Characterization of microsatellite markers in eastern white pine

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1102-1108 ◽  
Author(s):  
C. S. Echt ◽  
P. May-Marquardt ◽  
M. Hseih ◽  
R. Zahorchak
Keyword(s):  
Microsatellite Loci ◽  
Simple Sequence Repeat ◽  
Genome Mapping ◽  
Allelic Diversity ◽  
Sequence Repeat ◽  
White Pine ◽  
Eastern White Pine ◽  
The North ◽  
Central United States ◽  
Simple Sequence

An enrichment cloning method was evaluated for the isolation of microsatellite loci from eastern white pine and the resulting markers were examined for polymorphisms. A 200-fold enrichment was achieved for highly abundant (AC)n repeats, but for much less abundant (ACAG)n repeats an enrichment of only 20-fold was obtained. Using a single set of PCR conditions, 19 microsatellite loci were identified from 77 primer pairs evaluated. Genotyping of 16 (AC)n loci in 16 unrelated white pines from the north-central United States revealed an average of 5.4 alleles per locus and an average observed heterozygosity of 0.515. Five loci were scored among megagametophytes from a single pine to obtain a haploid genotype of the segregating female meiotic products. All loci segregated according to Mendelian expectations and linkage was established for two of the loci. It was concluded that (AC)n loci are highly variable in this species and that SSR (simple sequence repeat) markers can be efficiently developed for genome mapping and population genetics studies. Key words : Pinus strobus, forest genetics, simple sequence repeat, SSR, allelic diversity.

Microsatellite polymorphism in Dioscorea tokoro, a wild yam species

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 794-801 ◽  
Author(s):  
Ryohei Terauchi ◽  
Akihiro Konuma
Keyword(s):  
Microsatellite Loci ◽  
Simple Sequence Repeat ◽  
Population Genetic ◽  
Natural Populations ◽  
Allozyme Analysis ◽  
Sequence Repeat ◽  
Expected Heterozygosity ◽  
Simple Sequence ◽  
Paternity Exclusion ◽  
Wild Yam

Six microsatellite loci were characterized in Dioscorea tokoro, a wild yam species in East Asia. All six loci were polymorphic in a sample of 23 individuals from natural populations in Japan. The microsatellite loci displayed many alleles (6.2 alleles per locus on average), and the observed heterozygosity (Ho = 0.54) as well as expected heterozygosity (He = 0.68) were high. The heterozygosities were far more than that previously detected by allozyme analysis of D. tokoro (Ho = 0.23, He = 0.28). Five microsatellite loci were sufficient to provide a paternity exclusion rate (Q) of Q = 0.98, which enables monitoring of the pollen-mediated gene flow between plants in a population. Microsatellite loci are abundant and highly polymorphic in D. tokoro and other plants and are therefore ideal markers for plant population genetic studies.Key words: microsatellite, simple sequence repeat, population genetics, Dioscorea tokoro.

Simple sequence repeat analysis of a clonally propagated species: A tool for managing a grape germplasm collection

Genome ◽  
2001 ◽  
Vol 44 (3) ◽  
pp. 432-438 ◽  
Author(s):  
G Savage Dangl ◽  
Mary Lou Mendum ◽  
Bernard H Prins ◽  
M Andrew Walker ◽  
Carole P Meredith ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Middle Eastern ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Table Grape ◽  
Sequence Repeat ◽  
Crop Species ◽  
Simple Sequence ◽  
Grape Cultivars

The USDA germplasm repositories help to preserve the genetic variability of important crop species by collecting and maintaining representative cultivars and related germplasm. Simple sequence repeat markers with high allelic diversity were used to type 41 grapevines from 40 accessions. All vines were either seedless table grape cultivars or cultivars with names similar to table grape cultivars. The proportion of shared alleles was selected as the most appropriate statistical measure of genetic distance for this population. In conjunction with morphological traits, known synonyms were confirmed and a previously unknown synonym was discovered. An alleged synonym in the literature was disproved by the DNA data. The data were consistent with known parentage, where such data were available. Two mislabeled vines in the USDA collection were identified. UPGMA grouped the cultivars loosely into three groups: a group of nine mostly Middle Eastern cultivars, a group of 22 accessions mostly from Russia and Afghanistan that were morphologically similar to 'Thompson Seedless', and a third very loose group of 11 accessions consisting mostly of eastern European wine grape cultivars. The limitations and usefulness of this type of analysis are discussed.Key words: Vitis vinifera, grape, germplasm, simple sequence repeats, genetic distance.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea macrophylla

