scholarly journals Characterization of a mini core collection of Japanese wheat varieties using single-nucleotide polymorphisms generated by genotyping-by-sequencing

2016 ◽  
Vol 66 (2) ◽  
pp. 213-225 ◽  
Author(s):  
Fuminori Kobayashi ◽  
Tsuyoshi Tanaka ◽  
Hiroyuki Kanamori ◽  
Jianzhong Wu ◽  
Yuichi Katayose ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Core Collection ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Wheat Varieties ◽  
Single Nucleotide ◽  
Mini Core Collection

scholarly journals Genotipado por secuenciación de variedades tradicionales de Theobroma cacao (Malvaceae) del Estado de Tabasco, México

2019 ◽  
Vol 97 (3) ◽  
pp. 381
Author(s):  
Jorge Ricaño-Rodríguez ◽  
Enrique Hipólito-Romero ◽  
José M. Ramos-Prado ◽  
Eliezer Cocoletzi-Vásquez
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Theobroma Cacao ◽  
Genotyping By Sequencing ◽  
Restriction Enzymes ◽  
Nucleotide Polymorphisms ◽  
Minimum Evolution ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Traditional Agroforestry

<p><strong>Background:</strong> Single nucleotide polymorphisms (SNPs) have been identified in <em>Theobroma cacao</em> through a genotyping-by-sequencing approach. Through this research it is shared for the first time a set of results related to genetic variability and nature of conserved coding regions of reduced nucleotide sequences of mexican native varieties of cocoa.</p><p><strong>Hypothesis:</strong> Obtaining reduced genomes of <em>T. cacao</em> specimens by restriction enzymes (REs) allows the characterization of single nucleotide polymorphisms (SNPs) as well as conserved coding regions (CDs).</p><p><strong>Species of study and dates:</strong> <em>Theobroma cacao </em>L. (Malvaceae)</p><p>Study site: <em>Theobroma cacao</em> twigs came from traditional agroforestry plots located in the municipalities of Cardenas, Huimanguillo, Comalcalco, Paraiso, Jalpa de Mendez and Cunduacan, Tabasco, as well as Ixtacomitan and Pichucalco, Chiapas, Mexico; and they were collected and grafted among May and June from 2018.</p><p><strong>Methods:</strong> A method of genotyping-by-sequencing for the characterization of biobanks was developed. Filtering of crude sequences, genomic assembly, identification of SNPs, taxonomic molecular characterization and characterization of coding regions as well as minimum evolution of protein transcripts were performed.</p><p><strong>Results:</strong> <em>Theobroma cacao</em> samples showed different SNPs percentages (2 – 11 %) and the molecular evolution analyzes suggested similar maximum compound probabilities respect to their phylogeny. Conserved sequences were observed in the genomes´ coding regions, which suggest heuristic ontological predictions that have been evolutionarily regrouped in five clusters related to transcription processes and secondary metabolism.</p><strong>Conclusions:</strong> The GBS method allows to identify SNPs in cocoa. The characterization of reduced genomes determined the structural and transcriptional correlation between the samples and the reference genome of cacao Criollo.

scholarly journals DNA Variation in a Diversity Panel of Tomato Genetic Resources

2021 ◽  
pp. 1-7
Author(s):  
Joanne A. Labate
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Crop Improvement ◽  
Genotyping By Sequencing ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
Fresh Market ◽  
Single Nucleotide ◽  
Dna Variation ◽  
Diversity Panel ◽  
Home Gardening

A diversity panel of 190 National Plant Germplasm System (NPGS) tomato (Solanum lycopersicum) accessions was genotyped using genotyping by sequencing. These originated from 31 countries and included fresh market, ornamental, processing, breeders’ lines, landraces, and home gardening types, as well as six different accessions of the economically valuable cultivar San Marzano. Most of the 34,531 discovered single nucleotide polymorphisms were rare and therefore excluded from downstream analyses. A total of 3713 high-quality, mapped single nucleotide polymorphisms that were present in at least two accessions were used to estimate genetic distances and population structure. Results showed that these phenotypically and geographically diverse NPGS tomato accessions were closely related to each other. However, a subset of divergent genotypes was identified that included landraces from primary centers of diversity (South America), secondary centers of diversity (Italy, Taiwan, and France), and genotypes that originated from wild species through 20th century breeding for disease resistance (e.g., ‘VFNT Cherry’). Extreme variant accessions produce cultivated fruit traits in a background that contains many wild or primitive genes. These accessions are promising sources of novel genes for continued crop improvement.

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