Identification of Triazolo-quinazolinone Derivatives as Novel and Potent Chitinase OfChi-h Inhibitors Based on Structure-Based Virtual Screening.

Insect chitinase, OfChi-h, from Ostrinia furnacalis, is considered as a promising target for the development of green pesticides. On the basis of the crystal structure of OfChi-h, we successfully obtained a triazolo-quinazolinone scaffold as the novel class of OfChi-h inhibitor via a structure-based virtual screening approach. Rational compound screening enabled us to acquire a potent OfChi-h inhibitor TQ19 with a Ki value of 0.33 µM. Furthermore, the in vivo biological activity of target compounds was assayed. The results showed that compounds TQ8 and TQ19 could dramatically inhibit the growth and development of Ostrinia nubilalis larvae, and most of the compounds showed higher insecticidal activity than hexaflumuron. This present work reveals that triazolo-quinazolinone derivatives can serve as novel candidates for insect growth regulators.

Introgression of Bacterial Blight Resistance Genes in the Rice Cultivar Ciherang: Response against Xanthomonas oryzae pv. oryzae in the F6 Generation.

Bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae and is one of the most important diseases in rice. It results in significantly reduced productivity throughout all rice-growing regions of the world. Four BB resistance genes have been reported; however, introgression of a single gene into rice has not been able to sufficiently protect rice against BB infection. Pyramiding of effective BB resistance genes (i.e., Xa genes) into background varieties is a potential approach to controlling BB infection. In this study, combinations of four BB resistance genes, Xa4, xa5, xa13, and Xa21, were pyramided into populations. The populations were derived from crossing Ciherang (a widespread Indonesian rice variety) with IRBB60 (resistance to BB). Promising recombinants from the F6 generation were identified by scoring the phenotype against three virulent bacterial strains, C5, P6, and V, which cause widespread BB infection in most rice-growing countries. Pyramiding of genes for BB resistance in 265 recombinant introgressed lines (RILs) were confirmed through marker-assisted selection (MAS) of the F5 and F6 generations using gene-specific primers. Of these 265 RILs, 11, 34 and 45 lines had four, three, or two BB resistance genes, respectively. The RILs had pyramiding of two or three resistance genes, with the Xa4 resistance gene showing broad spectrum resistance against Xoo races with higher agronomic performance compared to their donor and recipients parents. The developed BB-resistant RILs have high yield potential to be further developed for cultivation or as sources of BB resistance donor material for varietal improvement in other rice lines.

Genomic variation in 3,010 diverse accessions of Asian cultivated rice.

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap.

BACKGROUND: Most agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs. RESULTS: Herein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions (Oryza sativa L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length. We scanned the Ho (observed heterozygosity per locus) index of coupled-parents of crosses mapping the same QTL, based on linkage and association mapping, and identified two new genes for grain length. We named this approach as Ho-LAMap. A simulation study of six known genes showed that Ho-LAMap could mine genes rapidly across a wide range of experimental variables using deep-sequencing data. We used Ho-LAMap to clone a new gene, OsLG3, as a positive regulator of grain length, which could improve rice yield without influencing grain quality. Sequencing of the promoter region in 283 rice accessions from a wide geographic range identified four haplotypes that seem to be associated with grain length. Further analysis showed that OsLG3 alleles in the indica and japonica evolved independently from distinct ancestors and low nucleotide diversity of OsLG3 in indica indicated artificial selection. Phylogenetic analysis showed that OsLG3 might have much potential value for improvement of grain length in japonica breeding. CONCLUSIONS: The results demonstrated that Ho-LAMap is a potential approach for gene discovery and OsLG3 is a promising gene to be utilized in genomic assisted breeding for rice cultivar improvement.

Harnessing the hidden genetic diversity for improving multiple abiotic stress tolerance in rice (Oryza sativa L.).

