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.

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.

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 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 Detection of simple sequence repeats in the chloroplast genome of Tetraphis pellucida Hedw.

2016 ◽  
Vol 3 (2) ◽  
pp. 207 ◽  
Author(s):  
Asheesh Shanker
Keyword(s):  
Chloroplast Genome ◽  
Simple Sequence Repeats ◽  
Average Length ◽  
Accession Number ◽  
Repeat Type ◽  
Perl Script ◽  
Repeat Units ◽  
Short Repeat ◽  
Diversity Studies ◽  
Simple Sequence

Simple sequence repeats (SSRs) consist of short repeat motifs of 1-6 nucleotides and are found in DNA sequences.The present study was conducted to detect SSRs in chloroplast genome of Tetraphis pellucida (Accession number: NC_024291), downloaded from the National Center for Biotechnology Information (NCBI). The sequence was mined with the help of MISA, a Perl script, to detect SSRs. The length of SSRs defined as ≥12 for mono, di, tri and tetranucleotide, ≥15 for pentanucleotide and ≥18 for hexanucleotide repeats. In total, 41 perfect microsatellites were identified in 127.489 kb sequence mined. An average length of 13.56 bp was calculated for mined SSRs with a density of 1 SSR/3.04 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 20 nt. Dinucleotides (14, 34.15%) were the most frequent repeat type, followed by tetranucleotides (10, 24.39%), trinucleotides (7, 17.07%), mononucleotides (6, 14.63%) and pentanucleotide (4, 9.76%) repeats. Hexanucleotide repeats were completely absent in chloroplast genome of Tetraphis pellucida. The mined SSRs can be used to develop molecular markers and genetic diversity studies in Tetraphis species.

Characterisation and inheritance of polymorphic plastid microsatellites in Abies

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 857-864 ◽  
Author(s):  
G. G. Vendramin ◽  
B. Ziegenhagen
Keyword(s):  
Population Genetics ◽  
Simple Sequence Repeats ◽  
Natural Populations ◽  
Abies Alba ◽  
Chloroplast Microsatellites ◽  
Length Variation ◽  
Pcr Products ◽  
Considerable Length ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Two polymorphic microsatellite loci were identified and sequenced in the genus Abies, using primer pairs derived from chloroplast simple sequence repeats (SSRs) of Pinus thunbergii. PCR products exhibited considerable length variation among six different Abies species and within Abies alba. F1 progeny of both an interspecific and an intraspecific reciprocal cross confirmed that the two SSRs were predominantly paternally inherited. The maternal size variant predominantly occurred in the megagametophytes analysed. First analysis of the two chloroplast microsatellites in seven natural populations of A. alba revealed 36 different haplotypes. The use of these highly polymorphic SSRs as potential markers in population genetics is discussed.Key words: Abies, chloroplast simple sequence repeats, sequences, inheritance, intraspecific variation, population genetics.

scholarly journals Simple Sequence Repeats and Genome Plasticity in Streptococcus agalactiae

2010 ◽  
Vol 192 (15) ◽  
pp. 3990-4000 ◽  
Author(s):  
Robert Janulczyk ◽  
Vega Masignani ◽  
Domenico Maione ◽  
Hervé Tettelin ◽  
Guido Grandi ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Streptococcus Agalactiae ◽  
Antigenic Variation ◽  
Phase Variation ◽  
Open Reading Frames ◽  
Genome Plasticity ◽  
Gram Negative ◽  
Ssr Loci ◽  
Gram Negative Organisms ◽  
Simple Sequence

ABSTRACT Simple sequence repeats (SSRs) and their role in phase variation have been extensively studied in Gram-negative organisms, where they have been associated with antigenic variation and other adaptation strategies. In this study, we apply comparative genomics in order to find evidence of slipped-strand mispairing in the human Gram-positive pathogen Streptococcus agalactiae. In two consecutive screenings, 2,233 (650 + 1,583) SSRs were identified in our reference genome 2603V/R, and these loci were examined in seven other S. agalactiae genomes. A total of 56 SSR loci were found to exhibit variation, where gain or loss of repeat units was observed in at least one other genome, resulting in aberrant genotypes. Homopolymeric adenine tracts predominated among the repeats that varied. Positional analysis revealed that long polyadenine tracts were overrepresented in the 5′ ends of open reading frames (ORFs) and underrepresented in the 3′ ends. Repeat clustering in ORFs was also examined, and the highest degree of clustering was observed for a capsule biosynthesis gene and a pilus sortase. A statistical analysis of observed over expected ratios suggested a selective pressure against long homopolymeric tracts. Altered phenotypes were verified for three genes encoding surface-attached proteins, in which frameshifts or fusions led to truncation of proteins and/or affected surface localization through loss or gain of the cell wall sorting signal. The data suggest that SSRs contributes to genome plasticity in S. agalactiae but that the bet-hedging strategy is different from Gram-negative organisms.

