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

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.

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North American Study on Essential Derivation in Maize: II. Selection and Evaluation of a Panel of Simple Sequence Repeat Loci

Crop Science ◽

10.2135/cropsci2009.03.0121 ◽

2010 ◽

Vol 50 (2) ◽

pp. 486-503 ◽

Cited By ~ 11

Author(s):

Alex L. Kahler ◽

Jonathan L. Kahler ◽

Steven A. Thompson ◽

Ronald S. Ferriss ◽

Elizabeth S. Jones ◽

...

Keyword(s):

North American ◽

Simple Sequence Repeat ◽

American Study ◽

Sequence Repeat ◽

North American Study ◽

Simple Sequence

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RAPD analysis of the relationship of North and South American subspecies of Fragaria chiloensis

Canadian Journal of Botany ◽

10.1139/b98-180 ◽

1998 ◽

Vol 76 (10) ◽

pp. 1812-1817 ◽

Cited By ~ 1

Author(s):

Sue Porebski ◽

Paul M Catling

Keyword(s):

North American ◽

Random Amplified Polymorphic Dna ◽

Molecular Evidence ◽

South American ◽

Cophenetic Correlation ◽

The North ◽

Fragaria Chiloensis ◽

Protection And Utilization ◽

Relationship Of ◽

North And South

To improve the intraspecific classification of Fragaria chiloensis (L.) Duchesne, 35 plants including 5 North American ssp. lucida, 15 North American ssp. pacifica, and 15 South American ssp. chiloensis were analysed using random amplified polymorphic DNA (RAPDs). From 100 primers screened, 12 were selected providing 62 scorable polymorphic bands. The phenogram (cophenetic correlation, r = 0.99) based on UPGMA clustering of Jaccard's coefficients revealed a clear division between North American and South American plants, but only partial separation was shown between the two North American subspecies. This is the first comprehensive molecular evidence for major genetic divergence between the North American and South American subspecies of F. chiloensis and suggests greater genetic variation within the Canadian material of the North American ssp. pacifica than within the South American ssp.chiloensis. These findings strongly support protection and utilization of wild Canadian Fragaria germplasm for crop improvement.Key words: strawberry, Fragaria chiloensis, ssp. chiloensis, ssp. pacifica, ssp. lucida, RAPD, variation, germplasm, Canada, United States, Chile.

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Characterization of microsatellite markers in eastern white pine

Genome ◽

10.1139/g96-138 ◽

1996 ◽

Vol 39 (6) ◽

pp. 1102-1108 ◽

Cited By ~ 103

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.

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Simple sequence repeat (SSR) markers for Elymus, Pseudoroegneria and Pascopyrum species (Triticeae: Gramineae)

Plant Genetic Resources ◽

10.1017/s1479262111000694 ◽

2011 ◽

Vol 9 (4) ◽

pp. 489-494 ◽

Cited By ~ 6

Author(s):

I. W. Mott ◽

S. R. Larson ◽

B. S. Bushman

Keyword(s):

Ssr Markers ◽

North American ◽

Simple Sequence Repeat ◽

Binary Data ◽

Expressed Sequence Tag ◽

Molecular Mapping ◽

Perennial Grass ◽

Grass Species ◽

Sequence Repeat ◽

Simple Sequence

The Triticeae tribe (Poaceae) includes several important cereal crops, cultivated forages, annual and perennial grass weeds and ecologically diverse native North American grasses. Elymus L. is the largest and most complex genus in the Triticeae tribe with approximately 150 polyploid perennial grass species occurring worldwide. The genomic constitutions of approximately 40% of the Elymus species are unknown. Molecular markers are needed to facilitate genetic analysis of diversity and functional traits in these species. We have developed simple sequence repeat (SSR) markers for use in Elymus based on Elymus expressed sequence tag sequences. To test the polymorphic content and transferability of these SSRs, 100 SSR primer pairs were tested on 84 plants representing seven North American Elymus, Pseudoroegneria and Pascopyrum species. The number of bands produced from each of the SSRs ranged from 1 to 11 with an average of 4.3 bands/SSR. A subset of the 23 most polymorphic SSRs produced 142 bands, an average of 6.2 bands/SSR. Binary data from the 100 SSRs successfully separated all individuals into their respective accessions in a neighbour-joining phylogram with a 100% confidence interval. Analysis of molecular variance showed that 29.9% of the total variation was within and 70.1% was among the accessions. These SSRs will be a useful tool for investigating genetic diversity, genome constitutions and molecular mapping in Elymus and other Triticeae grasses.

