scholarly journals Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum , based on simple sequence repeat and single nucleotide polymorphism

Mycoses ◽  
2020 ◽  
Vol 63 (11) ◽  
pp. 1244-1254
Author(s):  
Ivan M. Pchelin ◽  
Yuri V. Mochalov ◽  
Daniil V. Azarov ◽  
Sofya A. Romanyuk ◽  
Galina A. Chilina ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Fungal Pathogen ◽  
Simple Sequence Repeat ◽  
Trichophyton Rubrum ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Simple Sequence

scholarly journals Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

2020 ◽  
Author(s):  
Ivan M. Pchelin ◽  
Yuri V. Mochalov ◽  
Daniil V. Azarov ◽  
Sofya A. Romanyuk ◽  
Galina A. Chilina ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Simple Sequence Repeat ◽  
Trichophyton Rubrum ◽  
Sensu Stricto ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genetic Lineages ◽  
Aldolase Gene ◽  
Simple Sequence

AbstractBackgroundThe Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T. rubrum sensu stricto and T. violaceum, as well as other less well established or debatable taxa like T. soudanense, T. kuryangei and T. megninii. Our previous study provided limited evidence in favour of the existence of two genetic lineages in the Russian T. rubrum sensu stricto population.ObjectivesWe aimed to study the genetic structure of the Russian population of T. rubrum, and to identify factors shaping this structure.MethodsWe analysed the polymorphism of 12 simple sequence repeat (SSR, or microsatellite) markers and single-nucleotide polymorphism in the TERG_02941 protein-coding gene in 70 T. rubrum isolates and performed a phylogenomic reconstruction.ResultsAll three types of data provided conclusive evidence that the population consists of two genetic lineages. Clustering, performed by means of microsatellite length polymorphism analysis, was strongly dependent on the number of nucleotide repeats in the 5’-area of the fructose-1,6-bisphosphate aldolase gene. Analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22–48% of the variability was among groups within T. rubrum. There was no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression or urease activity.ConclusionOur results suggest that the Russian population of T. rubrum consists of two cosmopolitan genetic lineages.

scholarly journals Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 737
Author(s):  
Maja Žulj Mihaljević ◽  
Edi Maletić ◽  
Darko Preiner ◽  
Goran Zdunić ◽  
Marijan Bubola ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Simple Sequence Repeat ◽  
Genetic Erosion ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Simple Sequence

Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories.

scholarly journals Mapping Genes Governing Flower and Seedcoat Color in Asparagus Bean (Vigna unguiculata ssp. sesquipedalis) Based on Single Nucleotide Polymorphism and Simple Sequence Repeat Markers

HortScience ◽  
2011 ◽  
Vol 46 (8) ◽  
pp. 1102-1104 ◽  
Author(s):  
Pei Xu ◽  
Tingting Hu ◽  
Yuejian Yang ◽  
Xiaohua Wu ◽  
Baogen Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Simple Sequence Repeat ◽  
Recombinant Inbred Lines ◽  
Flower Color ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Asparagus Bean ◽  
Simple Sequence ◽  
T Locus

Colors of flower and seedcoat are interesting traits of asparagus bean, a cultivated subspecies of cowpea grown throughout Asia for its tender, long green pods. Little is known about the inheritance of these traits including their genome location. We report here the genetic analysis and mapping of the genes governing flower and seedcoat color in asparagus bean based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. Analysis of the F1 and F7:8 generation of recombinant inbred lines (RILs) population showed a monogenetic inheritance of both traits. Purple flower and brown seedcoat are dominant over white flower and cream seedcoat, respectively. We further show that genes governing flower color and seedcoat color are tightly linked on LG8, ≈0.4 cM apart. Synteny analysis showed that the gene controlling seedcoat color in our study is syntenic to the soybean T locus. The use of the mapping information in asparagus bean breeding is discussed.

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