scholarly journals Microsatellite analysis indicates the specific genetic basis of Czech bolting garlic

2014 ◽  
Vol 50 (No. 3) ◽  
pp. 226-234 ◽  
Author(s):  
J. Ovesná ◽  
L. Leišová-Svobodová ◽  
L. Kučera
Keyword(s):  
Cluster Analysis ◽  
Length Polymorphism ◽  
Microsatellite Loci ◽  
Genetic Basis ◽  
Allium Sativum ◽  
Microsatellite Analysis ◽  
Breeding Potential ◽  
Ssr Loci

Garlic, Allium sativum L., is a vegetable long used for culinary and medical purposes. A certain level of garlic quality is required by the local consumers, which is usually preserved by the varieties grown in that region. The aim was to establish an assay offering fast and inexpensive differentiation of garlic varieties. Length polymorphism of microsatellite loci (SSR, ILP markers) is often used in such a case. No assays have been described earlier. A set of SSR and newly used ILP markers has been assembled and verified. SSR loci ASM53, ASM072, ASA08 and ASA17 were the most polymorphic. Up to 18 alleles were scored per these loci. Monomorphic loci were identified, and excluded from the assay. The assay allows for the authenticity and confirmation of Czech garlic varieties. Moreover, a cluster analysis separated the Czech bolting varieties, indicating their specific genetic basis. The breeding potential of contemporary garlic varieties and lines is discussed.

scholarly journals Extensive Polymorphism in Cryptosporidium parvumIdentified by Multilocus Microsatellite Analysis

2000 ◽  
Vol 66 (8) ◽  
pp. 3344-3349 ◽  
Author(s):  
Xiaochuan Feng ◽  
Stephen M. Rich ◽  
Donna Akiyoshi ◽  
James K. Tumwine ◽  
Addy Kekitiinwa ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Dna Sequences ◽  
Microsatellite Loci ◽  
Single Copy ◽  
Microsatellite Analysis ◽  
Significant Length ◽  
Multilocus Fingerprint ◽  
Parasite Populations

ABSTRACT Restriction fragment length polymorphism and DNA sequence analysis discern two main types of Cryptosporidium parvum. We present a survey of length polymorphism at several microsatellite loci for type 1 and type 2 isolates. A total of 14 microsatellite loci were identified from C. parvum DNA sequences deposited in public databases. All repeats were mono-, di-, and trinucleotide repeats of A, AT, and AAT, reflecting the high AT content of the C. parvum genome. Several of these loci showed significant length polymorphism, with as many as seven alleles identified for a single locus. Differences between alleles ranged from 1 to 27 bp. Karyotype analysis using probes flanking three microsatellites localized each marker to an individual chromosomal band, suggesting that these markers are single copy. In a sample of 19 isolates for which at least three microsatellites were typed, a majority of isolates displayed a unique multilocus fingerprint. Microsatellite analysis of isolates passaged between different host species identified genotypic changes consistent with changes in parasite populations.

scholarly journals Terminal Restriction Fragment Length Polymorphism Data Analysis for Quantitative Comparison of Microbial Communities

2003 ◽  
Vol 69 (2) ◽  
pp. 926-932 ◽  
Author(s):  
Christopher B. Blackwood ◽  
Terry Marsh ◽  
Sang-Hoon Kim ◽  
Eldor A. Paul
Keyword(s):  
Cluster Analysis ◽  
Data Analysis ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Redundancy Analysis ◽  
Fragment Length Polymorphism ◽  
Peak Height ◽  
Relative Peak Height ◽  
Restriction Fragment Length

ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacterial communities. These samples included soil collected from three regions of the United States, soil fractions derived from three agronomic field treatments, soil samples taken from within one meter of each other in an alfalfa field, and replicate laboratory bioreactors. Cluster analysis by Ward's method and by the unweighted-pair group method using arithmetic averages (UPGMA) were compared. Ward's method was more effective at differentiating major groups within sets of profiles; UPGMA had a slightly reduced error rate in clustering of replicate profiles and was more sensitive to outliers. Most replicate profiles were clustered together when relative peak height or Hellinger-transformed peak height was used, in contrast to raw peak height. Redundancy analysis was more effective than cluster analysis at detecting differences between similar samples. Redundancy analysis using Hellinger distance was more sensitive than that using Euclidean distance between relative peak height profiles. Analysis of Jaccard distance between profiles, which considers only the presence or absence of a terminal restriction fragment, was the most sensitive in redundancy analysis, and was equally sensitive in cluster analysis, if all profiles had cumulative peak heights greater than 10,000 fluorescence units. It is concluded that T-RFLP is a sensitive method of differentiating between microbial communities when the optimal statistical method is used for the situation at hand. It is recommended that hypothesis testing be performed by redundancy analysis of Hellinger-transformed data and that exploratory data analysis be performed by cluster analysis using Ward's method to find natural groups or by UPGMA to identify potential outliers. Analyses can also be based on Jaccard distance if all profiles have cumulative peak heights greater than 10,000 fluorescence units.

