A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions

The 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.The 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.One of the largest ex situ germplasm collections in the world is comprised of rice accessions (Oryza sativa L.) [1]. Its two cultivated Asian subspecies, indica and japonica, have constituted one of the pillars of human diet for thousands of years. In Brazil, rice production and consumption is comparable to that of some Asian countries, and japonica rice accounts for 40% of the total rice production, a value above the 20% average observed in other parts of the world [2]. 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]. They may represent an extraordinary source of genes that