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 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.

Highly informative nature of inter simple sequence repeat (ISSR) sequences amplified using tri- and tetra-nucleotide primers from DNA of cauliflower (Brassica oleracea var. botrytis L.)

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 890-896 ◽  
Author(s):  
B Bornet ◽  
C Muller ◽  
F Paulus ◽  
M Branchard
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Oleracea ◽  
Simple Sequence Repeat ◽  
Dna Interaction ◽  
Inter Simple Sequence Repeat ◽  
Homology Search ◽  
Sequence Repeat ◽  
Pcr Products ◽  
Or Gene ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) sequences as molecular markers can lead to the detection of polymorphism and also be a new approach to the study of SSR distribution and frequency. In this study, ISSR amplification with nonanchored primer was performed in closely related cauliflower lines. Fourty-four different amplified fragments were sequenced. Sequences of PCR products are delimited by the expected motifs and number of repeats, which validates the ISSR nonanchored primer amplification technique. DNA and amino acids homology search between internal sequences and databases (i) show that the majority of the internal regions of ISSR had homologies with known sequences, mainly with genes coding for proteins implicated in DNA interaction or gene expression, which reflected the significance of amplified ISSR sequences and (ii) display long and numerous homologies with the Arabidopsis thaliana genome. ISSR amplifications revealed a high conservation of these sequences between Arabidopsis thaliana and Brassica oleracea var. botrytis. Thirty-four of the 44 ISSRs had one or several perfect or imperfect internal microsatellites. Such distribution indicates the presence in genomes of highly concentrated regions of SSR, or "SSR hot spots." Among the four nonanchored primers used in this study, trinucleotide repeats, and especially (CAA)5, were the most powerful primers for ISSR amplifications regarding the number of amplified bands, level of polymorphism, and their nature. Key words: inter simple sequence repeat (ISSR), nonanchored primer, DNA marker sequence, SSR, cluster of SSRs.

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

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 Microsatellite DNA markers in Populus tremuloides

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 293-297 ◽  
Author(s):  
Muhammad H Rahman ◽  
S Dayanandan ◽  
Om P Rajora
Keyword(s):  
Populus Tremuloides ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
Simple Sequence Repeat ◽  
Mendelian Inheritance ◽  
Inheritance Pattern ◽  
Sequence Repeat ◽  
Microsatellite Dna Markers ◽  
Ssr Loci ◽  
Simple Sequence

Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars. Key words: poplar, microsatellites, genetic mapping, simple sequence repeat (SSR) markers, DNA fingerprinting.

Identifi cation of Species-Diagnostic Inter Simple Sequence Repeat Markers for Ten Phyllanthus Species

2011 ◽  
Vol 66 (3-4) ◽  
pp. 167-172 ◽  
Author(s):  
Sunil Kumar Senapati ◽  
Subhashree Aparajita ◽  
Gyana Ranjan Rout
Keyword(s):  
Simple Sequence Repeat ◽  
Viral Infections ◽  
Pcr Amplification ◽  
Inter Simple Sequence Repeat ◽  
Diagnostic Markers ◽  
Sequence Repeat ◽  
Botanical Drug ◽  
Polymerase Chain ◽  
Medicinal Plant Material ◽  
Simple Sequence

Phyllanthus has been widely used in traditional medicine as an antipyretic, a diuretic, and to treat liver diseases and viral infections. Correct genotype identification of medicinal plant material remains important for the botanical drug industry. Limitations of chemical and morphological approaches for authentication have generated the need for newer methods in quality control of botanicals. In the present study, attempts were made to identify species- diagnostic markers for ten Phyllanthus species using the inter simple sequence repeat-polymerase chain reaction (ISSR-PCR) fingerprinting method. PCR amplification using seven ISSR primers resulted in significant polymorphism among the populations from different species. P. angustifolius and P. urinaria showed monomorphic frequency of maximum (63.88%) and minimum (20.64%), respectively. Seventeen species-diagnostic markers were identified for seven species (P. acidus, P. emblica, P. fraternus, P. urinaria, P. rotundifolius, P. amarus, and P. angustifolius) while no marker was detected for P. reticulatus, P. nivosus, and P. virgulatus. A maximum of six species-diagnostic markers were identified for P. acidus and a minimum of only one of 755 bp was available for P. amarus. Among the seventeen markers, nine were present in all individuals of particular species. The speciesspecific differences in fragment numbers and sizes could be used as diagnostic markers to distinguish the Phyllanthus species quickly

