Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice.

BACKGROUND: The African rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development. RESULTS: Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development. We uncovered evidence for a wider rachis meristem in O. glaberrima than in O. barthii. At the molecular level, spatial and temporal expression profiles of orthologs of O. sativa genes related to meristem activity and meristem fate control were obtained using in situ hybridization and qRT-PCR. Despite highly conserved spatial expression patterns between O. glaberrima and O. barthii, differences in the expression levels of these early acting genes were detected. CONCLUSION: The higher complexity of the O. glaberrima panicle compared to that of its wild relative O. barthii is associated with a wider rachis meristem and a modification of expression of branching-related genes. Our study indicates that the expression of genes in the miR156/miR529/SPL and TAW1 pathways, along with that of their target genes, is altered from the unbranched stage of development. This suggests that differences in panicle complexity between the two African rice species result from early alterations to gene expression during reproductive development.

Performance characteristics and clinical utility of diagnostic criteria proposals in bereaved treatment-seeking patients.

BACKGROUND: Persistent complex bereavement disorder (PCBD) is a protracted form of grief included in DSM Section 3 indicating a need for more research. Two other criteria sets [prolonged grief disorder (PGD) and complicated grief (CG) disorder] are also currently in use by researchers. This study evaluates rates of diagnosis of each proposed criteria set in a clinical sample of bereaved individuals participating in clinical research. METHOD: Two groups in which persistent grief was judged to be present or absent completed an assessment instrument that included items needed to diagnose PCBD as well as PGD and CG. One group included grief treatment-seeking participants in our multicenter National Institute of Mental Health (NIMH)-sponsored study who scored ⩾30 on the Inventory of Complicated Grief (ICG) and the other comprised bereaved adults enrolled in clinical research studies who scored <20 on the ICG. Rates of diagnosis were determined for proposed PCBD, PGD and CG criteria. RESULTS: PCBD criteria diagnosed 70 [95% confidence interval (CI) 64.2-75.8] % of the grief treatment-seeking group, PGD criteria identified 59.6 (95% CI 53.4-65.8) % of these individuals and CG criteria identified 99.6 (95% CI 98.8-100.0) %. None of the three proposed criteria identified any cases in the bereaved comparison group. CONCLUSIONS: Both proposed DSM-5 criteria for PCBD and criteria for PGD appear to be too restrictive as they failed to identify substantial numbers of treatment-seeking individuals with clinically significant levels of grief-related distress and impairment. Use of CG criteria or a similar algorithm appears to be warranted.

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species.

BACKGROUND: Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii. RESULTS: Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems. CONCLUSION: Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.

Consistency of crown rust evaluation in ryegrass cultivars.

Crown rust (Puccinia coronata) is the most important leaf disease in forage ryegrasses (Lolium spp.). In order to evaluate the stability in space and time of crown rust resistance a multisite rust evaluation trial was established by the European breeders association Eucarpia ( Fodder Crops Section). The same seed lots of 33 perennial ryegrass (Lolium perenne) and 18 Italian ryegrass (Lolium multiflorum) varieties were sown in April 2001, 2004 and 2007 at 27 European sites. This paper reports the temporal ranking of the ryegrass varieties for their crown rust susceptibility at the Belgian site and compares this ranking with the mean ranking over the European sites. The crown rust susceptibility was scored in September of each sowing year and of the year after. The rankings of both the perennial and the Italian ryegrass varieties were well correlated between the successive yearly observations at each sowing period. Also the rankings of the varieties of both species were similar over the 3 sowing periods. The rankings at the Belgian site corresponded very well with the mean ranking over the European sites. The crown rust resistance in ryegrass seems to be durable and consistent over a great part of Europe.

Characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice.

