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

Abstract

<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.

Molecular characterization of national cocoa collection from the leading traditional growing areas in Ecuador

“…Molecular markers have proven adequate for characterizing genetic variability in T. cocoa 17,18,[28][29][30][31][32][33] . In the present study, samples from a cocoa collection called National Centenarian cocoa collection (NCCC) were used, which is made up of 260 accessions collected from farms where trees with characteristics of National cocoa were found and whose ages were 75-100 years, located in the northern area of the province of Manabí, and in the province of Los Rios in Ecuador.…”

Ncbi: Generalidades Del Repositorio Y Breve Descripción De Recursos Aplicables Al Estudio De La Fitogenética

“…Las herramientas en mención son útiles en estudios de genotipeo por secuenciación; por ejemplo, a través del estudio de regiones sumamente conservadas de especímenes vegetales (e.g. Theobroma cacao L. y Aegilops umbellulata) se determinan variaciones genotípicas a nivel polimórfico, así como el mapeo de genes de resistencia a fitopatógenos, como la roya (Edae et al, 2016;Lima et al, 2009;Ricaño-Rodríguez et al, 2019); ésto permite a los investigadores dilucidar más a fondo las características genéticas distintivas de grupos de individuos que pertenecen a un mismo phylum.…”

“…Tomando en cuenta lo anterior, es importante mencionar que el estudio de los recursos fitogenéticos no se excluye de la mayoría de las disciplinas bioinformáticas, pues las herramientas disponibles en el NCBI son capaces de llevar a cabo estudios in silico, como por ejemplo la identificación de regiones genómicas conservadas (marcadores moleculares) para la clasificación de especímenes vegetales (Jorrin-Novo, 2020;Morgante y Salamini, 2003;Rensink y Buell, 2005;Ricaño-Rodríguez et al, 2019); o bien, evaluar la calidad de la secuenciación de genomas en especies de plantas utilizando etiquetas de secuencia expresada (Shangguan et al, 2013).…”

Quality differentiation of cocoa beans: implications for geographical indications

“…Third, the consumption of cocoa and its impact on human health was observed as a major research driver, with studies on the identification and validation of bioactivity, with conclusive benefits for cardiovascular health, insulin signaling and intestinal and mental health 26–30 . Fourth were genetic studies on genotyping and variance for subsequent breeding strategies, with a major emphasis on disease resistance 31–36 …”