To develop superior rice varieties with improved yield in most rainfed areas of Asia/Africa, we started an introgression-breeding program for simultaneously improving yield and tolerances of multiple abiotic stresses. Using eight BC1 populations derived from a widely adaptable recipient and eight donors plus three rounds of phenotypic selection, we developed 496 introgression lines (ILs) with significantly higher yield under drought, salt and/or non-stress conditions in 5 years. Six new varieties were released in the Philippines and Pakistan and many more are being evaluated in multi-location yield trials for releasing in several countries. Marker-facilitated genetic characterization revealed three interesting aspects of the breeding procedure: (1) the donor introgression pattern in specific BC populations was characteristic; (2) introgression frequency in different genomic regions varied considerably, resulting primarily from strong selection for the target traits; and (3) significantly lower heterozygosity was observed in BC progenies selected for drought and salinity tolerance. Applying strong phenotypic selection under abiotic stresses in early segregating generations has major advantages for not only improving multiple abiotic stress tolerance but also achieving quicker homozygosity in early generations. This breeding procedure can be easily adopted by small breeding programs in developing countries to develop high-yielding varieties tolerant of abiotic stresses. The large set of trait-specific ILs can be used for genetic mapping of genes/QTL that affect target and non-target traits and for efficient varietal development by designed QTL pyramiding and genomics-based recurrent selection in our Green Super Rice breeding technology.

A Cross-sectional Survey of HIV Transmission and Behavior among Men Who Have Sex with Men in Different Areas of Inner Mongolia Autonomous Region, China.

BACKGROUND: Little research has been conducted on the human immunodeficiency virus (HIV) epidemic and the sexual intercourse habits of men who have sex with men (MSM) in crowded places, both locally and abroad. This study conducted a survey of MSM in different locales of Inner Mongolia to provide a reference for developing strategies or measures to prevent and control HIV among this understudied population. METHODS: We conducted a cross-sectional survey of men aged 18 years and older at different venues popular among MSM in Inner Mongolia. Between April and July 2012, MSM volunteered to participate in this study, receive HIV/syphilis testing, and complete a questionnaire about their behavior. A total of 1611 MSM participated. Participants signed a voluntary informed consent form, completed an anonymous questionnaire and were tested for HIV and syphilis antibodies. RESULTS: Of the 1611 MSM surveyed, 6.83 and 23.65 % had HIV and syphilis, respectively, and the co-infection rate was 3.17 %. Sociodemographic factors such as age, culture, marital status, knowledge of acquired immune deficiency syndrome (AIDS) transmission, and peer education significantly differed between venues (P < 0.01). MSM who were under 22 years, 23-35 years, and over 36 years primarily contacted their potential partners online, at bars/other (streetwalkers), and at public baths/parks, respectively. MSM partners found in bars, in public baths, in parks and online were primarily high school students and technical secondary school students. MSM who were streetwalkers or cross-dressing male sex workers primarily had junior middle school education levels or below. Married MSM primarily had intercourse in public baths and parks, and MSM who had intercourse in public baths and parks also reported the greatest proportions of intercourse with women (39.1 and 35.0 %, respectively). Furthermore, MSM who had intercourse in parks reported having the most anal sex with same-sex partners and unprotected intercourse in the past 6 months. Unprotected intercourse with women in the past 6 months was also common among MSM who met partners in bathhouses or online. MSM were most likely to have anal sex with other men in public baths. MSM who had intercourse in bars were the least likely to have used a condom with female partners in the past 6 months. The culture of the MSM who had frequent intercourse with streetwalkers and cross-dressing male sex workers did not predict behavior. CONCLUSION: This study indicated that AIDS-related risky behaviors as well as HIV and syphilis infection were associated with the different locations frequented by MSM. When developing intervention strategies for AIDS, it is better to conduct targeted health education and behavioral interventions at bars/online for MSM aged 23-35 years and at public baths/parks for MSM over 36 years. Additionally, the current survey showed that information on AIDS/sexually transmitted diseases (STDs) must be popularized to reach streetwalkers and cross-dressing male sex workers, whose mobility limits their attainment of higher levels of health education.

Reference values of T lymphocyte subsets among health adults in Inner Mongolia Region.

Estimation of T-lymphocyte subsets continues to be an important aspect for monitoring HIV disease progression and response to antiretroviral therapy. Most of the diagnostic laboratories often rely on studies from western for CD4+T-lymphocyte reference values, which could, often be unreliable for usage in local settings. To establish the normal reference values of T lymphocyte subsets from healthy people of Inner Mongolia Autonomous Region, flow cytometry was performed to determine the reference ranges for lymphocyte subsets (CD3 and CD4 cells) in 400 healthy multiracial adult population from 12 League Cities in Inner Mongolia Region, China. The basic information including age, gender, nationality and history was collected. There were significant differences in the absolute counting, percentage of CD3+T lymphocytes, and CD4+T lymphocyte percentage counting among different age groups. There were significant differences in CD3+, CD4+T lymphocyte percentage in the groups with different genders. There were significant differences in CD3+T lymphocyte percentage count, absolute count of CD4+T lymphocytes and CD4+T lymphocyte percentage counting in the group with ages of 16-20. There were dramatic differences in CD3+T lymphocyte percentage count and CD4+T lymphocyte percentage counting in the group with ages of 31-40. There were significant differences in CD4+T lymphocyte percentage counting. By this study, age, gender and ethnic specific lymphocyte subset reference ranges have been locally established in Inner Mongolia Autonomous Region.

