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Agrobiodiversity / / From genomics to the field: Getting to know the genome of rice planted in America, to develop better varieties

From genomics to the field: Getting to know the genome of rice planted in America, to develop better varieties

Obtaining detailed genomic information about the rice cultivars most often planted today by rice producers in America was, broadly speaking, the goal of a research project whose results have just been announced in the Public Library of Science (PLOS One).


“This is a great story of collaboration, joint analysis with partners, and delivery of information to public databases, for the benefit of the rice community,” says Jorge Duitama, leader of CIAT’s Bioinformatics team, while he explains how important it is for the Center to have worked in a team with researchers from the entities that participated in the RiceCAP project, including Louisiana State University (LSU), the Genomics and Bioinformatics Research Unit of USDA-ARS, and the National Center for Genome Resources (NCGR) of the United States.

This research, which was started independently by the RiceCAP project and CIAT, focused on carrying out the complete sequencing of the genomes of 54 varieties, including two advanced lines from the Instituto Rio Grandense de Arroz [Rio Grande Rice Institute] (IRGA); two from Uruguay’s Instituto Nacional de Investigación Agropecuaria [National Institute of Agricultural Research] (INIA); three from the Colombia’s Federación de Productores de Arroz [Association of Rice Producers] (Fedearroz), and one from Venezuela’s Asociación de Productores Rurales del Estado Portuguesa [Association of Rural Producers of the Portuguesa State] (Asoportuguesa). This was also a chance to take advantage of the availability in the public databases of 50 additional varieties, corresponding to the main subspecies of rice.

Supported by state-of-the-art specialized tools, such as Next Generation Sequencing Eclipse Plugin (NGSEP), open source software developed at CIAT, with nearly 2,000 downloads since its launch in April 2014, and always keeping in mind the pressing need to use genomic tools to achieve a significant improvement in food production and hunger relief in the face of a rapidly increasing population, it was possible to generate a source of detailed information in terms of alleles and simple nucleotide polymorphisms (SNPs), which are useful for the development of future improved varieties through marker-assisted selection.

The scientists of this multi-institutional effort started with an initial approach to assess the potential of this database for rice improvement. From there, the variation observed within the GBSSI gene was investigated. This gene, located on chromosome 6, is known to be related to amylose content, which is one of the agricultural traits of greatest interest, both in Latin America and in the United States. This study made it possible to identify new SNPs that can be used in marker-assisted selection to develop improved varieties with high grain quality.

“Our hope is that both the analytical methods and the genomic information described in this study can be useful for the rice research community and for other groups that are carrying out similar sequencing efforts on other crops,” concludes Duitama.


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  • Reinhardt Howeler: Thanks, Keith. It was a pleasure writing this book as it brought back so many good memories of working with cassava, both in Latin America and in Asia. I was lucky that the Nippon Foundation suggested that I write this book and financed its publication. They also wanted a simplified version for farmers and extension workers that could be translated into various languages. The English version of this new book is now going to press in Hanoi, while the Khmer and Vietnamese translations are also ready for printing and the Thai and Chinese translations are still being worked on. In case you are interested in the English version, let me know. My email address is still And let me know where you are working now and what you are doing. Reinhardt
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