Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems.

Pith parenchyma cells store water in various plant organs. These cells are especially important for producing sugar and ethanol from the sugar juice of grass stems. In many plants, the death of pith parenchyma cells reduces their stem water content. Previous studies proposed that a hypothetical D gene might be responsible for the death of stem pith parenchyma cells in Sorghum bicolor, a promising energy grass, although its identity and molecular function are unknown. Here, we identify the D gene and note that it is located on chromosome 6 in agreement with previous predictions. Sorghum varieties with a functional D allele had stems enriched with dry, dead pith parenchyma cells, whereas those with each of six independent nonfunctional D alleles had stems enriched with juicy, living pith parenchyma cells. D expression was spatiotemporally coupled with the appearance of dead, air-filled pith parenchyma cells in sorghum stems. Among D homologs that are present in flowering plants, Arabidopsis ANAC074 also is required for the death of stem pith parenchyma cells. D and ANAC074 encode previously uncharacterized NAC transcription factors and are sufficient to ectopically induce programmed death of Arabidopsis culture cells via the activation of autolytic enzymes. Taken together, these results indicate that D and its Arabidopsis ortholog, ANAC074, are master transcriptional switches that induce programmed death of stem pith parenchyma cells. Thus, targeting the D gene will provide an approach to breeding crops for sugar and ethanol production.

Spatial kernel models capturing field heterogeneity for accurate estimation of genetic potential.

According to Fisher's principles, an experimental field is typically divided into multiple blocks for local control. Although homogeneity is supposed within a block, this assumption may not be practical for large blocks, such as those including hundreds of plots. In line evaluation trials, which are essential in plant breeding, field heterogeneity must be carefully treated, because it can cause bias in the estimation of genetic potential. To more accurately estimate genotypic values in a large field trial, we developed spatial kernel models incorporating genome-wide markers, which consider continuous heterogeneity within a block and over the field. In the simulation study, the spatial kernel models were robust under various conditions. Although heritability, spatial autocorrelation range, replication number, and missing plots directly affected the estimation accuracy of genotypic values, the spatial kernel models always showed superior performance over the classical block model. We also employed these spatial kernel models for quantitative trait locus mapping. Finally, using field experimental data of bioenergy sorghum lines, we validated the performance of the spatial kernel models. The results suggested that a spatial kernel model is effective for evaluating the genetic potential of lines in a heterogeneous field.

Impacts of dominance effects on genomic prediction of sorghum hybrid performance.

Non-additive (dominance and epistasis) effects have remarkable influences on hybrid performance, e.g., via heterosis. Nevertheless, only additive effects are often considered in genomic predictions (GP). In this study, we demonstrated the importance of dominance effects in the prediction of hybrid performance in bioenergy sorghum [Sorghum bicolor (L.) Moench]. The dataset contained more than 400 hybrids between 200 inbred lines and two testers. The hybrids exhibited considerable heterosis in culm length and fresh weight, and the degree of heterosis was consistent with the genetic distance from the corresponding tester. The degree of heterosis was further different among subpopulations. Conversely, Brix exhibited limited heterosis. Regarding GP, we examined three statistical models and four training dataset types. In most of the dataset types, genomic best linear unbiased prediction (GBLUP) with additive effects had lower prediction accuracy than GBLUP with additive and dominance effects (GBLUP-AD) and Gaussian kernel regression (GK). The superiority of GBLUP-AD and GK depended on the level of dominance variance, which was high for culm length and fresh weight, and low for Brix. Considering subpopulations, the influence of dominance was more complex. Our findings highlight the importance of considering dominance effects in GP models for sorghum hybrid breeding.

Effect of salt tolerance on biomass production in a large population of sorghum accessions.

