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 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.

Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 277-290 ◽  
Author(s):  
Eline van Zijll de Jong ◽  
Kathryn M Guthridge ◽  
German C Spangenberg ◽  
John W Forster
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Sequence Repeat ◽  
Pasture Grass ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity.

scholarly journals Length polymorphisms of simple sequence repeat DNA in soybean.

Genetics ◽  
1992 ◽  
Vol 132 (4) ◽  
pp. 1131-1139 ◽  
Author(s):  
M S Akkaya ◽  
A A Bhagwat ◽  
P B Cregan
Keyword(s):  
Genetic Markers ◽  
Simple Sequence Repeat ◽  
Pcr Amplification ◽  
Pcr Primers ◽  
F1 Hybrids ◽  
Sequence Repeat ◽  
Pcr Products ◽  
Soybean Genotypes ◽  
Ssr Loci ◽  
Simple Sequence

Abstract The objective of this work was to ascertain the presence and degree of simple sequence repeat (SSR) DNA length polymorphism in the soybean [Glycine max (L.) Merr.]. A search of GenBank revealed no (CA)n or (GT)n SSRs with n greater than 8 in soybean. In contrast, 5 (AT)n and 1 (ATT)n SSRs with n ranging from 14 to 27 were detected. Polymerase chain reaction (PCR) primers to regions flanking the six SSR loci were used in PCR amplification of DNA from 43 homozygous soybean genotypes. At three loci, amplification produced one PCR product per genotype and revealed 6, 7 and 8 product length variants (alleles) at the three loci, respectively. F1 hybrids between parents carrying different alleles produced two PCR products identical to the two parents. Codominant segregation of alleles among F2 progeny was demonstrated at each locus. A soybean DNA library was screened for the presence of (CA/GT)n SSRs. Sequencing of positive clones revealed that the longest such SSR was (CA)9. Thus, (CA)n SSRs with n of 15 or more are apparently much less common in soybean than in the human genome. In contrast to humans, (CA)n SSRs will probably not provide an abundant source of genetic markers in soybean. However, the apparent abundance of long (AT)n sequences should allow this SSR to serve as a source of highly polymorphic genetic markers in soybean.

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.

A Low Mutation Rate For Chloroplast Microsatellites

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 943-947
Author(s):  
Jim Provan ◽  
Nicole Soranzo ◽  
Neil J Wilson ◽  
David B Goldstein ◽  
Wayne Powell
Keyword(s):  
Chloroplast Genome ◽  
Mutation Rate ◽  
Simple Sequence Repeats ◽  
Mutation Rates ◽  
Chloroplast Microsatellites ◽  
Ssr Loci ◽  
Nuclear Ssr ◽  
Monomorphic Population ◽  
Simple Sequence ◽  
Pinus Torreyana

Abstract We used chloroplast simple sequence repeats (cpSSRs) to examine whether there is any variation present in the chloroplast genome of Pinus torreyana (Parry ex Carrière) that may previously not have been detected using RFLPs. Analysis of 17 cpSSR loci showed no variation, which is consistent with previous cpRFLP work and confirms that the species is descended from an original, highly monomorphic population following a bottleneck. This lack of biological variation in the chloroplast genome of P. torreyana allowed us to estimate the mutation rates at cpSSR loci as between 3.2 × 10-5 and 7.9 × 10-5. This estimate is lower than published mutation rates at nuclear SSR loci but higher than substitution rates elsewhere in the chloroplast genome.

scholarly journals Chloroplast microsatellites in barley: the reduction of variability spectrum in cultivated forms

2006 ◽  
Vol 4 (1) ◽  
pp. 17-21 ◽  
Author(s):  
Natalia V Lukhanina ◽  
Marina G Sinyavskaya ◽  
Inessa M Goloenko ◽  
Oleg G Davydenko
Keyword(s):  
Simple Sequence Repeat ◽  
Rare Variants ◽  
Chloroplast Microsatellites ◽  
Repeat Polymorphism ◽  
Hordeum Vulgare L ◽  
Chloroplast Genomes ◽  
Intergenic Regions ◽  
Ssr Loci ◽  
Cultivated Barley ◽  
Simple Sequence

The chloroplast genomes of 67 accessions of Hordeum vulgare L were surveyed for simple sequence repeat polymorphism. Seven SSR loci were investigated, trnL/trnF and psbI-trnS intergenic regions, as well as two regions 3' trnS genes were polymorphic. The rare variants of these loci were revealed and five rare accessions were found. Our results show an extremely low level of cpDNA polymorphism of cultivated barley.