scholarly journals A linkage of gene of resistance to a broomrape race G with microsatellite loci of a sunflower linedonor RGP1 of VNIIMK’s breeding

2021 ◽  
Vol 186 (2) ◽  
pp. 3-9
Author(s):  
S.Z. Guchetl ◽  
◽  
D.L. Savichenko ◽  
Keyword(s):  
Microsatellite Loci ◽  
Physical Map ◽  
Pcr Analysis ◽  
Sources Of Resistance ◽  
Resistant Varieties ◽  
Literary Sources ◽  
Ssr Loci ◽  
Environmentally Safe ◽  
Yield Formation ◽  
Sunflower Genome

Broomrape (Orobanche cumana Wallr.) is one of the main biotic factors limiting high sunflower yield formation. The most effective and environmentally safe method of protection is cultivation of resistant varieties and hybrids of sunflower. Development of resistant sunflower genotypes includes search and usage of sources of resistance in breeding process as well as accurate and productive procedures of material assessment. The purpose of the research is to analyze a linkage of a gene Or7 with microsatellite loci of the line-donor of resistance to broomrape race G from the VNIIMK’s collection. The objects of the research are the line RGP1 – a donor of resistance to broomrape race G and a susceptible to this race line VR 678 from the VNIIMK’s collection. Sunflower plants were crossed in field to produce F1. Also we conducted self-pollination of F1 plants to obtain F2 progeny. Plants were tested in a greenhouse in soil infected with seeds of broomrape race G using a method of early diagnostic. Sunflower DNA was extracted from the top leaves of the young sprouts of the vegetative plants. For PCR-analysis we used three SSR-primers demonstrated polymorphism in parental lines: ORS 683, ORS 1040, and ORS 1112. We tested joint inheritance of the gene Or7 and these loci, and inheritance between SSR-loci. An independent inheritance of the gene Or7 with DNA-loci ORS 683, ORS 1040, and ORS 1112, as well as SSR-loci between ORS 1040 and ORS 1112, ORS 1040 and ORS 683 was showed. Loci ORS683 – ORS 1112 are linked with a frequency of recombination of 0.27 ± 0.41 (27 cM). As a result of our research location of the gene Or7 in the nearest area to microsatellite loci ORS 683, ORS 1040, and ORS 1112 was excluded. Basing on studied literary sources and a representative sunflower genome HanXRQr2.0-SUNRISE we made a partial physical map LG3 for determination of an area for the further search of a localization of the Or7 and DNAmarkers co-segregating with this gene.

scholarly journals MICROSATELLITE POLYMORPHISM WITHIN TWO LAKE BAIKAL OILFISH SPECIES (COMEPHORUS LACEPEDE, 1801)

2007 ◽  
Vol 5 (2) ◽  
pp. 50-57 ◽  
Author(s):  
Veronika I Teterina ◽  
Lubov V Sukhanova ◽  
Sergey V Kirilchik
Keyword(s):  
Genetic Polymorphism ◽  
Genetic Differentiation ◽  
Lake Baikal ◽  
Microsatellite Loci ◽  
Passive Transfer ◽  
Microsatellite Analysis ◽  
Microsatellite Polymorphism ◽  
Baikal Lake ◽  
Water Currents ◽  
Cottus Gobio

Intraspecific genetic polymorphism of a Baikal Lake endemic, big Baikal oilfish (Comephorus baicalensis Pallas, 1776), was evaluated based on microsatellite analysis. The obtained results have compared to the results received earlier for a little Baikal oilfish (C. dybowski Korotneff, 1905). Six microsatellite loci designed for the European sculpin, Cottus gobio, were used. Big Baikal oilfish samples were tested from the three Baikal trenches (southern, middle, northern). Average values of F<sub>ST</sub> and R<sub>ST</sub>indexes between the samples did not exceed 0,02 that point to weak intraspecific genetic differentiation. Big Baikal oilfish had the smaller allele variety, the greater deficit of heterozygotes and presence of low-molecular alleles in comparison with little Baikal oilfish. The values of genetic differentiation were equaled F<sub>ST</sub> = 0,138 and R<sub>ST</sub> = 0,244 for all loci between cumulative samples of little and big Baikal oilfish. Analysis of microsatellite polymorphism has showed that both a big and little Baikal oilfishes are represented by single populations. The factor promoting panmixia within the Baikal oilfish species is apparently a passive transfer of juvenile and adult fishes by water currents.

