetic mean cluster analysis. The genotypes were clearly separated into three large groups, which reflected the three cultivated species, namely, C. mollissima, C. crenata, and C. sativa.

Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai)

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 433-441 ◽  
Author(s):  
R. L. Jarret ◽  
L. C. Merrick ◽  
T. Holms ◽  
J. Evans ◽  
M. K. Aradhya
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Genetic Relatedness ◽  
Genomic Library ◽  
Citrullus Lanatus ◽  
Dinucleotide Repeats ◽  
Length Polymorphisms ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total of 96 (0.53%) SSR-bearing clones were identified and the inserts from 50 of these were sequenced. The dinucleotide repeats (CT)n and (GA)n accounted for 82% of the SSRs sequenced. PCR primer pairs flanking seven SSR loci were used to amplify SSRs from 32 morphologically variable watermelon genotypes from Africa, Europe, Asia, and Mexico and a single accession of Citrullus colocynthis from Chad. Cluster analysis of SSR length polymorphisms delineated 4 groups at the 25% level of genetic similarity. The largest group contained C. lanatus var. lanatus accessions. The second largest group contained only wild and cultivated "citron"-type or C. lanatus var. citroides accessions. The third group contained an accession tentatively identified as C. lanatus var. lanatus but which perhaps is a hybrid between C. lanatus var. lanatus and C. lanatus var. citroides. The fourth group consisted of a single accession identified as C. colocynthis. "Egusi"-type watermelons from Nigeria grouped with C. lanatus var. lanatus. The use of SSRs for watermelon germplasm characterization and genetic diversity studies is discussed.Key words: Citrullus, watermelon, simple sequence repeats, genetic diversity.

Isolation and characterization of simple sequence repeat loci in the gray tree frog, Hyla chrysoscelis

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 676-680 ◽  
Author(s):  
J D Krenz ◽  
R D Semlitsch ◽  
H C Gerhardt ◽  
P A Mahoney
Keyword(s):  
Simple Sequence Repeat ◽  
Large Scale ◽  
Genomic Library ◽  
Tree Frog ◽  
Hyla Chrysoscelis ◽  
Sequence Repeat ◽  
Isolation And Characterization ◽  
Ssr Loci ◽  
Simple Sequence ◽  
Gray Tree Frog

A gray tree frog (Hyla chrysoscelis) genomic library was constructed and characterized with regard to the incidence and complexity of simple sequence repeat (SSR) loci. The partial genomic library, containing approximately 10 000 clones with an average-sized insert of 350 bp, was screened with six SSR repeat oligonucleotides (AC, AG, ACG, AGC, AAC, and AAG). Screening identified 31 unique positive clones containing 41 SSR loci. Sequences of tandemly arrayed dinucleotide repeats were more common (36 of 41) than trinucleotide repeats. Twenty-six loci were identified using the AC dinucleotide probe, while 7 loci were identified using the AG dinucleotide probe. An additional 3 AT dinucleotide loci were serendipitously identified. The AT repeats generally comprised the longest dinucleotide repeat loci. The SSR repeat loci reported here should provide potent markers for identity, parentage, and short-lineage determinations in large-scale experiments using gray tree frogs.Key words: Hyla chrysoscelis, simple sequence repeat, SSR, gray tree frog, microsatellite.

scholarly journals Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

2021 ◽  
Author(s):  
Júlia Halász ◽  
Noémi Makovics-Zsohár ◽  
Ferenc Szőke ◽  
Sezai Ercisli ◽  
Attila Hegedűs
Keyword(s):  
Simple Sequence Repeat ◽  
Principal Component ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Allele Number ◽  
Genetic Potential ◽  
Ssr Loci ◽  
High Level ◽  
Diversity Studies ◽  
Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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.

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.

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