Salinity causes major reductions in cultivated land area, crop productivity, and crop quality, and salt-tolerant crops have been required to sustain agriculture in salinized areas. The annual C4 crop plant Sorghum bicolor (L.) Moench is salt tolerant, with large variation among accessions. Sorghum's salt tolerance is often evaluated during early growth, but such evaluations are weakly related to overall performance. Here, we evaluated salt tolerance of 415 sorghum accessions grown in saline soil (0, 50, 100, and 150 mM NaCl) for 3 months. Some accessions produced up to 400 g per plant of biomass and showed no growth inhibition at 50 mM NaCl. Our analysis indicated that the genetic factors that affected biomass production under 100 mM salt stress were more different from those without salt stress, comparing to the differences between those under 50 mM and 100 mM salt stress. A genome-wide association study for salt tolerance identified two single-nucleotide polymorphisms (SNPs) that were significantly associated with biomass production, only at 50 mM NaCl. Additionally, two SNPs were significantly associated with salt tolerance index as an indicator for growth response of each accession to salt stress. Our results offer candidate genetic resources and SNP markers for breeding salt-tolerant sorghum.

Hand lesion after arthroscopic rotator cuff repair: Association with complex regional pain syndrome.

BACKGROUND: It is known that complex regional pain syndrome (CRPS) occurs after arthroscopic rotator cuff repair (ARCR); however, few studies have investigated this complication. Therefore, the purpose of the present study was to evaluate CRPS after ARCR. METHODS: A total of 182 patients who underwent ARCR were enrolled in this study. The average age of patients was 62.8 ± 10.0 years, with an average follow-up period of 21.5 ± 38.1 months. CRPS criteria outlined by the Ministry of Health, Labor, and Welfare study team for CRPS in Japan (MHLWJ) and International Association for the Study of Pain (IASP 2005) were utilized for diagnosis. There are two rating systems for the "clinical purpose" and "research purpose" in both criteria, respectively. Clinical outcomes, including Japanese Orthopedic Association (JOA) and University of California, Los Angeles scores, were evaluated using univariate and multivariate analysis. RESULTS: CRPS exclusively occurred in the hand of the operated limb, developing within 3 months of surgery. Two or more of the following symptoms were noted in patients with the hand lesion associated with CRPS: edema (93.4%), restricted range of motion (83.4%), hyperalgesia (30.1%), paridrosis (20.4%), and atrophic change (12.2%). Under these conditions, the incidences of CRPS were 24.2% (44/182) when evaluated by the MHLWJ rating system for the "clinical purpose;" 11% (22/182) by the MHLWJ rating system for the "research purpose;" 6% (11/182) by the IASP 2005 for the "clinical purpose;" and 0.5% (1/182) by the IASP 2005 for the "research purpose." Results of multivariate analysis demonstrated that "Function" in the JOA score was a risk factor for the development of CRPS after ARCR, when evaluated by a system for the "clinical purpose" of the MHLWJ. CONCLUSION: Following ARCR, CRPS-induced hand lesions occur more frequently than is generally believed, thereby suggesting that its impact on surgical outcomes should be clarified in the future.

Cutoff value of Japanese Orthopaedic Association shoulder score in patients with rotator cuff repair: Based on the University of California at Los Angeles shoulder score.

BACKGROUND: The Japanese Orthopaedic Association shoulder score cutoff values were calculated in patients with rotator cuff repair using the University of California at Los Angeles shoulder score. METHODS: Overall, 175 patients with rotator cuff repair were subjects in this study. The University of California at Los Angeles and Japanese Orthopaedic Association shoulder scores were evaluated before surgery and at 3, 6, 9, and 12 months after surgery. The cutoff value of the Japanese Orthopaedic Association shoulder score was determined using the 4-stage criteria of the University of California at Los Angeles shoulder score and a University of California at Los Angeles shoulder score of 28 points, which is the boundary between an excellent/good group and a fair/poor group. RESULTS: Both the JOA shoulder and UCLA shoulder scores showed significant improvement at 6, 9, and 12 months from the preoperative scores (p < 0.0001). There was a strong correlation between the total values of the two scores (r = 0.85, p < 0.0001). The cutoff value of the Japanese Orthopaedic Association shoulder score based on the highest accuracy from receiver operating characteristic curve analysis was 83 points. CONCLUSION: A Japanese Orthopaedic Association shoulder score cutoff value of 83 was equivalent to a University of California at Los Angeles shoulder score cutoff value of 28 for distinguishing between excellent/good and fair/poor outcomes after rotator cuff repair.

