SSR-Marker Analysis—A Method for S. cerevisiae Strain Characterization and Its Application for Wineries

Considering that many Saccharomyces cerevisiae strains exist and that they have different fermentation capacities, the challenge is to select the yeast strain that generates the most interesting wine character and wine flavor for the winemaker. A method based on simple sequence repeats (SSRs) markers, occurring in the yeast genome, was developed to differentiate the collected S.cerevisiae strains. For the amplification of the polymorphic SSR markers performed by polymerase chain reaction (PCR), two primer sets showing different size products for different S. cerevisiae strains were designed. The PCR-method with gel electrophoresis was validated using capillary sequencing and then used as a service for winegrowers combined with a sensory analysis via napping. This approach can be used for the preservation of the yeast diversity associated with given terroirs and as an option for an increased safety of fermentations. The application of S. cerevisiae strains collected in spontaneous fermentations and used for fermentation sustains the initial character of the wine and ensures a secure fermentation at the same time.

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Characterization of trypanosome infections by polymerase chain reaction (PCR) amplification in wild tsetse flies in Cameroon

Parasitology ◽

10.1017/s0031182098002625 ◽

1998 ◽

Vol 116 (6) ◽

pp. 547-554 ◽

Cited By ~ 23

Author(s):

I. MORLAIS ◽

P. GREBAUT ◽

J. M. BODO ◽

S. DJOHA ◽

G. CUNY

Keyword(s):

Polymerase Chain Reaction ◽

Infection Rate ◽

Forest Type ◽

Pcr Amplification ◽

Tsetse Flies ◽

Microscopical Examination ◽

Chain Reaction ◽

Pcr Method ◽

Polymerase Chain ◽

Primer Sets

The polymerase chain reaction (PCR) method was used to characterize trypanosome infections in tsetse flies from 3 sleeping sickness foci in Cameroon. The predominant tsetse species found was Glossina palpalis palpalis. An average infection rate of 12·1% was revealed by microscopical examination of 888 non-teneral tsetse flies. PCR amplification analyses for trypanosome identification were carried out on 467 flies, with primer sets specific for Trypanosoma (Trypanozoon) brucei s.l., T. (Duttonella) vivax, T. (Nannomonas) simiae and forest type T. (Nannomonas) congolense. Of 467 flies 93 were positive by microscopical analysis while PCR succeeded in identifying 89 positive flies. Of the PCR-positive flies 34 (38·2%) were negative by microscopical examination. PCR amplification, when compared to the parasitological technique, gave a higher estimate of infection rate of trypanosomes in natural tsetse populations. The PCR technique did, however, fail to identify 40·9% (38/93) of the parasitologically positive flies. The reasons for this failure are discussed. The overall prevalence of mixed infections, assessed by PCR, was 37·1%; the majority (72·7%) involved T. brucei and forest type T. congolense.

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Microsatellite DNA as shared genetic markers among conifer species

Canadian Journal of Forest Research ◽

10.1139/x99-009 ◽

1999 ◽

Vol 29 (3) ◽

pp. 365-371 ◽

Cited By ~ 39

Author(s):

C S Echt ◽

G G Vendramin ◽

C D Nelson ◽

P Marquardt

Keyword(s):

Pinus Radiata ◽

Picea Glauca ◽

Ssr Marker ◽

Allelic Variation ◽

Conifer Species ◽

Ssr Loci ◽

Polymerase Chain ◽

Shared Alleles ◽

Simple Sequence ◽

Shared Genetic

Polymerase chain reaction (PCR) primer pairs for 21 simple sequence repeat (SSR) loci in Pinus strobus L. and 6 in Pinus radiata D. Don. were evaluated to determine whether SSR marker amplification could be achieved in 10 other conifer species. Eighty percent of SSR primer pairs for (AC)n loci that were polymorphic in P. strobus also amplified SSR loci in two other soft pines of the subgenus Strobus but not in seven hard pines of the subgenus Pinus, nor in Picea glauca (Moench) Voss or Pseudotsuga menziesii (Mirb.) Franco. The six P. strobus SSR primer pairs that did amplify loci from conifers other than soft pines were those that were specific to loci monomorphic within P. strobus. These six loci were also monomorphic within seven other species tested, but four of the loci were polymorphic among species. A comparison of allelic variation among the three soft pine species found only 25 shared alleles among a total of 122 alleles at eight loci. Primer pairs for dinucleotide SSR loci that were polymorphic in Pinus radiata also specifically amplified loci from various other hard pines but not from the soft pines or from the other conifers tested.

