Paleo-Green Revolution for rice.

A central element of the Green Revolution was the widespread adoption of semidwarf rice cultivars (SRCs) that more than doubled worldwide rice production (1). The high-yield potentials of modern SRCs are attributed primarily to their improved harvest index, lodging resistance, and responsiveness to high inputs (primarily nitrogen and water) (1–3), contributing to their adoption in irrigated areas that occupy 57% of world rice lands (4). The short stature of SRCs is caused by sd1, a mutant allele in the gene encoding a key enzyme (gibberellin 20-oxidase) functioning in biosynthesis of the plant hormone gibberellic acid (GA) that greatly reduces content of the bioactive molecule GA1 (5, 6). In PNAS, Asano et al. (7) show that the SD1 locus (where the sd1 mutation resides) has been a target of humanmediated selection since prehistoric times. In a population of backcross inbred lines from a cross between an Oryza sativa paddy rice (subspecies japonica) variety Nipponbare and an upland rice (ssp. indica) variety Kasalath, a quantitative trait locus, qCL1, accounts for 20.9% of phenotypic variation in culm length. Study of 5,000 plants segregating at the qCL1 locus shows its phenotypic effects to result from at least two genes, with one (qCL1a) delimited to a 336-kb genomic region that included the SD1 locus and at least 40 other genes. The Nipponbare and Kasalath SD1 alleles differ by 2 aa-altering nucleotides. Plants transgenic for the respective alleles largely recapitulate the phenotypic difference in culm length. The Kasalath allele (SD1-GR) also has significantly higher catalytic activity than the Nipponbare allele SD1-EQ in the 13hydroxylated pathway of GA synthesis leading to GA1, which is consistent with its greater culm length. Levels and patterns of genetic diversity among primitive rice cultivars and wild relatives at the SD1 locus strongly suggest that the japonica allele of qCL1a was selected during domestication, perhaps 10,000 y ago. All 40 accessions of a wild progenitor, O. rufipogon, as well as most ssp. indica accessions contain SD1-GR, whereas all 16 diverse japonica accessions contain the Nipponbare allele (SD1-EQ). A 4-kb region encompassing the entire SD1 sequence shows 98% reduction in genetic diversity in ssp. japonica relative to O. rufipogon, a 10-fold greater reduction than in random genomic fragments (ruling out a population bottleneck). Indeed, diversity is reduced in subspecies japonica but not indica in a 404-kb region surrounding the locus, consistent