Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus)

Forty-eight kiwifruit cultivars and selections, representing more than 90% of total world kiwifruit production, were investigated using nine SSR markers to establish genetic identities, and evaluate genetic diversity and relatedness. These nine SSRs were polymorphic and a total of 213 alleles were detected, resulting in a mean number of 23.7 alleles per locus, ranging from nine to 38 alleles. One hundred and thirty-three alleles were found to be common to both A. chinensis and A. deliciosa, while 33 and 36 were specific to A. chinensis and A. deliciosa, respectively. In addition, 34 alleles were specific to one single genotype and provided a set of valuable alleles for cultivar identification. A single SSR locus UDK 96-414 could differentiate all 48 genotypes except two presumable clones. Mean number of alleles per locus (A), percentage of polymorphic loci (P), and direct count heterozygosity (Ho) assessed for each genotype over all loci revealed considerable differences among these 48 genotypes. On average, A = 2.6, P = 89.4% and Ho = 0.546 were found in A. chinensis cultivars, while A = 3.5, P = 97.0% and Ho = 0.671 in A. deliciosa cultivars. Consensus fingerprint profiling using SSR markers is a useful and reliable method for establishing genetic identities of kiwifruit cultivars and selections. It also improves evaluation effectiveness of genetic diversity and relatedness compared to RAPD markers.

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Molecular characterization of Pistacia atlantica Desf. subsp. atlantica (Anacardiaceae) in Algeria: Genome size determination, chromosome count and genetic diversity analysis using SSR markers

Scientia Horticulturae ◽

10.1016/j.scienta.2017.09.016 ◽

2018 ◽

Vol 227 ◽

pp. 278-287 ◽

Cited By ~ 7

Author(s):

Asma El Zerey-Belaskri ◽

Teresa Ribeiro ◽

M. Librada Alcaraz ◽

Wael EL Zerey ◽

Silvia Castro ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Size ◽

Molecular Characterization ◽

Ssr Markers ◽

Chromosome Count ◽

Diversity Analysis ◽

Size Determination ◽

Genetic Diversity Analysis ◽

Pistacia Atlantica

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Molecular Characterization of Apple Cultivars in Japan by S-RNase Analysis and SSR Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.6.885 ◽

2005 ◽

Vol 130 (6) ◽

pp. 885-892 ◽

Cited By ~ 14

Author(s):

Kentaro Kitahara ◽

Shogo Matsumoto ◽

Toshiya Yamamoto ◽

Junichi Soejima ◽

Tetsuya Kimura ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Ssr Markers ◽

Maternal Parent ◽

Golden Delicious ◽

Apple Cultivars ◽

Paternal Parent

We examined the genetic diversity and relatedness among apple (Malus ×domestica Borkh.) cultivars in Japan. The 42 apple cultivars, including major cultivars in Japan, were divided into five groups based on SSR genotypes. Most economically important cultivars belong in three groups: Fuji-Delicious, Golden Delicious, and Jonathan groups, and their genetic backgrounds seemed to be narrow. We also investigated the parent-offspring relationships of nine apple cultivars. `Jonathan', `Fuji', and `Rero 11' were identified as the respective paternal parents of three cultivars described as having unknown paternal parents (i.e., `Akagi', `Ambitious', and `Hokuto'). `Starking Delicious', `Senshu', and `Golden Delicious', rather than `Ralls Janet', `Hatsuaki', and `Indo', seemed to be the paternal parents of `Kinsei', `Kiou', and `Mellow', respectively. `Carolina Red June' was excluded as a paternal parent of `Ranzan'. Both attributed parents of `Scarlet' (`Akane' and `Starking Delicious') were excluded, and it was suggested that `Fuji' was used as either a maternal or a paternal parent of `Scarlet'. `Jonathan' rather than `McIntosh' seems to be a maternal parent of `Yukari'.

