ArticleBMC plant biology2007
A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions.
Article in BMC plant biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
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- Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India.BMC genetics · 2016Article
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- Genetic structure of Thai rice and rice accessions obtained from the International Rice Research Institute.Rice (New York, N.Y.) · 2012Article
- Development of a genome-wide multiple duplex-SSR protocol and its applications for the identification of selfed progeny in switchgrass.BMC genomics · 2012Article
- Development and application of a whole-genome simple sequence repeat panel for high-throughput genotyping in soybean.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
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- Functionally relevant microsatellites in sugarcane unigenes.BMC plant biology · 2010Article
- Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach.BMC plant biology · 2010Article
- Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups.BMC genomics · 2009Article
- Identification of drought-responsive genes in roots of upland rice (Oryza sativa L).BMC genomics · 2008Article
- Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference.BMC genomics · 2008Article
- Rice molecular breeding laboratories in the genomics era: Current status and future considerations.International journal of plant genomics · 2008Article
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5 authors.
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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 x 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.
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