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Genetic Diversity of Seashore Paspalum Revealed with Simple Sequence Repeat Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04860-19 ◽

2020 ◽

Vol 145 (4) ◽

pp. 228-235

Author(s):

Qing Shen ◽

Hua Bian ◽

Hai-yan Wei ◽

Li Liao ◽

Zhi-yong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Ssr Marker ◽

Diversity Index ◽

Polymorphic Information Content ◽

Principal Component ◽

Sequence Repeat ◽

Similarity Coefficients ◽

Seashore Paspalum ◽

Simple Sequence

Seashore paspalum (Paspalum vaginatum) is an important warm-season turfgrass distributed in tropical and coastal areas. It has excellent resistance to abiotic stresses, such as salinity, drought, and low temperature. However, the research on genetic diversity of local P. vaginatum collections from China is limited. In this study, the genetic diversity among 58 P. vaginatum accessions from four different provinces in China and four cultivars were assessed using simple sequence repeat (SSR) markers. The results indicated that a total of 45 alleles were detected by 19 polymorphic markers, with a range of 2 to 4 and an average of 2.4 alleles per marker. The genetic similarity coefficients between each pair of the 58 P. vaginatum accessions and four cultivars ranged from 0.51 to 1.00, with an average of 0.77. The range of variation of Shannon diversity index of each SSR marker was 0.047 to 1.075, with an average of 0.486. The polymorphic information content of each SSR marker varies from 0.016 to 0.577, with an average of 0.249. The results of cluster analysis and principal component analysis (PCA) showed that 58 P. vaginatum accessions and four cultivars were divided into four groups. These results provide the theoretical basis for the genetic diversity assessments and molecular marker–assisted breeding of P. vaginatum species.

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Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs05016-20 ◽

2021 ◽

pp. 1-11

Author(s):

Beibei Li ◽

Xiucai Fan ◽

Ying Zhang ◽

Chonghuai Liu ◽

Jianfu Jiang

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Ssr Markers ◽

Structure Analysis ◽

North American ◽

Simple Sequence Repeat ◽

North American Species ◽

Sequence Repeat ◽

Genetic Diversity And Structure ◽

Simple Sequence

Chinese wild Vitis is a useful gene source for resistance to biotic and abiotic stresses, although there is little research on its genetic diversity and structure. In this study, nine simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure among 100 Vitis materials. These materials included 77 indigenous accessions representing 23 of 38 wild Vitis species/cultivars in China, 18 V. vinifera cultivars, and the five North American species V. aestivalis, V. girdiana, V. monticola, V. acerifolia, and V. riparia. The SSR loci used in this study for establishing an international database (Vitis International Variety Catalogue) revealed a total of 186 alleles in 100 Vitis accessions. The mean values for the gene diversity (GD) and polymorphism information content (PIC) per locus were 0.91 and 0.90, respectively, which indicates that the discriminatory power of the markers is high. Based on the genetic distance data, the 100 Vitis accessions were divided into five primary clusters by cluster analysis, and five populations by structure analysis; these results indicate these Chinese wild grapes were more genetically close to European grapes than to North American species. In addition, the clustering patterns of most accessions correlated with the geographic distribution. An analysis of molecular variance (AMOVA) revealed that 3.28%, 3.27%, and 93.46% of the variance occurred between populations, between individuals within populations, and between individuals within the entire population, respectively. In addition, we identified three previously undescribed accessions (Wuzhi-1, MZL-5, and MZL-6) by cluster analysis. Our results reveal a high level of genetic diversity and variability in Vitis from China, which will be helpful in the use of genetic resources in future breeding programs. In addition, our study demonstrates that SSR markers are highly suitable for further genetic diversity analyses of Chinese wild grapes.

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European and Asian Pears: Simple Sequence Repeat–Polyacrylamide Gel Electrophoresis-based Analysis of Commercially Important North American Cultivars

HortScience ◽

10.21273/hortsci.41.2.304 ◽

2006 ◽

Vol 41 (2) ◽

pp. 304-309 ◽

Cited By ~ 9

Author(s):

Ashok K. Ghosh ◽

Lewis N. Lukens ◽

David M. Hunter ◽

Judith N. Strommer

Keyword(s):

North American ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Polyacrylamide Gel Electrophoresis ◽

Polyacrylamide Gel ◽

Sequence Repeat ◽

Ssr Loci ◽

Commercially Important ◽

Definition Of ◽

Simple Sequence

The genus Pyrus (pear) includes species and cultivars of great diversity. We have tested the feasibility of a polyacrylamide gel eletrophoresis (PAGE)-based +/– simple sequence repeat (SSR) screen as a means of defining relationships amongst pears of commercial importance in North America. The screen included 28 pear accessions, including economically important cultivars, numbered selections from breeding programs and interspecific hybrids. It relied on 18 SSR primer pairs, each of which produced polymorphic banding patterns in all the genotypes examined. Fragments were scored for presence or absence within genotypes. The results show that amplification and analysis of a small number of SSR loci enable identification of cultivars and reasonable definition of genetic relationships in North American pears. Seven primer pairs were sufficient to distinguish the 28 pear cultivars. Analyses using both distance and parsimony criteria grouped cultivars in a manner consistent with known pedigrees and sites of origin.

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Implementing molecular marker technology in forage improvement

Proceedings of the New Zealand Grassland Association ◽

10.33584/jnzg.2003.65.2498 ◽

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

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Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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