Abstract
BackgroundThis study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel. A sample of 548 accessions of traditional upland rice landraces collected in Brazil in the last 25 years was genotyped, a database of allelic frequencies was established, estimates of genetic parameters were performed and analysis of genetic structure of the collection was developed.ResultsThe three panels yielded a combined matching probability of 6.4 × 10-21, polymorphism information content (PIC) of 0.637, and a combined power of exclusion greater than 99.99%. A few samples presented a genetic background of indica rice. The 16 SSR loci produced a total of 229 alleles. Gene diversity values averaged 0.667, and PIC values averaged 0.637. Genetic structure analysis of the collection using a Bayesian approach detected three possible major clusters, with an overall FST value of 0.177. Important inputs on the knowledge about upland rice germplasm differentiations which happened in Brazil in the last few centuries were also achieved and are discussed.ConclusionThe three multiplex panels described here represent a powerful tool for rice genetic analysis, offering a rapid and efficient option for rice germplasm characterization. The data gathered demonstrates the feasibility of genotyping extensive germplasm collections using panels of multiplexed microsatellite markers. It contributes to the advancement of research on large scale characterization and management of germplasm banks, as well as identification, protection and assessments of genetic relationship of rice germplasm.
Highlights
This study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel
Genetic background of the rice accessions Initially, it was necessary to verify if the accessions of rice collected in different parts of Brazil belonged to the same genetic background, as indicated by previous information on each of the accessions
Garris and colleagues [15] detected a smaller average allele number than the results presented here for a sample of 234 rice accessions representing the geographic range of O. sativa
Summary
This study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel. EMBRAPA keeps a germplasm bank of landraces collected all around the country within a 25-year period. Most of these landraces have been collected in villages and isolated rural areas, where cultivated rice has been grown since its introduction in Brazil, centuries ago [3]. Technical information is limited to field observation, farmer testimony and descriptive data of the collection site. It is, an ideal material for genetic characterization based on molecular technology. Of particular interest is the understanding of the genetic structure of the collection and its potential exploitation for cultivar improvement
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