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

PLoS One. 2015 Apr 29;10(4):e0124617. doi: 10.1371/journal.pone.0124617. eCollection 2015.


Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the 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 identified 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 shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amylose / metabolism
  • Computational Biology
  • DNA Copy Number Variations
  • Genetic Markers / genetics*
  • Genetic Variation
  • Genome, Plant*
  • Genotype
  • Haplotypes
  • High-Throughput Nucleotide Sequencing
  • Oryza / genetics*
  • Plant Breeding / methods*
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Polymorphism, Single Nucleotide
  • Selection, Genetic*
  • Sequence Analysis, DNA
  • Starch Synthase / genetics
  • Starch Synthase / metabolism


  • Genetic Markers
  • Plant Proteins
  • Amylose
  • granule-bound starch synthase I
  • Starch Synthase

Grant support

This work was supported by the Agricultural Research Service of the United States Department of Agriculture (USDA/ARS); the RiceCAP project (USDA/CSREES http://www.uark.edu/ua/ricecap/) (2004-35317-14867 to J.O. and B.S.); The Mississippi Rice Promotion Board (http://rice.msstate.edu/members.html); The Rice Foundation (http://www.usarice.com/index.php); the Louisiana Rice Research Board (http://www.lsuagcenter.com/en/crops_livestock/crops/rice/Rice+Research+Board+Reports/From-the-Louisiana-Rice-Research-Board.htm); the International Center for Tropical Agriculture (http://ciat.cgiar.org/); the Global Rice Science Partnership (GRiSP) project (http://www.grisp.net/main/summary); and the National Science Foundation (NSF) (0965420 to J.T.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.