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Deepwater Rice GWAS Highlights Derived Signaling Haplotype

Deepwater rice in the Philippines.

NEW YORK (GenomeWeb) – A team from Japan and the US has tracked down a haplotype involving the gibberellin biosynthesis gene semidwarf1 (SD1) that contributes to the ability of "deepwater" rice to withstand being submerged in water.

The researchers did a genome-wide association study encompassing a panel of Asian and deepwater rice varieties, searching for variants that coincide with nine deepwater traits. The findings, appearing online today in Science, highlighted ties SD1 amplification and rice internode elongation — the growth of rice stems between nodes — in response to submergence in the water tolerant rice. Their analyses suggested that this adaptation arose through selection on existing genetic variation in rice in Bangladesh.

The latter result may be relevant to future rice developments in the face of extreme weather and other challenging environments linked to climate change, co-first author Takeshi Kuroha, a life sciences researcher at Tohoku University, said in a statement. "Farmers will need to diversify their methods, and the cryptic genetic variation found in wild rice genes may offer adaptive solutions for growing resilient crops," he added.

The researchers' initial GWAS led to half a dozen quantitative trait loci, which they whittled down to a candidate region that contained SD1. They then defined six SD1 haplogroups from variants found in and around this region. Among them: a haplotype called C928, containing variants found in the deepwater rice, which showed higher-than-usual SD1 expression in response to submergence.

In addition to experiments aimed at understanding the mechanism for the SD1 haplotype in deepwater rice, the team analyzed variants in 149 Oryza sativa rice varieties, pinning the deepwater rice-related SD1 haplotype exclusively in flood tolerant rice from Bangladesh. On the other hand, more than a dozen O. rufipogon wild rice accessions contained the haplotype, based on an analysis of available wild rice resequencing data.

These and other data from the study "support the hypothesis that [the deepwater rice haplotype] emerged in O. rufipogon during W1-W4 [rice population] differentiation; this conditionally functional haplotype was then a target of selection for the cultivation of O. sativa under deepwater environments in Bangladesh," the authors wrote.

The team's growth assays, PCR-based expression analyses, hormone treatment, and other experiments suggested deepwater rice-related SD1 haplotype amplifies the gene's signal in response to an ethylene-responsive transcription factor called OsEIL1a to promoted gibberellin hormone production and boost stem growth — in contrast to a loss-of-function SD1 allele associated with enhanced rice yield that has been shown to be subject to selection during the so-called Green Revolution.

"[A] transcriptional gain-of-function allele of the Green Revolution semidwarf gene triggers rapid stem elongation in deepwater rice, enabling it to survive adverse flooding conditions," the authors wrote, noting that "the same gene has been co-opted several times to permit rice cultivation in highly contrasting production systems via different molecular responses — decreasing enzymatic activity in one case and enhancing transactivation in the other."