Two genes with a common region that is characteristic of the TPSI1/Mt4 family were cloned from a Pi-starvationinduced cDNA library of rice roots using suppression subtracted hybridization (SSH). Based on the consensus sequence of these two genes, members of the TPSI1/Mt4 family were found in maize, wheat and barley. BLAST and a cluster analysis in the eight members of the TPSI1/Mt4 family showed two classes of four genes each among monocots. The first gene from rice was designated OsIPS1 based on a comparison of the consensus sequence with AtIPS1 , and consequently the second gene, which has been previously reported as OsPI1 , was designated OsIPS2 . Accumulation of the mRNA of OsIPS1/2 was examined by northern blotting and quantitative reverse transcriptasepolymerase chain reaction in whole-root and split-root experiments under treatment with phosphate (Pi) and the Pi analogue phosphite (Phi). OsIPS1 showed much higher mRNA accumulation in roots than OsIPS2 , and an opposite trend was seen in shoots. OsIPS1/2 showed both systemic and local responses to Pi starvation, and less than 10% of the overall induced mRNA level was due to the local Pi concentration in roots. The results indicate that Phi may interfere with earlier events in roots that are associated with a local Pi signalling pathway. An analysis of transgenic plants showed that OsIPS1/2 are independently responsive to Pi signalling and are mainly expressed in lateral roots and in the vascular cylinder in the primary root. Exogenous cytokinin (6-BA) almost completely suppressed systemic Pi starvation signalling and partially suppressed local Pi signalling. Exogenous abscisic acid remarkably reduced Pi starvation signalling. In contrast, exogenous auxin enhanced Pi signalling, especially local Pi signalling in roots. Exogenous ethylene (ethyphon) and the ratio of auxin to cytokinins did not appear to affect the expression of these two genes.

In this report we define the genes of two-component regulatory systems in rice through a comprehensive computational analysis of rice (Oryza sativa L.) genome sequence databases. Thirty-seven genes were identified, including 5 HKs (cytokinin-response histidine protein kinase) (OsHK1-4, OsHKL1), 5 HPs (histidine phosphotransfer proteins) (OsHP1-5), 15 type-A RRs (response regulators) (OsRR1-15), 7 type B RR genes (OsRR16-22), and 5 predicted pseudo-response regulators (OsPRR1-5). Protein motif organization, gene structure, phylogenetic analysis, chromosomal location, and comparative analysis between rice, maize, and Arabidopsis are described. Full-length cDNA clones of each gene were isolated from rice. Heterologous expression of each of the OsHKs in yeast mutants conferred histidine kinase function in a cytokinin-dependent manner. Nonconserved regions of individual cDNAs were used as probes in expression profiling experiments. This work provides a foundation for future functional dissection of the rice cytokinin two-component signaling pathway.

Main conclusionThis article provides an overview of the interactions between Phytophthora effectors and plant immune system components, which form a cross-linked complex network that regulates plant pathogen resistance.

Background Anthocyanins determinate the flower color of many plants. Tobacco is a model plant for studying the molecular regulation of flower coloration. We investigated the mechanism underlying flower coloration in tobacco by profiling flavonoid metabolites,expression of anthocyanin biosynthetic structural genes and their regulator genes in the pink-flowered tobacco cultivar Yunyan 87 and white-flowered Yunyan 87 mutant. Result Significant down-accumulation of anthocyanins, including cyanidin 3-O-glucoside, cyanin, cyanidin 3-O-rutinoside, pelargonidin 3-O-beta-D-glucoside, cyanidin O-syringic acid, pelargonin, and pelargonidin 3-O-malonylhexoside (log2 fold change < − 10), endowed the flower color mutation in Yunyan 87 mutant. Transcriptome analysis showed that the coordinately down-regulated anthocyanin biosynthetic genes including chalcone isomerase, naringenin 3-dioxygenase, dihydroflavonol 4-reductase and UDP-glucose:flavonoid 3-O-glucosyltransferase played critical roles in suppressing the formation of the aforesaid anthocyanins. Several genes encoding MYB and bHLH transcription factors were also found down-regulated, and probably the reason for the suppression of structural genes. Conclusion This is the first study of tobacco flower coloration combining metabolome and transcriptome analyses, and the results shed a light on the systematic regulation mechanisms of flower coloration in tobacco. The obtained information will aid in developing strategies to modify flower color through genetic transformation.