Dissecting genetic architecture underlying seed traits in multiple environments.

The seeds of flowering plants develop from double fertilization and play a vital role in reproduction and supplying human and animal food. The genetic variation of seed traits is influenced by multiple genetic systems, e.g., maternal, embryo, and/or endosperm genomes. Understanding the genetic architecture of seed traits is a major challenge because of this complex mechanism of multiple genetic systems, especially the epistasis within or between different genomes and their interactions with the environment. In this study, a statistical model was proposed for mapping QTL with epistasis and QTL-by-environment (QE) interactions underlying endosperm and embryo traits. Our model integrates the maternal and the offspring genomes into one mapping framework and can accurately analyze maternal additive and dominant effects, endosperm/embryo additive and dominant effects, and epistatic effects of two loci in the same or two different genomes, as well as interaction effects of each genetic component of QTL with environment. Intensive simulations under different sampling strategies, heritabilities, and model parameters were performed to investigate the statistical properties of the model. A set of real cottonseed data was analyzed to demonstrate our methods. A software package, QTLNetwork-Seed-1.0.exe, was developed for QTL analysis of seed traits.

Genome-Wide Responses to Selection and Genetic Networks Underlying Submergence Tolerance in Rice.

Submergence is an important factor limiting rice (Oryza sativa L.) yield in many rain-fed lowland areas of Asia. Here we explored the genetic basis of submergence tolerance (ST) in rice and facilitated simultaneous improvement of ST of rice. The genome-wide patterns of donor introgressions in 162 backcross (BC) progenies selected for ST from 12 populations of nine crosses between three recipients and three donors were characterized using simple sequence repeat (SSR) markers. The genome-wide responses of donor alleles to strong phenotypic selection for ST were reflected in three aspects: (i) significant over introgression of the donor alleles at 295 loci in 167 functional genetic units (FGUs) across the rice genome, (ii) greatly increased homozygosity or loss of heterozygosity genome-wide, and (iii) pronounced nonrandom associations between or among the detected ST loci, which led us to discovery of putative genetic networks (multilocus structures) underlying ST of rice. Our results suggest that ST of rice is controlled by large numbers of loci involved in multiple positively regulated signaling pathways. Restoration of one or more of these broken pathways in the BC progeny by genetic complementation from introgressed functional donor alleles at ST loci provide an appropriate explanation for transgressive segregation of ST and other complex traits in rice.

Genome-wide response to selection and genetic basis of cold tolerance in rice (Oryza sativa L.).

BACKGROUND: Cold stress is an important factor limiting rice yield in many areas of high latitude and altitude. Considerable efforts have been taken to genetically dissect cold tolerance (CT) in rice using DNA markers. Because of possible epistasis and gene × environment interactions associated with identified quantitative trait loci, the results of these genetic studies have unfortunately not been directly applicable to marker-assisted selection for improved rice CT. In this study, we demonstrated the utility of a selective introgression strategy for simultaneous improvement and genetic dissection of rice seedling CT. RESULTS: A set of japonica introgression lines (ILs) with significantly improved seedling CT were developed from four backcross populations based on two rounds of selection. Genetic characterization of these cold-tolerant ILs revealed two important aspects of genome-wide responses to strong phenotypic selection for rice CT: (1) significant over-introgression of donor alleles at 57 loci in 29 functional genetic units (FGUs) across the rice genome and (2) pronounced non-random associations between or among alleles at many unlinked CT loci. Linkage disequilibrium analyses of the detected CT loci allowed us to construct putative genetic networks (multi-locus structures) underlying the seedling CT of rice. Each network consisted of a single FGU, with high introgression as the putative regulator plus two to three groups of highly associated downstream FGUs. A bioinformatics search of rice genomic regions harboring these putative regulators identified a small set of candidate regulatory genes that are known to be involved in plant stress response. CONCLUSIONS: Our results suggest that CT in rice is controlled by multiple pathways. Genetic complementarity between parental-derived functional alleles at many loci within a given pathway provides an appropriate explanation for the commonly observed hidden diversity and transgressive segregation of CT and other complex traits in rice.