2007 ◽  
Vol 132 (3) ◽  
pp. 341-351 ◽  
Author(s):  
Sandra M. Reed ◽  
Timothy A. Rinehart
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Sequence Repeat ◽  
Hydrangea Macrophylla ◽  
Total Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Genetic diversity studies using 39 simple-sequence repeat (SSR) markers were carried out with 114 taxa of Hydrangea macrophylla (Thunb.) Ser., including 87 H. macrophylla ssp. macrophylla cultivars and 20 members of H. macrophylla ssp. serrata (Thunb.) Makino. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. H. macrophylla ssp. serrata contained nearly twice the allelic diversity of H. macrophylla ssp. macrophylla. The majority of genetic diversity was found to reside within the subspecies, with only 12% of the total genetic diversity observed occurring between subspecies. Although the elevation of H. macrophylla ssp. serrata to species level has recently been recommended by several hydrangea authorities, these data support the subspecies designation. Four cultivars (Preziosa, Pink Beauty, Tokyo Delight, and Blue Deckle) appeared to be hybrids between the two subspecies. Genetic similarities were found among five remontant cultivars (Bailmer, Oak Hill, David Ramsey, Decatur Blue, and Penny Mac) and several nonremontant cultivars, including General Vicomtesse de Vibraye, Nikko Blue, All Summer Beauty, and La France. No close genetic relationship was found between the remontant cultivar Early Sensation and other remontant cultivars. Genetic similarities were found among variegated and double-flower cultivars. Within H. macrophylla ssp. macrophylla, cultivars with mophead inflorescences clustered separately from most lacecap cultivars. This indicates the cultivars with lacecap inflorescences that were among some of the earliest introductions to Europe were not widely used in the breeding of mophead forms. Some presumed synonyms were found to be valid (‘Preziosa’ and ‘Pink Beauty’, ‘Rosalba’ and ‘Benigaku’, ‘Geoffrey Chadbund’ and ‘Mowe’), whereas others were not (‘Harlequin’ and ‘Monrey’, ‘Nigra’ and ‘Mandschurica’). This study identified potentially unexploited sources of germplasm within H. macrophylla and relationships between existing cultivars of this popular shrub. This information should be of value when selecting parents for breeding programs.

Simple Sequence Repeat Allelic Diversity in Virginia-Type Peanut Cultivars Released from 1943 to 2006

Crop Science ◽  
2010 ◽  
Vol 50 (4) ◽  
pp. 1348-1356 ◽  
Author(s):  
Susana R. Milla-Lewis ◽  
M. Carolina Zuleta ◽  
Thomas G. Isleib
Keyword(s):  
Simple Sequence Repeat ◽  
Allelic Diversity ◽  
Sequence Repeat ◽  
Peanut Cultivars ◽  
Simple Sequence

scholarly journals Novel polymorphic microsatellite markers from turmeric, Curcuma longa L. (Zingiberaceae)

2013 ◽  
Vol 72 (2) ◽  
pp. 407-412 ◽  
Author(s):  
Siju Senan ◽  
Dhanya Kizhakayil ◽  
Thotten E. Sheeja ◽  
Bhaskaran Sasikumar ◽  
Alangar I. Bhat ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Microsatellite Loci ◽  
Simple Sequence Repeat ◽  
Curcuma Longa ◽  
Sequence Repeat ◽  
Discrimination Power ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Abstract - Twenty one polymorphic microsatellite loci were isolated and characterized from turmeric (Curcuma longa L.). These markers were screened across thirty accessions. The number of alleles observed for each locus ranged from two to eight with an average of 4.7 alleles per locus. The discrimination power of these markers ranged from 0.25 to 0.67 (average 0.6). The simple sequence repeat (SSR) markers can complement the currently available SSR markers and would be useful for the genetic analysis of turmeric accessions.

scholarly journals INTER-SIMPLE SEQUENCE REPEAT ANALYSIS AND ALLELIC DIVERSITY AMONG GENOTYPES OF CULTIVATED Digitaria species

2018 ◽  
Vol 30 (2) ◽  
pp. 01-08
Author(s):  
D. A. Animasaun ◽  
K. F. Awujoola ◽  
R. Krishnamurthy ◽  
J. A. Morakinyo
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Similarity Index ◽  
Allelic Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Analysis ◽  
First Time ◽  
Simple Sequence