Dissecting the Genetic Architecture of Biofuel-Related Traits in a Sorghum Breeding Population.

In sorghum [Sorghum bicolor (L.) Moench], hybrid cultivars for the biofuel industry are desired. Along with selection based on testcross performance, evaluation of the breeding population per se is also important for the success of hybrid breeding. In addition to additive genetic effects, non-additive (i.e., dominance and epistatic) effects are expected to contribute to the performance of early generations. Unfortunately, studies on early generations in sorghum breeding programs are limited. In this study, we analyzed a breeding population for bioenergy sorghum, which was previously developed based on testcross performance, to compare genomic selection models both trained on and evaluated for the per se performance of the 3rd generation S0 individuals. Of over 200 ancestral inbred accessions in the base population, only 13 founders contributed to the 3rd generation as progenitors. Compared to the founders, the performances of the population per se were improved for target traits. The total genetic variance within the S0 generation progenies themselves for all traits was mainly additive, although non-additive variances contributed to each trait to some extent. For genomic selection, linear regression models explicitly considering all genetic components showed a higher predictive ability than other linear and non-linear models. Although the number and effect distribution of underlying loci was different among the traits, the influence of priors for marker effects was relatively small. These results indicate the importance of considering non-additive effects for dissecting the genetic architecture of early breeding generations and predicting the performance per se.

Diversity of Bradyrhizobium in Non-Leguminous Sorghum Plants: B. ottawaense Isolates Unique in Genes for N2O Reductase and Lack of the Type VI Secretion System.

Diverse members of Bradyrhizobium diazoefficiens, B. japonicum, and B. ottawaense were isolated from the roots of field-grown sorghum plants in Fukushima, and classified into "Rhizobia" with nodulated soybeans, "Free-living diazotrophs", and "Non-diazotrophs" by nitrogen fixation and nodulation assays. Genome analyses revealed that B. ottawaense members possessed genes for N2O reduction, but lacked those for the Type VI secretion system (T6SS). T6SS is a new bacterial weapon against microbial competitors. Since T6SS-possessing B. diazoefficiens and B. japonicum have mainly been isolated from soybean nodules in Japan, T6SS-lacking B. ottawaense members may be a cryptic lineage of soybean bradyrhizobia in Japan.

Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses.

Sorghum (Sorghum bicolor) is cultivated worldwide for food, bioethanol, and fodder production. Although nitrogen fixation in sorghum has been studied since the 1970s, N2-fixing bacteria have not been widely examined in field-grown sorghum plants because the identification of functional diazotrophs depends on the culture method used. The aim of this study was to identify functional N2-fixing bacteria associated with field-grown sorghum by using "omics" approaches. Four lines of sorghum (KM1, KM2, KM4, and KM5) were grown in a field in Fukushima, Japan. The nitrogen-fixing activities of the roots, leaves, and stems were evaluated by acetylene reduction and 15N2-feeding assays. The highest nitrogen-fixing activities were detected in the roots of lines KM1 and KM2 at the late growth stage. Bacterial cells extracted from KM1 and KM2 roots were analyzed by metagenome, proteome, and isolation approaches and their DNA was isolated and sequenced. Nitrogenase structural gene sequences in the metagenome sequences were retrieved using two nitrogenase databases. Most sequences were assigned to nifHDK of Bradyrhizobium species, including non-nodulating Bradyrhizobium sp. S23321 and photosynthetic B. oligotrophicum S58T. Amplicon sequence and metagenome analysis revealed a relatively higher abundance (2.9-3.6%) of Bradyrhizobium in the roots. Proteome analysis indicated that three NifHDK proteins of Bradyrhizobium species were consistently detected across sample replicates. By using oligotrophic media, we purified eight bradyrhizobial isolates. Among them, two bradyrhizobial isolates possessed 16S rRNA and nif genes similar to those in S23321 and S58T which were predicted as functional diazotrophs by omics approaches. Both free-living cells of the isolates expressed N2-fixing activity in a semi-solid medium according to an acetylene reduction assay. These results suggest that major functional N2-fixing bacteria in sorghum roots are unique bradyrhizobia that resemble photosynthetic B. oligotrophicum S58T and non-nodulating Bradyrhizobium sp. S23321. Based on our findings, we discuss the N2-fixing activity level of sorghum plants, phylogenetic and genomic comparison with diazotrophic bacteria in other crops, and Bradyrhizobium diversity in N2 fixation and nodulation.

Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology.

Seed shape is an important agronomic trait with continuous variation among genotypes. Therefore, the quantitative evaluation of this variation is highly important. Among geometric morphometrics methods, elliptic Fourier analysis and semi-landmark analysis are often used for the quantification of biological shape variations. Elliptic Fourier analysis is an approximation method to treat contours as a waveform. Semi-landmark analysis is a method of superimposed points in which the differences of multiple contour positions are minimized. However, no detailed comparison of these methods has been undertaken. Moreover, these shape descriptors vary when the scale and direction of the contour and the starting point of the contour trace change. Thus, these methods should be compared with respect to the standardization of the scale and direction of the contour and the starting point of the contour trace. In the present study, we evaluated seed shape variations in a sorghum (Sorghum bicolor Moench) germplasm collection to analyze the association between shape variations and genome-wide single-nucleotide polymorphisms by genomic prediction (GP) and genome-wide association studies (GWAS). In our analysis, we used all possible combinations of three shape description methods and eight standardization procedures for the scale and direction of the contour as well as the starting point of the contour trace; these combinations were compared in terms of GP accuracy and the GWAS results. We compared the shape description methods (elliptic Fourier descriptors and the coordinates of superposed pseudo-landmark points) and found that principal component analysis of their quantitative descriptors yielded similar results. Different scaling and direction standardization procedures caused differences in the principal component scores, average shape, and the results of GP and GWAS.

High-Throughput Phenotyping of Sorghum Plant Height Using an Unmanned Aerial Vehicle and Its Application to Genomic Prediction Modeling.

Genomics-assisted breeding methods have been rapidly developed with novel technologies such as next-generation sequencing, genomic selection and genome-wide association study. However, phenotyping is still time consuming and is a serious bottleneck in genomics-assisted breeding. In this study, we established a high-throughput phenotyping system for sorghum plant height and its response to nitrogen availability; this system relies on the use of unmanned aerial vehicle (UAV) remote sensing with either an RGB or near-infrared, green and blue (NIR-GB) camera. We evaluated the potential of remote sensing to provide phenotype training data in a genomic prediction model. UAV remote sensing with the NIR-GB camera and the 50th percentile of digital surface model, which is an indicator of height, performed well. The correlation coefficient between plant height measured by UAV remote sensing (PHUAV) and plant height measured with a ruler (PHR) was 0.523. Because PHUAV was overestimated (probably because of the presence of taller plants on adjacent plots), the correlation coefficient between PHUAV and PHR was increased to 0.678 by using one of the two replications (that with the lower PHUAV value). Genomic prediction modeling performed well under the low-fertilization condition, probably because PHUAV overestimation was smaller under this condition due to a lower plant height. The predicted values of PHUAV and PHR were highly correlated with each other (r = 0.842). This result suggests that the genomic prediction models generated with PHUAV were almost identical and that the performance of UAV remote sensing was similar to that of traditional measurements in genomic prediction modeling. UAV remote sensing has a high potential to increase the throughput of phenotyping and decrease its cost. UAV remote sensing will be an important and indispensable tool for high-throughput genomics-assisted plant breeding.

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data.

Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)).

Enamel matrix derivative stimulates core binding factor alpha1/Runt-related transcription factor-2 expression via activation of Smad1 in C2C12 cells.