Genomic distribution of MITEs in barley determined by MITE-AFLP mapping

Genome ◽  
2006 ◽  
Vol 49 (12) ◽  
pp. 1616-1620 ◽  
Author(s):  
H. Takahashi ◽  
H. Akagi ◽  
K. Mori ◽  
K. Sato ◽  
K. Takeda
Keyword(s):  
Fragment Length Polymorphism ◽  
Linkage Groups ◽  
Entire Genome ◽  
Ssr Loci ◽  
Plant Genes ◽  
Flanking Sequences ◽  
Average Marker Density ◽  
Simple Sequence ◽  
Map Distance ◽  
Hordeum Vulgare Ssp

Miniature inverted-repeat transposable elements (MITEs) represent a large superfamily of transposons that are moderately to highly repetitive and frequently found near or within plant genes. To elucidate the organization of MITEs in the barley genome, MITEs were integrated into the genetic map of barley. In this report, we describe the use of MITEs in amplified fragment length polymorphism (AFLP) mapping, and demonstrate their superiority over conventional AFLP mapping. Barley MITEs include members of the Stowaway, Barfly, and Pangrangja families. By amplifying the flanking sequences of these MITEs, a total of 214 loci were mapped from a population of 93 doubled-haploid segregating individuals between Hordeum vulgare ssp. vulgare and H. vulgare ssp. spontaneum. The 214 MITE-AFLP and 40 anchor simple sequence repeat (SSR) loci were distributed on 7 linkage groups, covering a total map distance of 1 165 cM. The average marker density on each chromosome ranged between 3.4 and 9.6 cM per locus. Only 1 MITE-based locus was frequently found to be associated with MITE loci from the same family, resulting in clusters in chromosomal subregions. In barley, it will be possible to cover the entire genome with a limited set of MITE-based primers and to build highly dense maps of specific regions.

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.

Cross-species microsatellite amplification in Vasconcellea and related genera and their use in germplasm classification

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 786-798 ◽  
Author(s):  
T Kyndt ◽  
B Van Droogenbroeck ◽  
A Haegeman ◽  
I Roldán-Ruiz ◽  
G Gheysen
Keyword(s):  
Population Genetics ◽  
Chloroplast Microsatellites ◽  
Microsatellite Data ◽  
Chloroplast Microsatellite ◽  
Diversity Assessment ◽  
Ssr Primers ◽  
Polymorphism Rate ◽  
Nuclear Ssr ◽  
Simple Sequence ◽  
Future Population

To generate inexpensive and efficient DNA markers for addressing a number of population genetics problems and identification of wild hybrids in Vasconcellea, we have evaluated the use of simple sequence repeat (SSR) primers previously developed for other species. A set of 103 Vasconcellea accessions and some individuals of the related genera Carica and Jacaratia were analyzed with 10 primer pairs directing amplification of chloroplast microsatellites in Nicotiana tabacum and 9 nuclear SSR primer pairs recently identified in Vasconcellea × heilbornii. Heterologous amplification of chloroplast SSRs was successful for 8 of the 10 loci, of which 6 showed polymorphism. Seven of the 9 nuclear SSR primer pairs were useful in Vasconcellea and often also in Jacaratia and Carica, all revealing polymorphism. Exclusive haplotypes for each described taxon were identified based on chloroplast microsatellite data. Clustering based on separate nuclear and chloroplast data resulted in a clear grouping per taxon, but only low resolution was obtained above species level. The codominancy of nuclear SSRs and the general high polymorphism rate of SSR markers will make them more useful in future population genetics studies and diversity assessment in conservation programs.Key words: Carica, Jacaratia, Vasconcellea, simple sequence repeats, cross-species amplification, classification, interspecific hybrids.

Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 757-763 ◽  
Author(s):  
Shanmukhaswami S. Salimath ◽  
Antonio C. de Oliveira ◽  
Jeffrey L. Bennetzen ◽  
Ian D. Godwin
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Finger Millet ◽  
Dna Marker ◽  
Fragment Length Polymorphism ◽  
Eleusine Coracana ◽  
Randomly Amplified Polymorphic Dna ◽  
Simple Sequence ◽  
Restriction Fragment Length

Finger millet (Eleusine coracana), an allotetraploid cereal, is widely cultivated in the arid and semiarid regions of the world. Three DNA marker techniques, restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), and inter simple sequence repeat amplification (ISSR), were employed to analyze 22 accessions belonging to 5 species of Eleusine. An 8 probe – 3 enzyme RFLP combination, 18 RAPD primers, and 6 ISSR primers, respectively, revealed 14, 10, and 26% polymorphism in 17 accessions of E. coracana from Africa and Asia. These results indicated a very low level of DNA sequence variability in the finger millets but did allow each line to be distinguished. The different Eleusine species could be easily identified by DNA marker technology and the 16% intraspecific polymorphism exhibited by the two analyzed accessions of E. floccifolia suggested a much higher level of diversity in this species than in E. coracana. Between species, E. coracana and E. indica shared the most markers, while E. indica and E. tristachya shared a considerable number of markers, indicating that these three species form a close genetic assemblage within the Eleusine. Eleusine floccifolia and E. compressa were found to be the most divergent among the species examined. Comparison of RFLP, RAPD, and ISSR technologies, in terms of the quantity and quality of data output, indicated that ISSRs are particularly promising for the analysis of plant genome diversity.Key words: Eleusine coracana, finger millet, genome analysis, microsatellites, randomly amplified polymorphic DNA, restriction fragment length polymorphism, simple sequence repeats.

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