Three genetic systems controlling growth, development and productivity of rice (Oryza sativa L.): a reevaluation of the 'Green Revolution'.

The Green Revolution (GR-I) included worldwide adoption of semi-dwarf rice cultivars (SRCs) with mutant alleles at GA20ox2 or SD1 encoding gibberellin 20-oxidase. Two series of experiments were conducted to characterize the pleiotropic effects of SD1 and its relationships with large numbers of QTLs affecting rice growth, development and productivity. The pleiotropic effects of SD1 in the IR64 genetic background for increased height, root length/mass and grain weight, and for reduced spikelet fertility and delayed heading were first demonstrated using large populations derived from near isogenic IR64 lines of SD1. In the second set of experiments, QTLs controlling nine growth and yield traits were characterized using a new molecular quantitative genetics model and the phenotypic data of the well-known IR64/Azucena DH population evaluated across 11 environments, which revealed three genetic systems: the SD1-mediated, SD1-repressed and SD1-independent pathways that control rice growth, development and productivity. The SD1-mediated system comprised 43 functional genetic units (FGUs) controlled by GA. The SD1-repressed system was the alternative one comprising 38 FGUs that were only expressed in the mutant sd1 backgrounds. The SD1-independent one comprised 64 FGUs that were independent of SD1. GR-I resulted from the overall differences between the former two systems in the three aspects: (1) trait/environment-specific contributions; (2) distribution of favorable alleles for increased productivity in the parents; and (3) different responses to (fertilizer) inputs. Our results suggest that at 71.4 % of the detected loci, a QTL resulted from the difference between a functional allele and a loss-of-function mutant, whereas at the remaining 28.6 % of loci, from two functional alleles with differentiated effects. Our results suggest two general strategies to achieve GR-II (1) by further exploiting the genetic potential of the SD1-repressed and SD1-independent pathways and (2) by restoring the SD1-mediated pathways, or 'back to the nature' to fully exploit the genetic diversity of those loci in the SD1-mediated pathways which are virtually inaccessible to most rice-breeding programs worldwide that are exclusively based on sd1.

Inhibition of WISE preserves renal allograft function.

Wnt-modulator in surface ectoderm (WISE) is a secreted modulator of Wnt signaling expressed in the adult kidney. Activation of Wnt signaling has been observed in renal transplants developing interstitial fibrosis and tubular atrophy; however, whether WISE contributes to chronic changes is not well understood. Here, we found moderate to high expression of WISE mRNA in a rat model of renal transplantation and in kidneys from normal rats. Treatment with a neutralizing antibody against WISE improved proteinuria and graft function, which correlated with higher levels of ß-catenin protein in kidney allografts. In addition, treatment with the anti-WISE antibody reduced infiltration of CD68(+) macrophages and CD8(+) T cells, attenuated glomerular and interstitial injury, and decreased biomarkers of renal injury. This treatment reduced expression of genes involved in immune responses and in fibrogenic pathways. In summary, WISE contributes to renal dysfunction by promoting tubular atrophy and interstitial fibrosis.

Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.).

Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in plant genomes. In this study, based on 54,465 SNPs between the genomes of two Indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, we identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing. From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 representative rice inbred lines from 22 rice growing countries worldwide. Using this set of SNPs, we were able to uncover the well-known Indica-Japonica subspecific differentiation and geographic differentiations within Indica and Japonica. Furthermore, our SNP results revealed some common and contrasting patterns of the haplotype diversity along different rice chromosomes in the Indica and Japonica accessions, which suggest different evolutionary forces possibly acting in specific regions of the rice genome during domestication and evolution of rice. Our results demonstrated that this set of SNPs can be used as anchor SNPs for large scale genotyping in rice molecular breeding research involving Indica-Japonica and Indica-Indica crosses.

Dissecting genetic networks underlying complex phenotypes: the theoretical framework.

Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many 'downstream' loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and "co-adapted" gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis.

Two doses of sclerostin antibody in cynomolgus monkeys increases bone formation, bone mineral density, and bone strength.