scholarly journals Genomic Relatedness of ChlamydiaIsolates Determined by Amplified Fragment Length Polymorphism Analysis

1999 ◽  
Vol 181 (15) ◽  
pp. 4469-4475 ◽  
Author(s):  
Adam Meijer ◽  
Servaas A. Morré ◽  
Adriaan J. C. Van Den Brule ◽  
Paul H. M. Savelkoul ◽  
Jacobus M. Ossewaarde
Keyword(s):  
Cluster Analysis ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Chlamydia Psittaci ◽  
Rrna Genes ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Genomic Relatedness

ABSTRACT The genomic relatedness of 19 Chlamydia pneumoniaeisolates (17 from respiratory origin and 2 from atherosclerotic origin), 21 Chlamydia trachomatis isolates (all serovars from the human biovar, an isolate from the mouse biovar, and a porcine isolate), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and 1 Chlamydia pecorum isolate was studied by analyzing genomic amplified fragment length polymorphism (AFLP) fingerprints. The AFLP procedure was adapted from a previously developed method for characterization of clinical C. trachomatis isolates. The fingerprints of all C. pneumoniae isolates were nearly identical, clustering together at a Dice similarity of 92.6% (± 1.6% standard deviation). The fingerprints of the C. trachomatis isolates of human, mouse, and swine origin were clearly distinct from each other. The fingerprints of the isolates from the human biovar could be divided into at least 12 different types when the presence or absence of specific bands was taken into account. The C. psittacifingerprints could be divided into a parakeet, a pigeon, and a feline type. The fingerprint of C. pecorum was clearly distinct from all others. Cluster analysis of selected isolates from all species revealed groups other than those based on sequence data from single genes (in particular, omp1 and rRNA genes) but was in agreement with available DNA-DNA hybridization data. In conclusion, cluster analysis of AFLP fingerprints of representatives of all species provided suggestions for a grouping of chlamydiae based on the analysis of the whole genome. Furthermore, genomic AFLP analysis showed that the genome of C. pneumoniae is highly conserved and that no differences exist between isolates of respiratory and atherosclerotic origins.

KERAGAMAN FENOTIPE DAN GENETIK TIGA VARIETAS KELAPA GENJAH KOPYOR ASAL PATI JAWA TENGAH

2016 ◽  
Vol 21 (1) ◽  
pp. 1 ◽  
Author(s):  
ISMAIL MASKROMO ◽  
ELSJE T. TENDA ◽  
MEITY A. TULALO ◽  
HENGKY NOVARIANTO ◽  
DEWI SUKMA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Biology ◽  
Plant Molecular Biology ◽  
Morphological Diversity ◽  
Local Varieties ◽  
Central Java ◽  
Variety Selection ◽  
Ssr Loci ◽  
Biology Laboratory

