ABSTRACT
El presente estudio evalua el gen de cloroplasto rbcL y la región espaciadora no codificante psbA-trnH de Arracacia xanthorrhiza como posible secuencia de código de barra. Se colectó material vegetal de A. xanthorrhiza en huertos de las provincias de Pichincha, Tungurahua y Cotopaxi, las cuales fueron sembradas en condiciones homogéneas en la Facultad de Ciencias Agropecuarias de la Universidad Técnica. El análisis del locus rbcL identificó los cinco materiales de A. xanthorrhiza con entre 97 y 99% de homología. La alineación de secuencias del locus rbcL y de psbA-trnH permitió diferenciar dos grupos, el primer grupo con SJ, QU, PP y B, observándose poca diversidad entre ellos, mientras que el segundo grupo está conformado por el material CH cultivado a 3260 m de altitud. En el segundo árbol, se demostró la divergencia entre los materiales colectados en diferentes provincias de la Sierra ecuatoriana, separándolos de acuerdo a su localidad, así como al color de la pulpa de la raíz. La región intergénica no codificadora (psbA-trnH) permitió identificar y obtener la diversidad genética de materiales cultivados de A. xanthorrhiza, provenientes de diversas zonas geográficas de la sierra ecuatoriana, con características morfológicas distintivas. Adicionalmente, esta secuencia pudo diferenciar a A. xanthorrhiza de otras especies de la familia Apiaceae, con lo cual se recomienda como código de barra.
The present study aimed to evaluate the Arracacia xanthorrhiza rbcL chloroplast gene and the non-coding spacer region psbA-trnH as a possible barcode sequence. Plant material of A. xanthorrhiza was collected in orchards of Pichincha, Tungurahua and Cotopaxi provinces. This material were cultivated in standard conditions in the la Facultad de Ciencias Agropecuarias de la Universidad Técnica. The rbcL locus analysis identified the five materials of A. xanthorrhiza with between 97 and 99% homology. The sequence alignment of rbcL locus and psbA-trnH allowed to differentiate two groups, the first group with SJ, QU, PP and B, showing low diversity among them, while the second group consisted of the CH material grown in 3260 m of altitude. In the second tree, the divergence between the materials collected in different provinces of the Ecuadorian Sierra was demonstrated, separating them according to their locality, as well as the color of the root pulp The non-coding intergenic region (psbA-trnH) allowed identify and obtain the genetic diversity of cultivated materials of A. xanthorrhiza, from various geographical areas of the Ecuadorian Sierra, with distinctive morphological characteristics. Additionally, this sequence was able to differentiate A. xanthorrhiza from other species of the Apiaceae family, which is recommended as a bar code.
ABSTRACT
BACKGROUND: Diversity estimates in cultivated plants provide a rationale for conservation strategies and support the selection of starting material for breeding programs. Diversity measures applied to crops usually have been limited to the assessment of genome polymorphism at the DNA level. Occasionally, selected morphological features are recorded and the content of key chemical constituents determined, but unbiased and comprehensive chemical phenotypes have not been included systematically in diversity surveys. Our objective in this study was to assess metabolic diversity in sesame by nontargeted metabolic profiling and elucidate the relationship between metabolic and genome diversity in this crop. RESULTS: Ten sesame accessions were selected that represent most of the genome diversity of sesame grown in India, Western Asia, Sudan and Venezuela based on previous AFLP studies. Ethanolic seed extracts were separated by HPLC, metabolites were ionized by positive and negative electrospray and ions were detected with an ion trap mass spectrometer in full-scan mode for m/z from 50 to 1000. Genome diversity was determined by Amplified Fragment Length Polymorphism (AFLP) using eight primer pair combinations. The relationship between biodiversity at the genome and at the metabolome levels was assessed by correlation analysis and multivariate statistics. CONCLUSION: Patterns of diversity at the genomic and metabolic levels differed, indicating that selection played a significant role in the evolution of metabolic diversity in sesame. This result implies that when used for the selection of genotypes in breeding and conservation, diversity assessment based on neutral DNA markers should be complemented with metabolic profiles. We hypothesize that this applies to all crops with a long history of domestication that possess commercially relevant traits affected by chemical phenotypes.
Subject(s)
Sesamum/genetics , Sesamum/metabolism , Amplified Fragment Length Polymorphism Analysis , DNA Primers/genetics , DNA, Plant/genetics , DNA, Plant/isolation & purification , Genetic Variation , Genome, Plant , Sesamum/classificationABSTRACT
La técnica de ADN polimórfico amplificado al azar (RAPD) fue utilizada en dos cultivares comerciales (Fonucla y UCLA-1) y 7 líneas (UCLA-249; UCLA-295; UCLA-37-1; UCLA-65; UCLA-83; UCLA-90; UCV-2) de ajonjolí (Sesamum indicum L) obtenidas por el programa de mejoramiento genético de la Universidad Centroccidental Lisandro Alvarado, Venezuela. Noventa y cuatro bandas polimórficas derivadas del uso de 12 deca-iniciadores indicaron un alto nivel de variabilidad. Tres de los iniciadores discriminaron 8 de los 9 materiales y, en combinación, pudieron resolverlos a todos. La probabilidad de que ocurrieran coincidencias idénticas fue de 5,22×10-29. El contenido de información de polimorfismo (CIP), el poder de resolución (PR) y el índice del marcador (IM) de cada iniciador no se correlacionaron de manera significativa con el número de genotipos resueltos. El coeficiente de similitud de Jaccard varió de 0,04 a 0,53. El agrupamiento realizado mediante UPGMA resultó en dos grupos principales relacionándose estrechamente con los grupos observados mediante el análisis de coordenadas principales (CP). Estos resultados demuestran que la técnica de RAPD es una herramienta útil para la identificación inequívoca de genotipos de ajonjolí y para evaluar la variabilidad de materiales genéticos usados en programas de mejoramiento genético
Subject(s)
Genetics , Random Amplified Polymorphic DNA Technique , Sequence Analysis, DNA , Agriculture , VenezuelaABSTRACT
BACKGROUND: Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia), and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP). RESULTS: Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA). This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied. CONCLUSION: We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres. Future germplasm collection strategies should focus on sampling a large number of plants. Covering many diversity centres is less important because each centre represents a major part of the total diversity in sesame, Central Asia centre being the only exception. The same recommendation holds for the choice of parents for segregant populations used in breeding projects. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in sesame.
