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.

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 ◽  
Tree Frog ◽  
Hyla Chrysoscelis ◽  
Sequence Repeat ◽  
Isolation And Characterization ◽  
Simple Sequence ◽  
Gray Tree Frog

Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.)

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 628-633 ◽  
Author(s):  
J. E. Bowers ◽  
G. S. Dangl ◽  
R. Vignani ◽  
C. P. Meredith
Keyword(s):  
Vitis Vinifera ◽  
Silver Staining ◽  
Simple Sequence Repeat ◽  
Pinot Noir ◽  
Sequence Repeat ◽  
Wine Grapes ◽  
Table Grapes ◽  
Isolation And Characterization ◽  
Ssr Loci ◽  
Simple Sequence

Four new simple sequence repeat (SSR) loci (designated VVMD5, VVMD6, VVMD7, and VVMD8) were characterized in grape and analyzed by silver staining in 77 cultivars of Vitis vinifera. Amplification products ranged in size from 141 to 263 base pairs (bp). The number of alleles observed per locus ranged from 5 to 11 and the number of diploid genotypes per locus ranged from 13 to 27. At each locus at least 75% of the cultivars were heterozygous. Alleles differing in length by only 1 bp could be distinguished by silver staining, and size estimates were within 1 or 2 bp, depending on the locus, of those obtained by fluorescence detection at previously reported loci. Allele frequencies were generally similar in wine grapes and table grapes, with some exceptions. Some alleles were found only in one of the two groups of cultivars. All 77 cultivars were distinguished by the four loci with the exception of four wine grapes considered to be somatic variants of the same cultivar, 'Pinot noir', 'Pinot gris', 'Pinot blanc', and 'Meunier'; two table grapes that are known to be synonymous, 'Keshmesh' and 'Thompson Seedless'; and three table grapes, 'Dattier', 'Rhazaki Arhanon', and 'Markandi', the first two of which have been suggested to be synonymous. Although the high polymorphism at grape SSR loci suggests that very few loci would theoretically be needed to separate all cultivars, the economic and legal significance of grape variety identification requires the increased resolution that can be provided by a larger number of loci. The ease with which SSR markers and data can be shared internationally should encourage their broad use, which will in turn increase the power of these markers for both identification and genetic analysis of grape. Key words : grape, Vitis, microsatellite, simple sequence repeat, DNA typing, identification.

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.

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 Evaluation of Genetic Diversity and Pedigree within Crapemyrtle Cultivars Using Simple Sequence Repeat Markers

2011 ◽  
Vol 136 (2) ◽  
pp. 116-128 ◽  
Author(s):  
Xinwang Wang ◽  
Phillip A. Wadl ◽  
Cecil Pounders ◽  
Robert N. Trigiano ◽  
Raul I. Cabrera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Interspecific Hybrids ◽  
Size Variation ◽  
Sequence Repeat ◽  
Allele Size ◽  
Low Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Estimates ◽  
Simple Sequence

Genetic diversity was estimated for 51 Lagerstroemia indica L. cultivars, five Lagerstroemia fauriei Koehne cultivars, and 37 interspecific hybrids using 78 simple sequence repeat (SSR) markers. SSR loci were highly variable among the cultivars, detecting an average of 6.6 alleles (amplicons) per locus. Each locus detected 13.6 genotypes on average. Cluster analysis identified three main groups that consisted of individual cultivars from L. indica, L. fauriei, and their interspecific hybrids. However, only 18.1% of the overall variation was the result of differences between these groups, which may be attributable to pedigree-based breeding strategies that use current cultivars as parents for future selections. Clustering within each group generally reflected breeding pedigrees but was not supported by bootstrap replicates. Low statistical support was likely the result of low genetic diversity estimates, which indicated that only 25.5% of the total allele size variation was attributable to differences between the species L. indica and L. fauriei. Most allele size variation, or 74.5%, was common to L. indica and L. fauriei. Thus, introgression of other Lagestroemia species such as Lagestroemia limii Merr. (L. chekiangensis Cheng), Lagestroemia speciosa (L.) Pers., and Lagestroemia subcostata Koehne may significantly expand crapemyrtle breeding programs. This study verified relationships between existing cultivars and identified potentially untapped sources of germplasm.

scholarly journals Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0127812 ◽  
Author(s):  
Jing Xiao ◽  
Jin Zhao ◽  
Mengjun Liu ◽  
Ping Liu ◽  
Li Dai ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Chinese Jujube ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence
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