A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice.

Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield. The qWS8/ipa1-2D locus is associated with reduced DNA methylation and a more open chromatin state at the IPA1 promoter, thus alleviating the epigenetic repression of IPA1 mediated by nearby heterochromatin. Our findings reveal that IPA traits can be fine-tuned by manipulating IPA1 expression and that an optimal IPA1 expression/dose may lead to an ideal yield, demonstrating a practical approach to efficiently design elite super rice varieties.

A practical protocol to accelerate the breeding process of rice in semitropical and tropical regions.

Breeding of excellent rice varieties is essential for modern rice production. Typical breeding procedures to introduce and maintain valuable agricultural traits require at least 8 generations from crossing to stabilization, always taking more than 4-5 years of work. This long and tedious process is the rate-limiting step in the development of new varieties, and therefore fast culturing methods are in urgent need. Taking advantage of early flowering characteristics of light-sensitive rice under short-day conditions, we have developed a practical protocol to accelerate the breeding cycle of rice, which we have termed the "1 + 2", "2 + 2", "1 + 3", and "0 + 5" methods according to the different rice varieties and different breeding purposes. We have also incorporated several techniques, including glume cutting, seed desiccation at 50°C in a drier seed dormancy breakage with low concentration of HNO3, and direct seeding. Using the above strategy, we have shortened the life cycle of light-sensitive rice varieties to about 70 days, making it possible for several rice cultivars to proliferate 4-5 generations in a single calendar year. This protocol greatly accelerates the process of new variety breeding, and can be used in rice research for shortening the process of genetic analysis and the construction of mapping populations.

Glabrous Rice 1, encoding a homeodomain protein, regulates trichome development in rice.

BACKGROUND: Glabrous rice, which lacks trichomes on the rice epidermis, is regarded as an important germplasm resource in rice breeding. Trichomes are derived from aerial epidermal cells and used as a model to study the cell fate determination in plant. In Arabidopsis, the molecular mechanisms of trichome development have been well studied. However, little is known about the molecular basis of trichome development in rice. RESULTS: In this study, near isogenic lines harboring the glabrous rice 1 locus were developed. By a map-based approach, we narrowed down the locus to a 21-kb DNA region harboring two genes. One of the genes named Glabrous Rice 1 (GLR1), which is most likely the candidate, encodes a homeodomain protein containing the WOX motif. Constitutive Expression of GLR1 could partially complement the glabrous phenotype of NILglr1. The knock down of GLR1 by RNA interference led to a significant decrease in trichome number on the leaves and glumes of the RNAi transgenic plants. CONCLUSION: GLR1 plays an important role in rice trichome development and will contribute to breeding of glabrous elite rice varieties.