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Biodiversity of some fig cultivars in Southern Syria

Journal of Phytology ◽

10.25081/jp.2021.v13.7339 ◽

2021 ◽

pp. 184-191

Author(s):

Sahara Abo Amin ◽

Faisal Hamed ◽

Seba Sarhan ◽

Nashaat Abo Tafish

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Significant Contribution ◽

Mean Value ◽

Local Fields ◽

The Mean ◽

Polymerase Chain ◽

Ssrs Markers ◽

Simple Sequence

This research has been conducted in the Biotechnology Laboratory in Damascus University_ Damascus, Syria where the genetic diversity of fourteen cultivars of figs (Ficus carica L.) growing in Swaida governorate which located in the south region of Syria were investigated using (Simple Sequence Repeats) SSRs technique, where 4 cultivars of them were genotypes scattered in the local fields without any scientific taxonomy and farmers did not classify them properly. Eight pairs of SSRs markers were used depend on their ability to separate between fig cultivars as mentioned in previous studies, six pairs of them gave amplified products in the polymerase chain reaction (PCR), while MFC3 and MFC6 primers did not give any amplification products. A total of 17 alleles were detected at six SSRs loci. The alleles number per locus ranged from 2 to 4 with an average of 2.83 alleles/locus. The observed heterozygosity (Ho) was 0.33, while the expected heterozygosity (He) was 0.17. The mean value of genetic similarity was 0.69 where fig cultivars has separated into two clusters in Cluster Analysis, which confirms a significant genetic similarity between most of the cultivars. MFC1 and MFC2 loci gave about 0.67 and 0.61 PIC (Polymorphism Information Content) values respectively, which confirms their ability to study the genetic diversity of fig cultivars more than other loci. F1 and F2 cultivars greatly affect the quality of the fruits as paternity traits as Caprifigs. Tammozi cultivar has low values of its genetic similarity with the rest of the cultivars which reflect great difference between it and other cultivars. Generally, the challenges in this study were in characterizing unrecognized fig cultivars in southern Syria to distinguish between them as they were not certified in agriculture ministry in Syria because the lack in studies related to the same topic as these cultivars were not studied before, thus, we managed to make a significant contribution in certifying fig cultivars in Syria using SSR technique.

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Investigation of duck plague virus in hoar areas of Bangladesh

Bangladesh Journal of Livestock Research ◽

10.3329/bjlr.v26i1-2.49939 ◽

2020 ◽

Vol 26 (1-2) ◽

pp. 73-78

Author(s):

A Hossen ◽

MH Rahman ◽

MZ Ali ◽

MA Yousuf ◽

MZ Hassan ◽

...

Keyword(s):

Cytopathic Effect ◽

Clinical Sample ◽

Chorioallantoic Membrane ◽

Clinical Samples ◽

Isolation And Identification ◽

Duck Plague Virus ◽

Pcr Method ◽

Polymerase Chain ◽

The Individual ◽

Free Ranging

Duck plague (DP) is the most important infectious disease of geese, ducks and free-ranging water birds. The present study was conducted to determine the prevalence of duck plague virus followed by isolation and identification. For these purposes, a total of 155 cloacal swabs samples were collected randomly from duck of different haor areas of Bangladesh including 45 (41 surveillance and 4 clinical) samples from Netrokona; 42 (40 surveillance and 2 clinical) samples from Kishoregonj; 30 samples from Brahmanbaria and 38 samples from Sunamganj. The samples were processed and pooled (1:5 ratio) for initial screening of target polymerase gene of duck plague virus by polymerase chain reaction (PCR) method. All the samples of a positive pool were then tested individually for identifying the individual positive samples. The result showed that out of 155 samples, 41 (26.45%) were found positive in which 17 were from Netrokona, where 15 (36.58%) were from surveillance samples and 2 (50%) were from clinical sample; 16 were from Kishoregonj, where 14 (35%) were from surveillance samples and 2 (100%) were from clinical sample; 2 (6.6%) were from Brahmanbaria and 5 (13.15%) were from Sunamganj. These positive samples were inoculated into 9-10 days embryonated duck eggs (EDE) through chorioallantoic membrane (CAM) route for the isolation of virus. The EDE died earlier was also chilled, and in a similar way, the CAMs were collected and again performed PCR for id entification of virus. Out of 41 PCR positive samples, 26 samples were isolated and reconfirmed by PCR. Subsequently, DPV was isolated in primary duck embryo fibroblasts cell culture and confirmed by observing cytopathic effect (CPE). Bang. J. Livs. Res. Vol. 26 (1&2), 2019: P. 73-78

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Prevalence of SHV-extended spectrum β-lactamase producing carbapenem –resistantKlebsiellapneumoniae among patients with lower respiratory tractinfections in Babylon Province-Iraq.

International Journal of Research in Pharmaceutical Sciences ◽

10.26452/ijrps.v9ispl1.1299 ◽

2018 ◽

Vol 9 (SPL1) ◽

Author(s):

Fatima Moeen Abbas

Keyword(s):

Resistance Rate ◽

Combination Method ◽

Diffusion Method ◽

Disk Diffusion Method ◽

Carbapenem Resistant ◽

Extended Spectrum ◽

Pcr Method ◽

Polymerase Chain ◽

Tract Infections ◽

Positive Results

This study was carried out to screen the prevalence of Klebsiella pneumoniae isolated from patients with lower respiratory tract infections in Babylon province.From December,2015 to the end of March,2016,a total of 100 sputum samples were collected from patients visited or hospitalized Merjan Teaching Hospital and Al- Hashimya General Hospital. Fifteenth (65%) isolates were identified as Klebsiellapneumoniae. All bacterial isolates were evaluated for extended spectrum β-lactamase (ESBL) production phenotypically using disk combination method. Eleven (73.3%) isolates were detected as ESBL-producers. Kirby-Bauer disk diffusion method was employed to determine resistance profile of ESBLs-positive isolates. Higher rates of resistance were observed for ampicillin and piperacillin antibiotics with (81.8%) and (72.7%) resistance rate, respectively, while the lowest rate was noticed for imipenem antibiotic (14.28%). Carbapenem-resistant isolates were investigated for blaSHV gene by Polymerase Chain Reaction (PCR) method, 2 (100%) isolates gave positive results.

