scholarly journals Identification of Simple-sequence Repeats in Malus (Apple)

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 855D-855 ◽  
Author(s):  
Amy K. Szewc-McFadden ◽  
Sharon Bliek ◽  
Christopher G. Alpha ◽  
Warren F. Lamboy ◽  
James R. McFerson
Keyword(s):  
Simple Sequence Repeats ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Germplasm Characterization ◽  
The Core ◽  
Marker Data ◽  
Core Subset ◽  
Germplasm Collections ◽  
Ssr Loci ◽  
Simple Sequence

Simple-sequence repeats (SSRs) are efficient and informative DNA markers with great potential for germplasm characterization. When used to characterize large arrays of accessions, such as the core subset of the USDA/ARS Malus collection, SSRs may be more effective than other approaches, such as restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD). For example, SSRs can be PCR-amplified and fluorescence-based detected; they also appear to be abundantly disbursed throughout plant genomes and yield abundant polymorphisms in most taxa studied. We are conducting an extensive screening of a size-fractionated library of Malus ×domestica cv. Golden Delicious to identify and characterize selected SSR loci. We are applying genetic information revealed by SSR loci in combination with passport and horticultural data to better comprehend genetic identity and relatedness in Malus germplasm collections and help develop the Malus core subset. Ultimately, application of molecular marker data will permit improved conservation and use of genetic resources.

scholarly journals Utilization of Identified Simple Sequence Repeats (SSRs) in Malus ×domestica (Apple) for Germplasm Characterization

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 619b-619 ◽  
Author(s):  
Amy K. Szewc-McFadden ◽  
Warren F. Lamboy ◽  
James R. McFerson
Keyword(s):  
Germplasm Collection ◽  
Ex Situ ◽  
Dna Library ◽  
The Core ◽  
Core Subset ◽  
Ssr Loci ◽  
Dna Fragment ◽  
Simple Sequence

To comprehend genetic identity and relatedness in Malus germplasm held in situ and ex situ, we are employing simple sequence repeat (SSR) DNA fragment information in combination with passport and horticultural data. SSRs offer certain advantages for characterizing large arrays of germplasm efficiently. They are abundantly dispersed throughout plant genomes and are exceedingly polymorphic. In addition, they can be PCR-amplified and detected by automated fluorescence-based technology. A size-fractionated DNA library of M. ×domestica cv Golden Delicious was screened to identify SSR loci. Eight loci were found to be reliably informative and were used to prepare locus-specific primer pairs. Characterization of the 75 M. ×domestica accessions included in the core subset of the USDA-ARS Malus germplasm collection revealed six of the eight loci were polymorphic within the array. The number of alleles per locus ranged from two to 21. Throughput was enhanced by multiplexing, allowing simultaneous use of two or three primer pairs. With improved genetic characterization of Malus germplasm, we intend to better develop and relate the core subset to the rest of the collection and to in situ Malus genetic resources. SSR markers appear to be an efficient and reliable tool to expedite this process.

scholarly journals Genepool Variation in Genus Glycine Subgenus Soja Revealed by Polymorphic Nuclear and Chloroplast Microsatellites

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 793-803 ◽  
Author(s):  
W Powell ◽  
M Morgante ◽  
J J Doyle ◽  
J W McNicol ◽  
S V Tingey ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Diversity Indices ◽  
Chloroplast Microsatellites ◽  
The Core ◽  
Phenetic Relationships ◽  
Allelic Variability ◽  
Soybean Genotypes ◽  
Ssr Loci ◽  
Nuclear Ssrs ◽  
Simple Sequence

Abstract A combination of nuclear and chloroplast simple sequence repeats (SSRs) have been used to investigate the levels and pattern of variability detected in Glycine max and G. soja genotypes. Based on the analysis of 700 soybean genotypes with 115 restriction fragment length polymorphism (RFLP) probes, 12 accessions were identified that represent 92% of the allelic variability detected in this genepool. These 12 core genotypes together with a sample of G. max and G. soja accessions were evaluated with 11 nuclear SSRs that detected 129 alleles. Compared with the other G. max and G. soja genotypes sampled, the core genotypes represent 40% of the allelic variability detected with SSRs. Despite the multi-allelic nature of soybean SSRs, dendrograms representing phenetic relationships between accessions clustered according to their subspecies origin. In addition to biparentally inherited nuclear SSRs, two uniparentally (maternally) transmitted chloroplast SSRs were also studied. A total of seven haplotypes were identified, and diversity indices of 0.405 ± 0.088 and 0.159 ± 0.071 were obtained for the two chloroplast SSRs. The availability of polymorphic SSR loci in the chloroplast genome provides new opportunities to investigate cytonuclear interactions in plants.

scholarly journals Simple Sequence Repeats (SSRs) in Watermelon (Citrullus lanatus L.)