Molecular markers and genetic maps are useful tools for genetic research and molecular breeding. Although significant progress has been made recently on molecular marker development and genetic map construction in tobacco (Nicotiana tabacum), more efforts are still required to meet the needs of genetic research and breeding in this allotetraploid species. In this study, based on the expressed sequence tag (EST) data and genome sequence data of N. tabacum, we developed a total of 4886 simple sequence repeat (SSR) markers (including 1365 genomic SSRs and 3521 EST-SSRs), which were functional in a set of eight tobacco varieties of four different types and were basically novel. Using these newly developed SSR markers as well as published SSR markers and a population of 207 double haploid (DH) lines derived from a cross between two flue-cured tobacco varieties ÔHonghua DajinyuanÕ and ÔHicks Broad LeafÕ, we constructed a genetic map consisting of 611 SSR loci distributed on 24 tentative linkage groups and covering a total length of 1882.1 cM with an average distance of 3.1 cM between adjacent markers.

Tobacco (Nicotiana tabacum L.), particularly flue-cured tobacco, is one of the most economically important nonfood crops and is also an important model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping, and breeding. Simple sequence repeats (SSR) are one of the most widely-used molecular markers, having significant advantages including that they are generally co-dominant, easy to use, abundant in eukaryotic organisms, and produce highly reproducible results. In this study, based on the genome sequence data of flue-cured tobacco (K326), we developed a total of 13,645 mostly novel SSR markers, which were working in a set of eighteen tobacco varieties of four different types. A mapping population of 213 backcross (BC1) individuals, which were derived from an intra-type cross between two flue-cured tobacco varieties, Y3 and K326, was selected for mapping. Based on the newly developed SSR markers as well as published SSR markers, we constructed a genetic map consisting of 626 SSR loci distributed across 24 linkage groups and covering a total length of 1120.45 cM with an average distance of 1.79 cM between adjacent markers, which is the highest density map of flue-cured tobacco till date.

Using degenerate primers based on the conserved nucleotide binding site (NBS) and protein kinase domain (PKD), 100 resistance gene analogs (RGAs) were isolated from tobacco variety Nicotiana repanda. BLASTx search against the GenBank database revealed that 27 belong to the NBS class and 73 belong to the protein kinase (PK) class. Cluster analysis and multiple sequence alignment of the deduced protein sequences indicate that RGAs of the NBS class can be divided into two groups: toll/interleukin receptor (TIR) and non-TIR types. Both types possess 6 conserved motifs (P-loop, RNBS-A, Kinase-2, RNBS-B, RNBS-C, GLPL). Based on their sequence similarity, the tobacco RGAs of the PK class were assigned to 8 subclasses. We examined their expression after infection with either Tobacco mosaic virus (TMV) or the tobacco black shank pathogen (Phytophthora parasitica var. nicotianae). The expression levels of 4 RGAs of the PK class were significantly elevated by TMV and 1 RGA of the PK class and 3 RGAs of the NBS class were up-regulated by P. parasitica var. nicotianae. The expression of two RGAs of the PK class was induced by P. parasitica var. nicotianae. Infection by either TMV or P. parasitica var. nicotianae enhanced the expression of NtRGA2, a RGA of the PK class. The present study shows that RGAs are abundant in the tobacco genome and the identification of tobacco RGAs induced by pathogens should provide valuable information for cloning related resistance genes in tobacco.

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