scholarly journals Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 143
Author(s):  
Lei Zhu ◽  
Huayu Zhu ◽  
Yanman Li ◽  
Yong Wang ◽  
Xiangbin Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Motif Length ◽  
Pair Group ◽  
Ssr Loci ◽  
Ssr Frequency ◽  
Basic And Applied Research ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

scholarly journals Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

2020 ◽  
Author(s):  
Lei Zhu ◽  
Hua yu Zhu ◽  
Yan man Li ◽  
Xiang bin Wu ◽  
Jin tao Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomics ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Diversity Analysis ◽  
Motif Length ◽  
Genetic Diversity Analysis ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Background The Cucurbita genus contains important economic crops in the world, while limited molecular markers have been developed in the past years. Simple sequence repeats (SSR) markers are powerful tools for the study of genetic mapping construction, genetic diversity analysis and genome wide association. The availability of pumpkin genome information has made it possible to analyze SSRs in genome wide across three Cucurbita species. Results In this paper, based on the whole genome sequences, 34,375 SSR loci were found in C. moschata, 30,577 SSR loci were found in C. maxima and 38,104 SSR loci were found in C. pepo. C. pepo has the maximum density of SSRs with an average of 145 SSR/Mb. In general, the frequency in total SSR loci decreased with the increase of the motif length, dinucleotide motifs were the most common motifs in the three species, and for the same repeat types, the SSR frequency decreased sharply with the increase of the repeat number. Most of those SSR loci were suitable for marker development (84.75% in C. moscata, 94.53% in C. maxima and 95.09% in C. pepo). Based on those markers, we compared and analyzed the cross-species SSR markers between C. pepo and other Cucurbitaceae species by silico-PCR. Using these cross-species primers, the high collinear relationships between C. pepo and the other two species were detected, respectively. Furthermore, the application of SSR markers in genetic diversity analysis was tested in C. pepo, the results showed that they were good tools to be used in genetic diversity analysis. Conclusion In this study, the genome wide SSR markers were detected from three Cucurbita species, and some of their applications were proved by comparative genomics and genetic diversity analysis. The large number of genome-wide SSR markers and crossspecies markers would promote the basic and applied studies of Cucurbita species, such as gene mapping, QTLs mapping, comparative genomics and marker-assisted breeding.

scholarly journals Molecular polymorphism in SSR loci of the RB92579 variety: perspectives for use in sugarcane improvement and industrial sector

2020 ◽  
pp. 729-738
Author(s):  
Rodrigo Desordi ◽  
Claudete Aparecida Mangolin ◽  
Gustavo Barizon Maranho ◽  
Rone Charles Maranho ◽  
Maria de Fátima Pires da Silva Machado
Keyword(s):  
Simple Sequence Repeats ◽  
Genetic Divergence ◽  
Agricultural Productivity ◽  
Dna Amplification ◽  
Industrial Sector ◽  
Sugarcane Variety ◽  
Mato Grosso ◽  
South Central ◽  
Ssr Loci ◽  
Simple Sequence

The sugarcane variety RB92579 has excellent agricultural productivity, very low flowering, efficient water use, and a high content of sucrose. Despite its excellent agricultural productivity, the RB92579 has not been used as a direct parent in sugarcane improvement. The main goal of the present study was to investigate polymorphisms at the SSR and EST-SSR loci of the RB92579 sugarcane variety to evaluate its potential for breeding and generating new varieties and to guide better use by the industrial sector. A total of 92 samples of the RB92579 variety were collected from plants in the fourth cutting stage grown in two Brazilian states: Paraná (PR; South region) and Mato Grosso do Sul (MS; South-Central region). Four primers for DNA simple sequence repeats (SSRs) and eight primers for expressed sequence tags for simple sequence repeats (EST-SSR) were used for DNA amplification. The polymorphism occurrence in the 12 SSR loci was 28% in the PR and MS populations, with a total of 25 alleles and an average of 2.08 alleles/loci. High values for mean observed heterozygosity, a high value for genetic identity and a low level of population differentiation was found in samples from the PR and MS states. The number of polymorphisms in the EST-SSR and noncoding SSR loci as well as the genetic divergence was low. However, the high heterozygosity in both populations indicates that the RB92579 variety can be used as a parent to generate new cultivars. On the other hand, the low coefficient of genetic divergence and high identity coefficient indicate that there is genetic uniformity; therefore, there is no need for differential industrial adaptations for pretreatment or enzymatic hydrolysis of the sugarcane bagasse from RB92579 at the same cutting stage and planted in the two regions (PR and MS).

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