Acha (Digitaria exilis Kipps. and D. iburua Stapf.) are valuable indigenous food crops in West Africa, but despite several economic potentials of this crop, little or no attention is paid to its germplasm evaluation and improvement. In this study, we assessed genetic diversity and relationship among genotypes of cultivated acha in Nigeria using Inter-Simple Sequence Repeat (ISSR) markers for the first time. Genomic DNA were extracted from the genotypes and we performed fragment amplification by Polymerase Chain Reaction (PCR). A total of 95 loci consisting of 790 bands were amplified by 13 ISSR primers, out of which 53.37% were polymorphic. Loci amplification per primer ranged from 5-10, with an average of 7.30 loci per primer. Eight of the primers had above 50% polymorphism. Cluster analysis separated the genotypes into two major groups; a group consisting of two D. exilis genotypes and the other comprising a mixture of genotypes. The D. exilis in the latter group were distant members and was only similar at 0.72 similarity index. The polymorphism we obtained in the present study showed that the ISSR markers are effective for assessment of genetic diversity of the genotypes. Clustering of D. exilis and D. iburua together suggests a common progenitor but could have been separated by geographical isolation mechanism

Relationships among subspecies of New World octoploid strawberry species, Fragaria virginiana and Fragaria chiloensis, based on simple sequence repeat marker analysis

2006 ◽  
Vol 84 (12) ◽  
pp. 1829-1841 ◽  
Author(s):  
K.E. Hokanson ◽  
M.J. Smith ◽  
A.M. Connor ◽  
J.J. Luby ◽  
James F. Hancock
Keyword(s):  
North American ◽  
Simple Sequence Repeat ◽  
Distinct Species ◽  
South American ◽  
Sequence Repeat ◽  
Similarity Coefficients ◽  
The North ◽  
Fragaria Chiloensis ◽  
Fragaria Virginiana ◽  
Simple Sequence

Simple sequence repeat (SSR) markers, developed from Fragaria  ×ananassa Duchesne ex Rozier ‘Earliglow’, were used to assess diversity among all of the proposed taxa of Fragaria virginiana Mill. and Fragaria chiloensis (L.) Mill. to facilitate strawberry germplasm utilization and conservation and to help resolve taxonomic relationships. DNA was obtained from 111 individuals representing F. chiloensis subsp. pacifica Staudt, F. chiloensis subsp. lucida (E. Vilm. ex Gray) Staudt, F. virginiana subsp. virginiana Mill., F. virginiana subsp. glauca (S. Watson) Staudt, F. virginiana subsp. grayana (Vilm. ex J. Gay) Staudt, and F. virginiana subsp. platypetala (Rydb.) Staudt from North America, F. chiloensis subsp. chiloensis f. chiloensis and F. chiloensis subsp. chiloensis f. patagonica from South America, F. chiloensis subsp. s andwicensis (Decne.) Staudt from Hawaii, as well as F. ×ananassa subsp. cuneifolia (Nutt ex Howell), and F. ×ananassa subsp. ananassa . A total of 108 bands were scored among all accessions using the five SSR primer pairs, for a mean of 21.6 bands per primer pair with 3–8 bands in individual accessions. Cluster analysis and principal coordinate analysis using Jaccard similarity coefficients based on presence or absence of bands supported the separation of F. virginiana and F. chiloensis as distinct species. The various F. virginiana subspecies were not distinguishable. The two South American forms of F. chiloensis subsp. chiloensis are very similar to each other and distinct from the North American subspecies. The F. chiloensis subsp. sandwicensis accessions were distinct from other taxonomic classes. The F. ×ananassa cultivars clustered most closely with the South American F. chiloensis supporting the origin of F. ×ananassa primarily from South American rather than North American F. chiloensis. While the North and South American F. chiloensis subspecies should remain separated based on their molecular distinction, consideration should be given to classifying F. chiloensis subsp. pacifica and subsp. lucida as different forma of a single North American F. chiloensis subspecies, rather than as separate subspecies. This is similar to the current classification of the two South American forma of F. chiloensis subsp. chiloensis (L.) Mill. Similarly, the F. virginiana subspecies should be reclassified as forms of a single subspecies, F. virginiana subsp. virginiana, rather than separate subspecies.

Implementing molecular marker technology in forage improvement

2003 ◽  
pp. 229-238
Author(s):  
M. Faville ◽  
B. Barrett ◽  
A. Griffiths ◽  
M. Schreiber ◽  
C. Mercer ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Genetic Variation ◽  
White Clover ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Seedling Vigour ◽  
Genome Map ◽  
Trait Locus ◽  
Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence

Mapping Unequal Crossing over Hotspot Region of Simple Sequence Repeat in Maize

2009 ◽  
Vol 35 (5) ◽  
pp. 958-961
Author(s):  
Ji-Hua TANG ◽  
Xi-Qing MA ◽  
Wen-Tao TENG ◽  
Jian-Bing YAN ◽  
Jing-Rui DAI ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Crossing Over ◽  
Sequence Repeat ◽  
Unequal Crossing Over ◽  
Simple Sequence
Sign in / Sign up

Export Citation Format

Share Document