Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza.

The wild Oryza species are rich in genetic diversity and are good resources for modern breeding of rice varieties. The reliable ex situ conservation of various genetic resources supports both basic and applied rice research. For this purpose, we developed PCR-based and co-dominant insertion/deletion (INDEL) markers which enable the discrimination of the genome types or species in the genus Oryza. First, 12,107 INDEL candidate sequences were found in the BAC end sequences for 12 Oryza species available in public databases. Next, we designed PCR primers for INDEL-flanking sequences to match the characteristics of each INDEL, based on an assessment of their likelihood to give rise to a single or few PCR products in all 102 wild accessions, covering most Oryza genome types. Then, we selected 22 INDEL markers to discriminate all genome types in the genus Oryza. A phylogenetic tree of 102 wild accessions and two cultivars according to amplicon polymorphisms for the 22 INDEL markers corresponded well to those in previous studies, indicating that the INDEL markers developed in this study were a useful tool to improve the reliability of identification of wild Oryza species in the germplasm stocks.

Ovule is a lateral organ finally differentiated from the terminating floral meristem in rice.

The floral meristem is the homeostatic source of floral organs in angiosperms. In rice, after stamen and carpel differentiation, the floral meristem is terminated and exhausted to produce an ovule. To elucidate underlying mechanisms controlling the continuous process from floral meristem termination to ovule formation, we investigated two rice mutants showing abnormalities in ovule formation. In the weak mutant of the lonely guy gene, responsible for cytokinin activation to maintain the floral meristem, ovule formation was abolished inside the normally developing carpel. The loss-of-function of the OsMADS13 gene, encoding a MADS-box transcription factor, resulted in the replacement of ovule with extra carpels. The in situ expression of tissue-specific markers in both mutants revealed that a lateral region of the terminating floral meristem adjacent to the site of carpel initiation exclusively differentiated the ovule and is apparently distinct from the remainder of the floral meristem, in contrast to previous assumptions. Our findings also suggest that primordial germ cells are initiated independently of ovule formation, but dependently on the presence of active cytokinin. We propose a novel pattern of ovule formation in angiosperms, in which the ovule is a lateral organ finally differentiated from the terminating floral meristem in rice.

Rice expression atlas in reproductive development.

Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. A decrease in expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes which appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several cyclin-dependent kinases (CDKs), cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the most extensive and most comprehensive data set available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed.

Rice plant development: from zygote to spikelet.

Rice is becoming a model plant in monocotyledons and a model cereal crop. For better understanding of the rice plant, it is essential to elucidate the developmental programs of the life cycle. To date, several attempts have been made in rice to categorize the developmental processes of some organs into substages. These studies are based exclusively on the morphological and anatomical viewpoints. Recent advancement in genetics and molecular biology has given us new aspects of developmental processes. In this review, we first describe the phasic development of the rice plant, and then describe in detail the developmental courses of major organs, leaf, root and spikelet, and specific organs/tissues. Also, for the facility of future studies, we propose a staging system for each organ.