The development of bone-rebuilding anabolic agents for treating bone-related conditions has been a long-standing goal. Genetic studies in humans and mice have shown that the secreted protein sclerostin is a key negative regulator of bone formation. More recently, administration of sclerostin-neutralizing monoclonal antibodies in rodent studies has shown that pharmacologic inhibition of sclerostin results in increased bone formation, bone mass, and bone strength. To explore the effects of sclerostin inhibition in primates, we administered a humanized sclerostin-neutralizing monoclonal antibody (Scl-AbIV) to gonad-intact female cynomolgus monkeys. Two once-monthly subcutaneous injections of Scl-AbIV were administered at three dose levels (3, 10, and 30 mg/kg), with study termination at 2 months. Scl-AbIV treatment had clear anabolic effects, with marked dose-dependent increases in bone formation on trabecular, periosteal, endocortical, and intracortical surfaces. Bone densitometry showed that the increases in bone formation with Scl-AbIV treatment resulted in significant increases in bone mineral content (BMC) and/or bone mineral density (BMD) at several skeletal sites (ie, femoral neck, radial metaphysis, and tibial metaphysis). These increases, expressed as percent changes from baseline were 11 to 29 percentage points higher than those found in the vehicle-treated group. Additionally, significant increases in trabecular thickness and bone strength were found at the lumbar vertebrae in the highest-dose group. Taken together, the marked bone-building effects achieved in this short-term monkey study suggest that sclerostin inhibition represents a promising new therapeutic approach for medical conditions where increases in bone formation might be desirable, such as in fracture healing and osteoporosis.

[Meta-analysis of relationship of vitamin D receptor gene polymorphism and tuberculosis susceptibility].

OBJECTIVE: To provide a quantitative summary in estimating the association between polymorphisms of 2 loci of FokI and TaqI in vitamin D receptor gene and susceptibility to tuberculosis by means of meta-analysis. METHODS: Databases CNKI, CBM, WanFang DATA, MEDLINE and PubMed were searched using "VDR", "polymorphisms" or "alleles", in combination with "tuberculosis", and a manual search of citations from relevant original studies and literature was also performed between January 1980 and November 2007. RevMan 4.2 was applied in the process of analyzing the data of 14 case-control studies. RESULTS: The summary ORs for studies with polymorphisms of FokI, TaqI loci of the VDR gene were 1.12 (95%CI: 0.98 - 1.28) in Ff vs FF, 1.66 (95%CI: 1.12 - 2.46) in ff vs FF, 0.97 (95%CI: 0.82 - 1.14) in Tt vs TT, 1.27 (95%CI: 0.96 - 1.69) in tt vs TT. The fail-safe number was 109.69 for FokI and 75.24 for TaqI. The analysis result was reliable. CONCLUSION: Polymorphisms at FokI loci (VDR-ff) showed statistically significant association between the VDR variants and susceptibility to tuberculosis, and variant in the TaqI locus failed to show statistically significant association.

Sclerostin antibody treatment increases bone formation, bone mass, and bone strength in a rat model of postmenopausal osteoporosis.

The development of bone-rebuilding anabolic agents for potential use in the treatment of bone loss conditions, such as osteoporosis, has been a long-standing goal. Genetic studies in humans and mice have shown that the secreted protein sclerostin is a key negative regulator of bone formation, although the magnitude and extent of sclerostin's role in the control of bone formation in the aging skeleton is still unclear. To study this unexplored area of sclerostin biology and to assess the pharmacologic effects of sclerostin inhibition, we used a cell culture model of bone formation to identify a sclerostin neutralizing monoclonal antibody (Scl-AbII) for testing in an aged ovariectomized rat model of postmenopausal osteoporosis. Six-month-old female rats were ovariectomized and left untreated for 1 yr to allow for significant estrogen deficiency-induced bone loss, at which point Scl-AbII was administered for 5 wk. Scl-AbII treatment in these animals had robust anabolic effects, with marked increases in bone formation on trabecular, periosteal, endocortical, and intracortical surfaces. This not only resulted in complete reversal, at several skeletal sites, of the 1 yr of estrogen deficiency-induced bone loss, but also further increased bone mass and bone strength to levels greater than those found in non-ovariectomized control rats. Taken together, these preclinical results establish sclerostin's role as a pivotal negative regulator of bone formation in the aging skeleton and, furthermore, suggest that antibody-mediated inhibition of sclerostin represents a promising new therapeutic approach for the anabolic treatment of bone-related disorders, such as postmenopausal osteoporosis.

Targeted deletion of the sclerostin gene in mice results in increased bone formation and bone strength.