scholarly journals Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat

2014 ◽  
Vol 139 (5) ◽  
pp. 507-517 ◽  
Author(s):  
Xiaoying Li ◽  
Hongxia Xu ◽  
Jianjun Feng ◽  
Junwei Chen
Keyword(s):  
Large Scale ◽  
Trinucleotide Repeat ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Eriobotrya Japonica ◽  
Pcr Products ◽  
Ssr Loci ◽  
Trait Locus ◽  
High Level ◽  
Simple Sequence

Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotrya japonica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pairs were designed from partial SSRs and used for polymerase chain reaction (PCR) amplification. Of these primer pairs, 54 exhibited amplification and 33 were polymorphic. The number of alleles at these loci ranged from two to 17, and the polymorphism information content values ranged from 0.24 to 0.89. We tested the transferability of 33 SSR polymorphic primer pairs in apple and pear, and the transferability rates in these two species were 90.9% and 87.9%, respectively. A high level of marker polymorphism was observed in apple [Malus ×domestica (66.7%)], whereas a low level was observed in pear [Pyrus sp. (51.5%)]. In addition, the PCR products from seven SSR primer pairs were selected for sequence analysis, and 89.2% of the fragments were found to contain SSRs. SSR motifs were conserved among loquat, apple, and pear. According to our sequencing results for real SSR loci, ≈12,490 SSR loci were present in these loquat unigenes. The cluster dendrogram showed a distinct separation into different groups for these three species, indicating that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the species of Maloideae in the Rosaceae. The results of our identified SSRs should be useful for genetic linkage map construction, quantitative trait locus mapping, and molecular marker-assisted breeding of loquat and related species.

scholarly journals Does plant –microbe’s common Inter Simple Sequence Repeat lead to a new recombination? A novel mechanism of pathogenicity

2021 ◽  
Author(s):  
Purvi M. Rakhashiya ◽  
Pritesh P. Bhatt ◽  
Vrinda S. Thaker
Keyword(s):  
Simple Sequence Repeat ◽  
Plant Pathogens ◽  
Pcr Amplification ◽  
Inter Simple Sequence Repeat ◽  
Hybridization Technique ◽  
Sequence Repeat ◽  
Plant Host ◽  
Host Pathogen ◽  
Monomorphic Band ◽  
Simple Sequence

AbstractA total of eight varieties of the mango from an orchard were studied using molecular markers to understand the host-pathogen interaction. From the infected leaves of the plant, a total of the 8 bacterial pathogens (Exiguobacterium arabatum, Pseudomonas mendocina, Pantoea dispersa, Bacillus sp. Pantoea ananatis, Micrococcous luteus, Microbacterium_sp., Enterobacter cloacae) were isolated and identified. All the host varieties of mango were distinguished for the genetic diversity using the Inter Simple Sequence Repeat (ISSR) DNA markers. This set of ISSR marker primers were also used for the mango pathogens. PCR amplification of the ISSR primers showed polymorphic and monomorphic band patterns in the host plants and in their pathogens. The monomorphic band generated by PCR amplification in the host and in the pathogen, by the common primer, is selected and used for PCR hybridization technique. PCR products obtained from the host, pathogen and hybridization were cloned, sequenced and compared. A multiple sequence alignment of these sequences revealed that the product of hybridization PCR was mixture of host and pathogen sequences. On this basis, we hypothesize a possibility for the recombination of host-microbes DNA as one of the mechanisms of pathogenicity for the plant pathogens using hybrid PCR technique. The possible mechanism of recombination for plant host and its pathogen is discussed.HighlightsInter Simple Sequence Repeat markers used to (i) Fingerprint the pathogens and their host (mango) and (ii) for study of the possibilities for the recombination as mechanism of pathogenicity.

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