<p>ABSTRAK<br />Kelapa Genjah kopyor asal Pati, Jawa Tengah merupakan<br />kekayaaan hayati asli Indonesia dengan nilai ekonomi tinggi. Informasi<br />keragaman genetik kelapa kopyor masih terbatas. Data keragaman<br />morfologi dan genetik diperlukan dalam program pemuliaan kelapa<br />kopyor. Penelitian ini mempelajari keragaman tiga varietas kelapa genjah<br />kopyor asal Pati yang telah dilepas berdasarkan karakter morfologi,<br />kuantitas endosperma, dan keragaman alel marka SSR. Penelitian<br />dilakukan di Pati dan di Laboratorium Plant Molecular Biology,<br />Departemen Agronomi dan Hortikultura, IPB. Evaluasi dilakukan terhadap<br />tiga populasi kelapa Genjah kopyor (hijau, coklat, dan kuning) dengan 30<br />tanaman sampel untuk setiap populasi. Rataan data morfologi digunakan<br />untuk menyusun dendogram. Kuantitas endosperma diamati pada satu<br />buah kelapa kopyor per tanaman yang dievaluasi. Karakteristik<br />endosperma dikelompokkan sesuai kategori yang telah ditetapkan. Untuk<br />setiap populasi, analisis marka dengan lima pasang primer SSR dilakukan<br />pada 10 tanaman sampel. Data yang didapat digunakan untuk menentukan<br />keragaman genetik kelapa Genjah kopyor asal Pati. Hasil pengamatan<br />menunjukkan keragaman morfologis dan alel SSR antar tanaman dalam<br />varietasnya (keragaman intra-varietas) rendah. Sebaliknya, keragaman<br />morfologis dan alel SSR antar varietasnya tinggi. Kuantitas endosperma<br />kelapa Genjah kopyor asal Pati bervariasi antara skor 1–6. Keragaman<br />genetik yang rendah dalam varietas dan tinggi antar ketiga varietas (coklat,<br />hijau, dan kuning) memperkuat pelepasan ketiganya sebagai varietas lokal.<br />Selain itu, keragaman genetik antar tanaman dalam varietas yang rendah<br />mendukung penggunaan ketiga varietas lokal sebagai tetua dalam program<br />perakitan varietas kelapa kopyor unggul baru. Tetua yang dipilih dapat<br />diseleksi intra-varietas berdasarkan persentase buah kopyor per tandan<br />dan skor kuantitas endosperma yang tinggi.<br />Kata kunci: Keragaman morfologis, keragaman intra dan antar varietas,<br />kuantitas endosperma</p><p>ABSTRACT<br />Kopyor dwarf coconuts are mutants from Pati, Central Java having<br />high economic values. However, morphological and genetic diversities of<br />this coconut were still limited. Morphological and genetic diversity data<br />are needed for breeding program. The research objectives were to evaluate<br />intra and inter-specific diversity based on morphology, endosperm<br />quantity, and SSR alleles. Field evaluations were conducted in Pati while<br />laboratory activities were at Plant Molecular Biology Laboratory,<br />Department of Agronomy and Horticulture, IPB. Three populations of<br />kopyor dwarf varieties (brown, green, and yellow) were evaluated. Thirty<br />trees were sampled for each population. The average of morphological<br />data were used to construct cluster analysis. Endosperm quantity was<br />scored (0 – 9) based on a single nut sample. Ten palms were analyzed<br />using five SSR loci for each population and used to determine genetic<br />diversity of populations. Results of observations indicated intra-variety<br />morphological and SSR allele variations among kopyor dwarf was low.<br />However, inter-variety variations were high. The endosperm quantity<br />scores among kopyor dwarf coconut ranged from 1–6. The low intra-<br />variety and high inter-variety variations among the three kopyor dwarf<br />coconut supported their release as different local varieties. Moreover, the<br />low intra-variety phenotypic and genotypic diversities among kopyor<br />brown, green, and yellow dwarf coconut support their use as parents for<br />new and superior kopyor coconut variety development in the future. For<br />such purpose, however, it is necessary to conduct intra-variety selection to<br />identify desirable parents based on high kopyor fruit percentage per bunch<br />and for high kopyor endosperm quantity.<br />Key words: Morphological diversity, intra and inter variety diversities,<br />quantity, endosperm</p>

Restriction Fragment Length Polymorphism Assessment of the Heterogeneous Nature of Maize Population GT-MAS:gk and Field Evaluation of Resistance to Aflatoxin Production by Aspergillus flavus

2002 ◽  
Vol 65 (1) ◽  
pp. 167-171 ◽  
Author(s):  
B. Z. GUO ◽  
A. BUTRON ◽  
H. LI ◽  
N. W. WIDSTROM ◽  
R. E. LYNCH
Keyword(s):  
Cluster Analysis ◽  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Field Evaluation ◽  
Aflatoxin Production ◽  
Inbred Lines ◽  
Rflp Markers ◽  
Maize Population ◽  
Restriction Fragment Length

Aflatoxin, produced by Aspergillus flavus, is one of the most toxic and carcinogenic substances known and contaminates many agricultural commodities such as corn, peanuts, cottonseed, and tree nuts. The challenge to breeders/plant pathologists is to identify lines that have resistance to aflatoxin production. Maize population GT-MAS:gk has been identified and released as a germplasm with resistance to aflatoxin contamination. In the present study, we assessed genetic divergence in the GT-MAS:gk population using restriction fragment length polymorphism (RFLP) DNA markers to survey 11 selfed inbred lines and conducted field evaluations for the dissimilarities in aflatoxin production among these inbred lines in comparison with a sister population, GT-MAS:pw,nf. The 11 selfed inbred lines were assayed for DNA polymorphism using 113 RFLP markers in 10 linkage groups covering 1,518.2 centimorgans (cM; unit of gene or chromosome size). Considerable variation among the inbreds was detected with RFLP markers, of which 42 probe-enzyme combinations gave 102 polymorphic bands. Cluster analysis based on genetic similarities revealed associations and variations among the tested lines. Three polymorphic groups were distinguished by cluster analysis. Two years of field evaluation data showed that aflatoxin concentrations among the lines were significantly different in both years (P &lt; 0.001). Maturity data were also different. Thus, this study demonstrates that the maize population GT-MAS:gk is heterogeneous and that individuals may be different in resistance to A. flavus infection and aflatoxin production. Therefore, the most resistant lines should be inbred to increase homogeneity, and resistance should be confirmed through progeny testing.

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