In Asian cultivated rice (Oryza sativa L.), aroma is one of the most valuable traits in grain quality and 2-ACP is the main volatile compound contributing to the characteristic popcorn-like odour of aromatic rices. Although the major locus for grain fragrance (frg gene) has been described recently in Basmati rice, this gene has not been characterised in true japonica varieties and molecular information available on the genetic diversity and evolutionary origin of this gene among the different varieties is still limited. Here we report on characterisation of the frg gene in the Azucena variety, one of the few aromatic japonica cultivars. We used a RIL population from a cross between Azucena and IR64, a non-aromatic indica, the reference genomic sequence of Nipponbare (japonica) and 93-11 (indica) as well as an Azucena BAC library, to identify the major fragance gene in Azucena. We thus identified a betaine aldehyde dehydrogenase gene, badh2, as the candidate locus responsible for aroma, which presented exactly the same mutation as that identified in Basmati and Jasmine-like rices. Comparative genomic analyses showed very high sequence conservation between Azucena and Nipponbare BADH2, and a MITE was identified in the promotor region of the BADH2 allele in 93-11. The badh2 mutation and MITE were surveyed in a representative rice collection, including traditional aromatic and non-aromatic rice varieties, and strongly suggested a monophylogenetic origin of this badh2 mutation in Asian cultivated rices. Altogether these new data are discussed here in the light of current hypotheses on the origin of rice genetic diversity.

Clinical comparison of an adhesive precoated vs. an uncoated ceramic bracket system.

OBJECTIVES: To clinically evaluate the bond characteristics of the adhesive precoated ceramic (APC) Clarity bracket and compare it with the uncoated Clarity bracket used with Transbond XT bonding system. Design - A randomized clinical trial. SETTINGS AND SAMPLE POPULATION: Department of Orthodontics, Katholieke Universiteit Leuven. Twenty patients requiring bonded fixed orthodontic appliance from central incisor to second bicuspid. EXPERIMENTAL VARIABLE: APC Clarity brackets were bonded in the first and fourth quadrant of group 1 and in the second and third quadrant of group 2. Uncoated Clarity brackets were bonded with Transbond XT in the second and third quadrant of group 1 and in the first and fourth quadrant of group 2. OUTCOME MEASURE: During orthodontic treatment, bracket failures were registered. At debonding, the tooth surfaces were intraorally scored according to the Adhesive Remnant Index. RESULTS: During treatment one tie wing fractured in the APC group and no bond failures occurred. At debonding, no significant differences between the APC and Transbond XT could be shown in any of the quadrants. CONCLUSION: The two groups performed identically.

Analysis of the transcriptional response to Rice Yellow Mottle Virus infection in Oryza sativa indica and japonica cultivars.

Several cDNA libraries were constructed using mRNA isolated from roots, panicles, cell suspensions and leaves of non-stressed Oryza sativa indica (IR64) and japonica (Azucena) plants, from wounded leaves, and from leaves of both cultivars inoculated with Rice Yellow Mottle Virus (RYMV). A total of 5549 cleaned expressed sequence tags (ESTs) were generated from these libraries. They were classified into functional categories on the basis of homology, and analyzed for redundancy within each library. The expression profiles represented by each library revealed great differences between indica and japonica backgrounds. EST frequencies during the early stages of RYMV infection indicated that changes in the expression of genes involved in energy metabolism and photosynthesis are differentially accentuated in susceptible and partially resistant cultivars. Mapping of these ESTs revealed that several co-localize with previously described resistance gene analogs and QTLs (quantitative trait loci).

Linkage mapping of Hsa-1(Og), a resistance gene of African rice to the cyst nematode, Heterodera sacchari.

Inheritance of resistance to cyst nematode (Heterodera sacchari) in Oryza sativa was investigated by inoculation tests with isolate 244 from Congo in segregating populations derived from hybridisation between O. sativa and its African sister cultivated species, O. glaberrima. We found that the resistance was controlled by one major gene, Hsa-1(Og), with codominance of susceptible and resistant alleles. To map Hsa-1(Og) on the rice genome, we pooled the data obtained from segregation of the resistance trait and microsatellite markers in three kinds of progeny: BC(1)F(3), BC(1)F(4), and pseudo-F(2) populations. Hsa-1(Og) was unambiguously located between Cornell University's RM206 and RM254 markers on chromosome 11. Two additional microsatellite markers derived from Monsanto publicly available sequences were found to be tightly linked to the Hsa-1(Og) gene. It is possible that numerous plant resistances to a pathogen in fact exhibit a codominant inheritance, possibly explaining misleading conclusions in several reports on resistance segregation.

Fine genetic mapping of a gene required for Rice yellow mottle virus cell-to-cell movement.

