Abstract
BackgroundGenetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fragment length polymorphisms, DNA sequence analysis, chloroplast DNA, and microsatellite markers. Yet, little is known about whether these traits, which distinguish among genetically distinct types of common bean, can be evaluated using omics technologies.ResultsThree 'omics' approaches: transcriptomics, proteomics, and metabolomics were used to qualitatively evaluate the diversity of common bean from two Centers of Domestication (COD). All three approaches were able to classify common bean according to their COD using unsupervised analyses; these findings are consistent with the hypothesis that differences exist in gene transcription, protein expression, and synthesis and metabolism of small molecules among common bean cultivars representative of different COD. Metabolomic analyses of multiple cultivars within two common bean gene pools revealed cultivar differences in small molecules that were of sufficient magnitude to allow identification of unique cultivar fingerprints.ConclusionsGiven the high-throughput and low cost of each of these 'omics' platforms, significant opportunities exist for their use in the rapid identification of traits of agronomic and nutritional importance as well as to characterize genetic diversity.
Highlights
Genetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fragment length polymorphisms, DNA sequence analysis, chloroplast DNA, and microsatellite markers
Original classification of common bean germplasm was performed by Singh et al [9] into two primary Centers of Domestication (COD); namely Middle American from Central and North America and Andean from South America
The approach used was sequential; transcriptomics experiments were performed first, followed by proteomics, and metabolomics, with increasing complexity of the experimental design as work progressed to each new platform
Summary
Genetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fragment length polymorphisms, DNA sequence analysis, chloroplast DNA, and microsatellite markers. Original classification of common bean germplasm was performed by Singh et al [9] into two primary Centers of Domestication (COD); namely Middle American from Central and North America and Andean from South America. The commercial market classes that represent Race Nueva Granada in the USA, include light red kidney, dark red kidney, white kidney, and cranberry beans. Andean beans such as Calima, Azufrado, sugar bean, and other mottled types are widely grown in Africa and the Caribbean. Beans from the Middle American COD were domesticated in West-Central Mexico [10] and include Durango (central highlands of Mexico), Jalisco (coastal Mexico near the state of Jalisco), and Mesoamerican (lowland tropical Central America) Races.
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