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The SUSPECT SYMPTOMS OF INBREEDING DEPRESSION AND THE HOMOZYGOSITY LEVEL OF FOURTH GENERATION OF SP450T AND FIFTH GENERATION OF DURA DELI OIL PALM SELFING POPULATION

Jurnal Penelitian Kelapa Sawit ◽

10.22302/10.22302/iopri.jur.jpks.v24i2.8 ◽

2018 ◽

Vol 24 (2) ◽

pp. 55-66

Author(s):

Rokhana Faizah ◽

Sri Wening ◽

Hernawan Yuli Rahmadi ◽

Abdul Razak Purba

Keyword(s):

Inbreeding Depression ◽

Oil Palm ◽

Recurrent Selection ◽

Fourth Generation ◽

Depression Symptoms ◽

Reciprocal Recurrent Selection ◽

Chain Reaction ◽

Fifth Generation ◽

Polymerase Chain ◽

Simple Sequence

Inbreeding is a common method used to reproduce candidate mother plant from selected parental lines for commercial seeds in Reciprocal Recurrent Selection (RRS) oil palm breeding program. However this practice may increased homozigosity level of selected population. This study concerned the level of homozygosity of SP540T fourth generations and Dura Deli Dolok Sinumbah fifth generations (3 crosses respectively) and their correlation with inbreeding depression symptoms. Polymerase Chain Reaction-Simple Sequence Repeat (PCR-SSR) with 16 markers developed for oil palm was used to analyze 327 samples. The result shows that the levels of homozigosity of SP540T fourth selfing generation were ranged between 0.44-0.84 or 0.61 in average. While the levels of homozygosity of Dura Deli fifth selfing generations were ranged between 0.60-0.93 or 0.78 in average. The homozygosity level in Dura Deli was 1.27% higher than SP540T populations. Correlation analysis showed that the higher the level of homozygosity, the higher of the inbreeding symptoms 2 observed (R =0.95).

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Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Plants ◽

10.3390/plants10071386 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1386

Author(s):

Soyun Kim ◽

Keunho Yun ◽

Han Yong Park ◽

Ju Young Ahn ◽

Ju Yeon Yang ◽

...

Keyword(s):

Molecular Markers ◽

Raphanus Sativus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cosmetic Industry ◽

Natural Colorants ◽

Health Promoting ◽

Primer Sets ◽

Red Radish ◽

Simple Sequence

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

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Diversity and Relationships among Neglected Apricot (Prunus armeniaca L.) Landraces Using Morphological Traits and SSR Markers: Implications for Agro-Biodiversity Conservation

Plants ◽

10.3390/plants10071341 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1341

Author(s):

Giandomenico Corrado ◽

Marcello Forlani ◽

Rosa Rao ◽

Boris Basile

Keyword(s):

Prunus Armeniaca ◽

Ex Situ ◽

Skin Colour ◽

Maintenance Breeding ◽

Prunus Armeniaca L ◽

Ex Situ Collection ◽

Loss Of Diversity ◽

Ssrs Markers ◽

On Farm ◽

Simple Sequence

Apricot (Prunus armeniaca L.) is an economically important tree species globally cultivated in temperate areas. Italy has an ample number of traditional varieties, but numerous landraces are abandoned and at risk of extinction because of increasing urbanization, agricultural intensification, and varietal renewal. In this work, we investigated the morphological and genetic diversity present in an ex-situ collection of 28 neglected varieties belonging to the so-called “Vesuvian apricot”. Our aim was to understand the level of diversity and the possible link between the promotion of specific fruit types (e.g., by public policies) and the intraspecific variation in apricot. The combination of five continuous and seven categorical traits allowed us to phenotypically distinguish the varieties; while fruit quality-related attributes displayed high variation, both apricot size and skin colour were more uniform. The twelve fluorescent-based Simple Sequence Repeats (SSRs) markers identified cultivar-specific molecular profiles and revealed a high molecular diversity, which poorly correlated with that described by the morphological analysis. Our results highlighted the complementary information provided by the two sets of descriptors and that DNA markers are necessary to separate morphologically related apricot landraces. The observed morphological and genetic differences suggest a loss of diversity influenced by maintenance breeding of specific pomological traits (e.g., skin colour and size). Finally, our study provided evidence to recommend complementary strategies to avoid the loss of diversity in apricot. Actions should pivot on both the promotion of easily identified premium products and more inclusive biodiversity-centred on-farm strategies.

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