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Molecular characterization of avocado germplasm with a new set of SSR and EST-SSR markers: genetic diversity, population structure, and identification of race-specific markers in a group of cultivated genotypes

Tree Genetics & Genomes ◽

10.1007/s11295-012-0577-5 ◽

2012 ◽

Vol 9 (2) ◽

pp. 539-555 ◽

Cited By ~ 22

Author(s):

Eduardo Gross-German ◽

Maria Angeles Viruel

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Characterization ◽

Ssr Markers

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Molecular Characterization of Staphylococcus aureus Isolated from Bovine Mastitis and Close Human Contacts in South African Dairy Herds: Genetic Diversity and Inter-Species Host Transmission

Frontiers in Microbiology ◽

10.3389/fmicb.2017.00511 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 34

Author(s):

Tracy Schmidt ◽

Marleen M. Kock ◽

Marthie M. Ehlers

Keyword(s):

Genetic Diversity ◽

Staphylococcus Aureus ◽

South African ◽

Molecular Characterization ◽

Bovine Mastitis ◽

Dairy Herds

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Molecular characterization of echovirus 13 uncovering high genetic diversity and identification of new genotypes in Pakistan

Infection Genetics and Evolution ◽

10.1016/j.meegid.2016.12.017 ◽

2017 ◽

Vol 48 ◽

pp. 102-108

Author(s):

Shahzad Shaukat ◽

Mehar Angez ◽

Tariq Mahmood ◽

Muhammad Masroor Alam ◽

Salmaan Sharif ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

High Genetic Diversity

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Molecular Characterization of Pathogenicity Locus (PaLoc) and tcdC Genetic Diversity Among tcdA+B+ Clostridioides Difficile Clinical Isolates in Tehran, Iran

10.21203/rs.3.rs-56651/v1 ◽

2020 ◽

Author(s):

Mansoor Kodori ◽

Zohreh Ghalavand ◽

Abbas Yadegar ◽

Gita Eslami ◽

Masoumeh Azimirad ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Disease Severity ◽

Genetic Variants ◽

Rflp Analysis ◽

Clostridioides Difficile ◽

Pcr Rflp ◽

The Common ◽

Healthcare Associated

Abstract Background: Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs).Methods: Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene.Results: Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene.Conclusions: The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/ toxinotype 0 and the RT 126/ toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.

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Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers

Molecular Biology Reports ◽

10.1007/s11033-021-07030-4 ◽

2021 ◽

Author(s):

S. P. Jeevan Kumar ◽

C. Susmita ◽

K. V. Sripathy ◽

Dinesh K. Agarwal ◽

Govind Pal ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Ssr Markers ◽

Crop Yield ◽

Gene Pool ◽

Stress Factors ◽

Soybean Cultivars ◽

Genetic Base ◽

Purity Analysis ◽

Breeding Programmes

Abstract Background The genetic base of soybean cultivars in India has been reported to be extremely narrow, due to repeated use of few selected and elite genotypes as parents in the breeding programmes. This ultimately led to the reduction of genetic variability among existing soybean cultivars and stagnation in crop yield. Thus in order to enhance production and productivity of soybean, broadening of genetic base and exploring untapped valuable genetic diversity has become quite indispensable. This could be successfully accomplished through molecular characterization of soybean genotypes using various DNA based markers. Hence, an attempt was made to study the molecular divergence and relatedness among 29 genotypes of soybean using SSR markers. Methods and results A total of 35 SSR primers were deployed to study the genetic divergence among 29 genotypes of soybean. Among them, 14 primer pairs were found to be polymorphic producing a total of 34 polymorphic alleles; and the allele number for each locus ranged from two to four with an average of 2.43 alleles per primer pair. Polymorphic information content (PIC) values of SSRs ranged from 0.064 to 0.689 with an average of 0.331. The dendrogram constructed based on dissimilarity indices clustered the 29 genotypes into two major groups and four sub-groups. Similarly, principal coordinate analysis grouped the genotypes into four major groups that exactly corresponded to the clustering of genotypes among four sub-groups of dendrogram. Besides, the study has reported eight unique and two rare alleles that could be potentially utilized for genetic purity analysis and cultivar identification in soybean. Conclusion In the present investigation, two major clusters were reported and grouping of large number of genotypes in each cluster indicated high degree of genetic resemblance and narrow genetic base among the genotypes used in the study. With respect to the primers used in the study, the values of PIC and other related parameters revealed that the selected SSR markers are moderately informative and could be potentially utilized for diversity analysis of soybean. The clustering pattern of dendrogram constructed based on SSR loci profile displayed good agreement with the cultivar’s pedigree information. High level of genetic similarity observed among the genotypes from the present study necessitates the inclusion of wild relatives, land races and traditional cultivars in future soybean breeding programmes to widen the crop gene pool. Thus, hybridization among diverse gene pool could result in more heterotic combinations ultimately enhancing genetic gain, crop yield and resistance to various stress factors.

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