INTRODUCTION: Sclerosteosis is a rare high bone mass genetic disorder in humans caused by inactivating mutations in SOST, the gene encoding sclerostin. Based on these data, sclerostin has emerged as a key negative regulator of bone mass. We generated SOST knockout (KO) mice to gain a more detailed understanding of the effects of sclerostin deficiency on bone. MATERIALS AND METHODS: Gene targeting was used to inactivate SOST and generate a line of SOST KO mice. Radiography, densitometry, microCT, histomorphometry, and mechanical testing were used to characterize the impact of sclerostin deficiency on bone in male and female mice. Comparisons were made between same sex KO and wildtype (WT) mice. RESULTS: The results for male and female SOST KO mice were similar, with differences only in the magnitude of some effects. SOST KO mice had increased radiodensity throughout the skeleton, with general skeletal morphology being normal in appearance. DXA analysis of lumbar vertebrae and whole leg showed that there was a significant increase in BMD (>50%) at both sites. microCT analysis of femur showed that bone volume was significantly increased in both the trabecular and cortical compartments. Histomorphometry of trabecular bone revealed a significant increase in osteoblast surface and no significant change in osteoclast surface in SOST KO mice. The bone formation rate in SOST KO mice was significantly increased for trabecular bone (>9-fold) at the distal femur, as well as for the endocortical and periosteal surfaces of the femur midshaft. Mechanical testing of lumbar vertebrae and femur showed that bone strength was significantly increased at both sites in SOST KO mice. CONCLUSIONS: SOST KO mice have a high bone mass phenotype characterized by marked increases in BMD, bone volume, bone formation, and bone strength. These results show that sclerostin is a key negative regulator of a powerful, evolutionarily conserved bone formation pathway that acts on both trabecular and cortical bone.

Mapping QTLs of root morphological traits at different growth stages in rice.

Roots are a vital organ for absorbing soil moisture and nutrients and influence drought resistance. The identification of quantitative trait loci (QTLs) with molecular markers may allow the estimation of parameters of genetic architecture and improve root traits by molecular marker-assisted selection (MAS). A mapping population of 120 recombinant inbred lines (RILs) derived from a cross between japonica upland rice 'IRAT109' and paddy rice 'Yuefu' was used for mapping QTLs of developmental root traits. All plant material was grown in PVC-pipe. Basal root thickness (BRT), root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW) and root volume (RV) were phenotyped at the seedling (I), tillering (II), heading (III), grain filling (IV) and mature (V) stages, respectively. Phenotypic correlations showed that BRT was positively correlated to MRL at the majority of stages, but not correlated with RN. MRL was not correlated to RN except at the seedling stage. BRT, MRL and RN were positively correlated to RFW, RDW and RV at all growth stages. QTL analysis was performed using QTLMapper 1.6 to partition the genetic components into additive-effect QTLs, epistatic QTLs and QTL-by-year interactions (Q x E) effect. The results indicated that the additive effects played a major role for BRT, RN and MRL, while for RFW, RDW and RV the epistatic effects showed an important action and Q x E effect also played important roles in controlling root traits. A total of 84 additive-effect QTLs and 86 pairs of epistatic QTLs were detected for the six root traits at five stages. Only 12 additive QTLs were expressed in at least two stages. This indicated that the majority of QTLs were developmental stage specific. Two main effect QTLs, brt9a and brt9b, were detected at the heading stage and explained 19% and 10% of the total phenotypic variation in BRT without any influence from the environment. These QTLs can be used in breeding programs for improving root traits.

Identification of functional candidate genes for drought tolerance in rice.

Drought tolerance (DT) in rice is known to be controlled by many quantitative trait loci (QTLs) and involved differential expression of large numbers of genes, but linking QTLs with their underlying genes remains the most challenging issue in plant molecular biology. To shed some light on this issue, differential gene expression in response to PEG simulated drought in 3 unique genetic materials (a lowland rice, IR64 and its derived line, PD86 which has 11 introgressed DT QTLs, and a upland rice IRAT109) was investigated using a PCR-based subtractive hybridization strategy. More than 300 unique subtracted cDNA sequences, covering genes of diverse cellular activities and functions, were identified and confirmed by semi-quantitative and quantitative RT-PCR. Detailed bioinformatics analyses of the data revealed two interesting results. First, the levels and mechanisms of DT of the three rice lines were associated with the number and types of differentially expressed genes, suggesting different DT mechanisms in rice are controlled by different sets of genes and different metabolic pathways, and most differentially expressed genes under drought were able to contribute to DT. Second, there appeared a high correspondence in genomic location between DT QTLs and clusters of differentially expressed genes in rice, suggesting some DT QTLs may represent clusters of co-regulated and functionally related genes. Thus, differential gene expression analyses using genetically characterized materials can provide additional insights into the molecular basis of QTLs and convergent evidence to shortlist the candidate genes for target QTLs.