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Resequencing Study Characterizes Variation in Wild, Cultivated Rice Genomes

NEW YORK (GenomeWeb News) – By sequencing and comparing the genomes of 50 cultivated and wild rice strains, an international team has identified millions of genetic variants for distinguishing between rice strains and exploring their population histories.

In a paper in the early, online edition of Nature Biotechnology yesterday, researchers from China, Denmark, the US, and Switzerland described the strategy that they used to resequence 40 Asian cultivated rices, Oryza sativa, accessions and 10 accessions of two related wild species, O. rufipogon and O. nivara.

By inspecting and comparing these genomes, the investigators uncovered examples of structural variants in genomes, found thousands of new rice genes, and tracked down genes with distinct diversity patterns in cultivated rice. They also found some 6.5 million high-quality SNPs that they have already started using to discern rice population patterns. Down the road, the variants are expected to serve as a resource for those interested in improving rice crops, the study authors noted.

"The high-quality variation data will greatly facilitate the identification of functional variations and be useful for marker-assisted breeding and gene mapping of rice," co-first author Xun Xu, a researcher with the Chinese Academy of Sciences and vice president of BGI-Shenzhen's research and development department, said in a statement.

"The millions of SNP data generated in this study not only provide tremendous opportunity to unravel the domestication history of rice," he added, "but they also could serve as a valuable source for researchers to rapidly identify agronomically important genes in rice."

Plants in the rice lineage morphed dramatically during the process of domestication, both in their physical features and physiology, the researchers explained. But the genetic patterns behind these changes are not well understood.

To explore these features in more detail than previously possibly, researchers used Illumina GAII paired-end sequencing to resequence 40 cultivated rice accessions, including a dozen cultivars from the indica sub-species of O. sativa and two-dozen cultivars from the japonica sub-species. They also resequenced 10 strains of O. rufipogon or O. nivara, wild plants from which rice was domesticated.

After mapping the sequence reads back to an International Rice Genome Sequencing Project reference genome, the team had a mapped genome coverage of around 10 times for each of the resequenced strains. Unmapped reads, meanwhile, were assembled into contigs containing more than 2,000 previously unknown rice genes.

More than 1,400 of these new genes corresponded to plant gene homologs in the NCBI sequence database. Even so, the presence of those genes varied widely by rice strain: most showed up in fewer than five of the resequenced rice accessions, nearly 700 genes turned up in just one of the strains, and 319 were specific to wild rice strains.

On the other hand, the team's analyses indicated that more than 1,300 of the genes found in the rice reference genome were missing from one or more of the resequenced accessions.

Within the resequenced genomes, the team detected 94,700 structural variants, 808,000 small insertions and deletions, and roughly 50 million potential SNPs, including 6.5 million high-quality variants.

"To our knowledge, this represents the largest high-quality SNP data set obtained in rice," the study's authors noted. "The data may be used to identify important rice genes by serving as molecular markers for designing rice SNP arrays and for breeding."

When they analyzed the rice populations using these SNPs, for example, researchers found thousands of genes showing significantly less genetic diversity in cultivated than in wild strains — patterns that may reflect artificial selective pressures placed on these parts of the genome during domestication.

Findings from the team's phylogenetic analyses were also consistent with distinct domestication events for the indica and japonica rice sub-species, suggesting that indica sub-species are most closely related to the wild O. nivara plants while japonica sub-species are more similar to O. rufipogon.

"[T]he tree showed that all japonica rices were closer to the five Chinese O. rufipogon accessions, especially Dongxiang wild rice from the low Yangtze region," the team explained, "strongly supporting the conjecture that japonica might have been independently domesticated from a Chinese O. rufipogon population in the Yangtze region."