BACKGROUND: Although enamel matrix derivative (EMD) can promote osteogenic differentiation of the pluripotent mesenchymal precursor cell line, C2C12, the molecular mechanism that underlies this phenomenon is unclear. The purpose of this study was to determine which molecules in EMD stimulate osteogenic differentiation. METHODS: C2C12 cells were cultured in 5% serum-containing medium to induce differentiation, either with or without the addition of EMD. The expression of core binding factor alpha1/runtrelated transcription factor-2 (Cbfa1/Runx2) was measured using Northern blot, Western blot, and/or real-time polymerase chain reaction (R-PCR) analysis. Phosphorylation of mothers against decapentaplegic homolog 1 (Smad1) and bone morphogenetic protein (BMP)-like molecules in EMD was determined by Western blot. RESULTS: EMD increased Cbfa1/Runx2 mRNA and protein expression substantially. EMD also induced phosphorylation of Smad1. Noggin inhibited the EMD-induced phosphorylation of Smad1 markedly, and also partially blocked EMD-induced Cbfa1/ Runx2 mRNA expression. In the Western blot analysis, single bands that corresponded to approximately 15 and approximately 17.5 kDa proteins were recognized in EMD by anti-BMP-2/4 and anti-BMP-7 antibodies, respectively. CONCLUSIONS: Our study demonstrates that EMD stimulates Cbfa1/Runx2 expression and the phosphorylation of Smad1, and that both of these processes can be blocked by noggin. Therefore, the osteogenic activity of EMD may be mediated by BMPlike molecules in EMD.

Effects of serum on hepatocyte growth factor secretion and activation by periodontal ligament and gingival fibroblasts.

BACKGROUND: Hepatocyte growth factor (HGF)/scatter factor is a paracrine growth factor secreted by mesenchymal cells, which exerts an effect on a variety of epithelial cell types. Our recent study revealed that periodontal ligament fibroblasts (PLF) and gingival fibroblasts (GF) cultured in the presence of serum which contains various stimulants produced HGF or HGF-like factor, a predominant chemoattractant for gingival epithelial cells, and suggested that it could be involved in epithelial down-growth in periodontitis. METHODS: To clarify whether serum in medium stimulates PLF and GF to synthesize or activate HGF, the effect of fetal bovine serum (FBS) on HGF production was determined by enzyme-linked immunoabsorbent assay (ELISA), and its chemotactic activity for gingival epithelial cells was examined by modified Boyden chamber assay. RESULTS: One to 10% FBS in the culture medium stimulated HGF secretion in a dose-dependent manner and the chemotactic activity was decreased by treatment with anti-hHGF neutralizing antibody. Furthermore, fibroblast-conditioned medium incubated with FBS and aprotinin reduced its chemotactic activity. Interestingly, serum-free culture of PLF and GF produced potent chemoattractants for gingival epithelial cells other than HGF. CONCLUSIONS: These results show that FBS stimulates both HGF secretion and activation by PLF and GF.

Gibberellin deficiency pleiotropically induces culm bending in sorghum: an insight into sorghum semi-dwarf breeding.

Regulation of symmetrical cell growth in the culm is important for proper culm development. So far, the involvement of gibberellin (GA) in this process has not yet been demonstrated in sorghum. Here, we show that GA deficiency resulting from any loss-of-function mutation in four genes (SbCPS1, SbKS1, SbKO1, SbKAO1) involved in the early steps of GA biosynthesis, not only results in severe dwarfism but also in abnormal culm bending. Histological analysis of the bent culm revealed that the intrinsic bending was due to an uneven cell proliferation between the lower and upper sides of culm internodes. GA treatment alleviated the bending and dwarfism in mutants, whereas the GA biosynthesis inhibitor, uniconazole, induced such phenotypes in wild-type plants--both in a concentration-dependent manner, indicating an important role of GA in controlling erectness of the sorghum culm. Finally, we propose that because of the tight relationship between GA deficiency-induced dwarfism and culm bending in sorghum, GA-related mutations have unlikely been selected in the history of sorghum breeding, as could be inferred from previous QTL and association studies on sorghum plant height that did not pinpoint GA-related genes.