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Team Reports on Rice Resequencing Resource Containing 3,000 Genomes

NEW YORK (GenomeWeb News) – In a study published online today in GigaScience, members of a research team from China and the Philippines presented findings from a population re-sequencing study focused on some 3,000 rice strains.

As part of the first phase of the 3,000 Rice Genomes Project, investigators from the Chinese Academy of Agricultural Sciences, BGI-Shenzhen, and the International Rice Research Institute in the Philippines sequenced 3,000 Oryza sativa rice plants, representing accessions grown in nearly 90 countries. By tapping into almost 19 million SNPs detected in the genomes, they subsequently performed a phylogenetic analysis that verified the presence of five main rice varieties.

Although additional work is needed to more fully explore how genetic features in various rice strains impact plant features, those involved in the study are optimistic that the slew of new sequence data will ultimately aid efforts to improve rice crops and boost yields.

"Our ultimate goal is to establish, through collective efforts by the international scientific community, a public rice database containing genetic and genomic information suitable for advancing rice breeding technology," the study's authors wrote.

"The expected information explosion from follow-up studies of the project will provide a foundation to revolutionize rice genetics and breeding research," they added. "Ultimately that could lead to a more thorough understanding of the molecular, cellular, and physiological machineries/networks responsible for the growth and development of rice plants and their responses to various abiotic and biotic stresses."

To that end, the team has deposited some 13.4 terabytes of rice sequence information into a publicly available database through the GigaDB site as well as the National Center for Biotechnology Information's Sequence Read Archive. A collection of seeds representing the re-sequenced strains is reportedly available through the International Rice Research Institute's International Rice Genebank Collection.

The original rice reference genome — produced using DNA from the O. sativa sub-species japonica — was published in Nature in 2005, following the release of a draft sequence a few years earlier. Since then, several studies have started documenting genetic diversity in rice plants.

For example, investigators involved in the OryzaSNP Consortium used array-based approaches to tally up variants in 20 rice varieties or landraces — work they reported in the Proceedings of the National Academy of Sciences in 2009.

In a Nature Biotechnology study published in 2011, meanwhile, a team from China, Denmark, the US, and Switzerland presented findings from a genome re-sequencing study centered on 40 O. sativa strains commonly cultivated in Asia and 10 accessions representing related wild plants.

In an effort to get an even broader and deeper view of rice diversity, members of the 3,000 Rice Genomes Project used Illumina's HiSeq 2000 instrument to generate genomic DNA sequence for 3,000 rice accessions from 89 countries, covering between 92.5 and 94 percent of the rice reference genome to 14-fold depth, on average.

The re-sequenced set included 2,466 of the International Rice Genebank Collection's accessions, the researchers noted, along with 534 accessions housed at the Chinese Academy of Agricultural Sciences' China National Crop Gene Bank.

Within the genome sequences for these accessions, the team pinpointed 18.9 million SNPs. The variants tended to turn up across a few rice chromosomes in particular — such as chromosomes 1, 4, and 11 — but were less common on chromosomes 5, 9, and 10.

When they incorporated such variants into a phylogenetic analysis of the rice strains, the researchers found five main genetic clusters coinciding with known O. sativa varieties: tropical japonica, temperature japonica, indica, aus/boro, and basmatic/sadri.

The split between japonica and indica varieties was most pronounced, they reported. The aus/boro and basmatic/sadri varieties made up smaller groups, as did a set of admixed rice accessions.

In a related commentary article in GigaScience, study leaders from the Chinese Academy of Agricultural Sciences, BGI-Shenzhen, and the International Rice Research Institute provided more information on future directions of the 3,000 Rice Genomes Project, which is focused on developing genetic and genomic resources for rice with an eye to aiding rice farmers in more than a dozen countries in Africa and Asia.

"With decreasing resources (water and land), food security is — and will be — the most challenging issue in these countries, both currently and in the future," co-corresponding author Zhi-Khang Li, project director of the Chinese Academy of Agricultural Sciences, said in a statement. "As a scientist in rice genetics, breeding and genomics, it would be a dream to help to solve this problem."