Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

Authors: DUITAMA, JORGE - International Center For Tropical Agriculture (CIAT); SILVA, ALEXANDER - International Center For Tropical Agriculture (CIAT); SANABRIA, YAMID - Louisiana State University Agcenter; CRUZ, DANIEL - International Center For Tropical Agriculture (CIAT); QUINTERO, CONSTANZA - International Center For Tropical Agriculture (CIAT); BALLEN, CAROLINA - International Center For Tropical Agriculture (CIAT); LORIEUX, MATHIAS - International Center For Tropical Agriculture (CIAT); Scheffler, Brian; FARMER, ANDREW - National Center For Genome Resources; TORRES, EDGAR - International Center For Tropical Agriculture (CIAT); OARD, JAMES - Louisiana State University Agcenter; TOHME, JOE - International Center For Tropical Agriculture (CIAT)

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/2/2015
Publication Date: 4/29/2015
Citation: Duitama, J., Silva, A., Sanabria, Y., Cruz, D., Quintero, C., Ballen, C., Lorieux, M., Scheffler, B.E., Farmer, A., Torres, E., Oard, J., Tohme, J. 2015. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One. 10(4):e0124617. doi:10.1371/journal.pone.0124617.

Interpretive Summary: Rice is an extremely important carbohydrate crop worldwide. However, there are several rice species or sub-species grown in the world to meet these caloric needs. In part this is because diverse rice quality traits are desired in various parts of the world and there are different environmental growing conditions. This array of needs is presently meet with using rice cultivars from genetically different backgrounds. In the Americas and especially the US, the type of rice grown is relatively unique and limited in genetic variation. In this study, the DNA sequence of 104 rice varieties was analyzed. The DNA sequences were either generated for this project or were gathered for open data sources. Genetic difference between these varieties were identified by comparing sequences between these accessions and the reference genome of rice. This information provides a look at the genome structure of elite varieties grown in the Americas which will be an invaluable tool to the rice research community. In addition to looking at whole genome structure, the major gene involved in starch content was examined which helped identify novel DNA markers for varieties with high amylose content. High amylose content has been associated with rice varieties with a lower glycemic index.

Technical Abstract: Current advances in sequencing technologies and bioinformatics allow to determine a nearly complete genomic background of rice, a staple food for the poor people. Consequently, comprehensive databases of variation among thousands of varieties is currently being assembled and released. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to produce significant improvements for development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We built a database of repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns that constitute the genomic background of elite varieties commonly used by farmers throughout the Americas. Based on a nearly complete reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.