The very high resistance to Rice yellow mottle virus observed in the two rice varieties Gigante ( Oryza sativa) and Tog 5681 ( O. glaberrima) is monogenic and recessive. Bulked segregant analysis was carried out to identify AFLP markers linked to the resistance gene. Mapping of PCR-specific markers, CAPS and microsatellite markers on 429 individuals of an IR64 x Gigante F(2) population pinpointed this resistance gene on the long arm of chromosome 4 in a 3.7-cM interval spanned by PCR markers. These markers also flanked the resistance gene of the O. glaberrima accession Tog 5681 and confirmed previous allelism tests. The rarity of this recessive natural resistance was in line with a resistance mechanism model based on point mutations of a host component required for cell-to-cell movement of the virus. Preliminary data on the genetic divergence between the two cultivated rice species in the vicinity of the resistance locus suggested that two different resistance alleles are present in Gigante and Tog 5681. A large set of recombinants is now available to envisage physical mapping and cloning of the gene.

Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy.

Rice progenies used for the construction of genetic maps permit exhaustive identification and characterization of resistance genes present in their parental cultivars. We inoculated a rice progeny derived from the cross IR64 x Azucena with different Magnaporthe grisea isolates that showed differential responses on the parental cultivars. By QTL mapping, nine unlinked loci conferring resistance to each isolate were identified and named Pi-24( t) to Pi-32( t). They could correspond to nine specific resistance genes. Five of these resistance loci (RLs) were mapped at chromosomal locations where no resistance gene was previously reported, defining new resistance genes. Using degenerate primers of the NBS (nucleotide binding site) motif found in many resistance genes, two resistance gene analogues (RGAs) IR86 and IR14 were identified and mapped closely to two blast RLs (resistance identified in this study, i.e. Pi-29(t) and Pi-30(t) respectively). These two RLs may correspond to the Pi-11 and Pi-a blast resistance genes previously identified. Moreover, the ir86 and ir14 genes have been identified "in silico" on the indica rice cultivar 93-11, recently sequenced by Chinese researchers. Both genes encodes NBS-LRR-like proteins that are characteristics of plant-disease resistance genes.

The effect of type 1 astrocytes on neuronal complexity: a fractal analysis.

Embryonic, ventral spinal cord neurons were grown on poly(d-lysine) (PDL) or on a monolayer of type 1 astrocytes. At various times from 6 h to 2 weeks postplating, cells were fluorescently labeled and fixed with 4% paraformaldehyde. The cell surface immunoreaction allowed visualization of neurons in their entirety, namely, cell bodies and various membranous extensions that included lamellipodia, growth cones, axons, and dendrites. Outlines were drawn for individual neurons and their fractal dimension (D) was calculated. Neurons on poly(d-lysine) reached a peak D at 3 days in vitro, 1 day later than neurons on astrocytes (2 days in vitro). The maximum D was greater for cells on poly(d-lysine) when compared with neurons on astrocytes. In a second experiment the maximum D was similar for neurons on both surfaces but neurons on PDL maintained a higher D for a much longer period than neurons on astrocytes. An examination of fluorescent images revealed that neurons on poly(d-lysine) exhibited lamellipodia and large growth cones for several days and these structures were likely responsible for the high D seen in these cells. These structures were rarely observed in neurons plated on astrocytes. Interestingly, D on both surfaces decreased to a similar value at between 1 and 2 weeks in vitro. The trend for D in these cultures, an initial increase to a peak value followed by a decrease to a stable value, is discussed in light of the chemical nature of the two surfaces and synapse formation and stabilization.

Distribution, Pathogenicity, and Interactions of Two Strains of Rice yellow mottle virus in Forested and Savanna Zones of West Africa.

In Côte d'Ivoire, the S2 strain of Rice yellow mottle virus (RYMV) predominated in the forested zones, including the "rice belt" to the west, in each of the cropping systems where rice was grown. The S1 strain occurred more frequently in the northern Guinean savanna, and only S1 isolates were found further north in the Sahelo-Soudanian zones. In mixed infection, S2 dominated over S1 both in viral capsid and RNA contents under temperature regimes encompassing those observed in savanna and forested zones of Côte d'Ivoire. There was no evidence of interactions in virus accumulation between the West African strains S1 or S2 with the more distantly related East African strain S4. Field trials emphasized the impact of RYMV, which induced yield losses of 40 to 60% in several widely grown cultivars of Oryza sativa indica and O. sativa japonica. We report the high resistance of the O. indica cv. Gigante under field conditions which was apparent with all the S1 and S2 isolates tested. Responses to RYMV infection of several cultivars were isolate dependent. With most differential cultivars, responses were not strain specific, with the exception of the O. japonica cv. Idsa6, in which the S2 isolates always induced higher yield losses than the S1 isolates.