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 840E-840
Author(s):  
R.L. Jarret ◽  
S. Kresovich ◽  
T. Holms ◽  
Janelle Evans ◽  
Z. Liu
Keyword(s):  
New Hampshire ◽  
Simple Sequence Repeats ◽  
Genomic Dna ◽  
Citrullus Lanatus ◽  
Germplasm Characterization ◽  
Dna Library ◽  
Automated Dna Sequencing ◽  
Ssr Loci ◽  
Genomic Dna Library ◽  
Simple Sequence

Simple sequence repeats (SSRs) were isolated from a size-fractionated genomic DNA library of watermelon (Citrullus lanatus L. cv. New Hampshire Midget). Screening of the library with five oligonucleotide probes, including (GT)11, (AT)11, (CT)11, (GC)11, and (TAA)8, detected the occurrence of 96 positive colonies among ≈8000 recombinants. Automated DNA sequencing revealed the presence of SSRs. PCR primer pairs homologous to the regions flanking the SSR loci were synthesized commercially and used to screen 56 watermelon genotypes for the occurrence of SSR polymorphisms. Amplification products were separated using nondenaturing PAGE. Eighty percent of the primer pairs produced amplification products of the expected size and detected polymorphisms among the genotypes examined. The use of SSRs for watermelon germplasm characterization is discussed.

scholarly journals Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

scholarly journals Comparative Analysis of Genetic Similarity between Perennial Ryegrass Genotypes Investigated With AFLPs, ISSRs, RAPDs and SSRs

2011 ◽  
Vol 42 (No. 3) ◽  
pp. 87-94 ◽  
Author(s):  
U.K. Posselt ◽  
P. Barre ◽  
G. Brazauskas ◽  
L.B. Turner
Keyword(s):  
Perennial Ryegrass ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Correlation Coefficients ◽  
Inter Simple Sequence Repeat ◽  
Grass Species ◽  
Sequence Repeat ◽  
Simple Sequence

Perennial ryegrass (Lolium perenne L.) is the most important grass species used in temperate grassland agriculture. Our objective was to obtain an overview of the genetic relationships between 20 individual genotypes of perennial ryegrass of diverse origins, using amplified fragment length polymorphism (AFLP), inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD) and two sets of simple sequence repeat (SSR) markers. All 20 individuals were uniquely fingerprinted by all four marker systems and comparisons were made on the basis of 85 markers each. Mean genetic similarities were estimated at 0.31, 0.43, 0.23 and 0.15 for AFLPs, ISSRs, RAPDs and SSRs, respectively. Cophenetic values resulted in good (AFLP and SSR-B = 0.88) to moderately good fits (ISSR = 0.76, RAPD = 0.70, and SSR-A = 0.79). Comparing the four marker systems to each other, AFLP and SSR-A were correlated best (r = 0.57). All other comparisons revealed rather low correlation coefficients in the Mantel Z test. With twice as many markers cophenetic values increased to a very good fit for AFLPs (0.90) and SSRs (0.92).      

scholarly journals Identificación de híbridos de Citrus aurantifolia X Citrus limon utilizando marcadores de Secuencias Simples Repetidas (SSR)

2017 ◽  
Vol 8 (6) ◽  
pp. 1397
Author(s):  
Manuel De Jesús Bermúdez Guzmán ◽  
Luis Felipe Guzmán Rodríguez ◽  
Karina De la Paz García Mariscal ◽  
Paola Andrea Palmeros Suárez ◽  
Mario Orozco Santos
Keyword(s):  
Simple Sequence Repeats ◽  
Random Amplified Polymorphic Dna ◽  
Citrus Limon ◽  
Citrus Aurantifolia ◽  
Simple Sequence

  La apomixis es un tipo de reproducción asexual donde la formación de semillas porta embriones genéticamente idénticos al progenitor, constituyendo un obstáculo en programas de mejoramiento genético de muchas especies vegetales, incluyendo cítricos. La identificación de plantas híbridas se realiza mediante caracteres morfológicos, ensayos isoenzimáticos y marcadores moleculares. Estos últimos se han utilizado con mayor frecuencia debido a su precisión, destacando el uso del DNA polimórfico amplificado al azar (RAPD, “Random Amplified Polymorphic DNA”) y Secuencias Simples Repetidas (SSR, “Simple Sequence Repeats”). En limón mexicano (C. aurantifolia) únicamente se han utilizado marcadores RAPD para la identificación de híbridos, por lo que no existen reportes que hagan uso de marcadores SSR para este fin. El objetivo del presente trabajo fue identificar híbridos derivados de la polinización controlada entre C. aurantifolia var. “Colimex” X C. limon var. “Rosenberg” y su recíproca utilizando marcadores moleculares SSR. Durante el año 2014-2016 se colectaron hojas de árboles de limón de aproximadamente 12 meses de edad, que se encuentran establecidos en el Campo Experimental Tecomán del INIFAP. Se evaluaron en total ocho marcadores moleculares SSR sobre los progenitores utilizados en este estudio y fueron seleccionados los oligonucleótidos TAA45 y cAGG09 para la identificación de híbridos en las dos poblaciones progenie. De un total de 40 y 43 individuos F1 procedentes de la cruza bidireccional entre “Colimex” X “Rosenberg”, se lograron identificar 17 y 35 plantas híbridas, respectivamente. Los resultados indican que los marcadores SSR son eficientes y confiables para la identificación de híbridos de limón mexicano.

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