Seed dormancy provides a strategy for flowering plants to survive adverse natural conditions. It is also an important agronomic trait affecting grain yield, quality, and processing performance. We cloned a rice quantitative trait locus, Sdr4, which contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. These results are discussed with respect to possible selection of the allele during the domestication process.domestication | preharvest sprouting | quantitative trait locus

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To understand the genetic basis of yield-related traits of rice, we developed 39 chromosome segment substitution lines (CSSLs) from a cross between an average-yielding japonica cultivar, Sasanishiki, as the recurrent parent and a high-yielding indica cultivar, Habataki, as the donor. Five morphological components of panicle architecture in the CSSLs were evaluated in 2 years, and 38 quantitative trait loci (QTLs) distributed on 11 chromosomes were detected. The additive effect of each QTL was relatively small, suggesting that none of the QTLs could explain much of the phenotypic difference in sink size between Sasanishiki and Habataki. We developed nearly isogenic lines for two major QTLs, qSBN1 (for secondary branch number on chromosome 1) and qPBN6 (for primary branch number on chromosome 6), and a line containing both. Phenotypic analysis of these lines revealed that qSBN1 and qPBN6 contributed independently to sink size and that the combined line produced more spikelets. This suggests that the cumulative effects of QTLs distributed throughout the genome form the major genetic basis of panicle architecture in rice.

Highlight qEMF3, a novel QTL for the early-morning flowering trait to mitigate heat-induced spikelet sterility at flowering in rice, was identified using a wild rice, Oryza officinalis, as a genetic resource.