The Genetic Basis of High Resistance to Rice Yellow Mottle Virus (RYMV) in Cultivars of Two Cultivated Rice Species.

Three cultivars of Oryza sativa (IR64, Azucena, and Gigante) and four cultivars of O. glaberrima (Tog5681, Tog5673, CG14, and SG329) were evaluated for their resistance to two isolates of rice yellow mottle virus (RYMV) by enzyme-linked immunosorbent assay (ELISA) and symptomatology. Cultivars Tog5681 and Gigante were highly resistant, and no symptoms were observed when either virus isolate was inoculated at 10 or 20 days postgermination and assayed by ELISA at 7, 14, 22, 35, 50, or 64 days postinoculation. Azucena showed a partial resistance, whereas the other cultivars were susceptible. Symptom appearance was associated with increase in ELISA absorbance in the systemically infected leaves. The best discrimination among the cultivars occurred when the plants were inoculated at 10 days postgermination. Crosses were made between the highly resistant (Gigante and Tog5681) and the susceptible (IR64) cultivars to determine the genetic basis of resistance to RYMV. Evaluation of F1 hybrids and interspecific progenies, as well as the segregation of resistance in F2 and F3 lines of the IR64 × Gigante cross, provided results consistent with the presence of a single recessive resistance gene common to Tog5681 and Gigante.

A major quantitative trait locus for rice yellow mottle virus resistance maps to a cluster of blast resistance genes on chromosome 12.

ABSTRACT Two doubled-haploid rice populations, IR64/Azucena and IRAT177/ Apura, were used to identify markers linked to rice yellow mottle virus (RYMV) resistance using core restriction fragment length polymorphism (RFLP) maps. Resistance was measured by mechanical inoculation of 19-day-old seedlings followed by assessment of virus content by enzyme-linked immunosorbent assay tests 15 days after inoculation. IR64/Azucena and IRAT177/Apura populations, 72 and 43 lines, respectively, were evaluated, and resistance was found to be polygenic. Resistance was expressed as a slower virus multiplication, low symptom expression, and limited yield loss when assessed at the field level. Bulked segregant analysis using the IR64/Azucena population identified a single random amplified polymorphic DNA marker that mapped on chromosome 12 and corresponded to a major quantitative trait locus (QTL) evidenced by interval mapping. When pooling RFLP data, integrated mapping of this chromosome revealed that the QTL was common to the two populations and corresponded to a small chromosomal segment known to contain a cluster of major blast resistance genes. This region of the genome also reflected the differentiation observed at the RFLP level between the subspecies indica and japonica of Oryza sativa. This is consistent with the observation that most sources of RYMV resistance used in rice breeding are found in upland rice varieties that typically belong to the japonica subspecies.

Aroma in rice: genetic analysis of a quantitative trait.

A new approach was developed which succeeded in tagging for the first time a major gene and two QTLs controlling grain aroma in rice. It involved a combination of two techniques, quantification of volatile compounds in the cooking water by gas chromatography, and molecular marker mapping. Four types of molecular marker were used (RFLPs, RAPDs, STSs, isozymes). Evaluation and mapping were performed on a doubled haploid line population which (1) conferred a precise character evaluation by enabling the analysis of large quantities of grains per genotype and (2) made possible the comparison of gas chromatography results and sensitive tests. The population size (135 lines) provided a good mapping precision. Several markers on chromosome 8 were found to be closely linked to a major gene controlling the presence of 2-acetyl-1-pyrroline (AcPy), the main compound of rice aroma. Moreover, our results showed that AcPy concentration in plants is regulated by at least two chromosomal regions. Estimations of recombination fractions on chromosome 8 were corrected for strong segregation distortion. This study confirms that AcPy is the major component of aroma. Use of the markers linked to AcPy major gene and QTLs for marker-assisted selection by successive backcrosses may be envisaged.