Pangenome-Wide Association Study and Transcriptome Analysis Reveal a Novel QTL and Candidate Genes Controlling both Panicle and Leaf Blast Resistance in Rice.

Cultivating rice varieties with robust blast resistance is the most effective and economical way to manage the rice blast disease. However, rice blast disease comprises leaf and panicle blast, which are different in terms of resistance mechanisms. While many blast resistant rice cultivars were bred using genes conferring resistance to only leaf or panicle blast, mining durable and effective quantitative trait loci (QTLs) for both panicle and leaf blast resistance is of paramount importance. In this study, we conducted a pangenome-wide association study (panGWAS) on 9 blast resistance related phenotypes using 414 international diverse rice accessions from an international rice panel. This approach led to the identification of 74 QTLs associated with rice blast resistance. One notable locus, qPBR1, validated in a F4:5 population and fine-mapped in a Heterogeneous Inbred Family (HIF), exhibited broad-spectrum, major and durable blast resistance throughout the growth period. Furthermore, we performed transcriptomic analysis of 3 resistant and 3 sensitive accessions at different time points after infection, revealing 3,311 differentially expressed genes (DEGs) potentially involved in blast resistance. Integration of the above results identified 6 candidate genes within the qPBR1 locus, with no significant negative effect on yield. The results of this study provide valuable germplasm resources, QTLs, blast response genes and candidate functional genes for developing rice varieties with enduring and broad-spectrum blast resistance. The qPBR1, in particular, holds significant potential for breeding new rice varieties with comprehensive and durable resistance throughout their growth period.

The Function of SD1 on Shoot Length and its Pyramiding Effect on Shoot Length and Plant Height in Rice (Oryza sativa L.).

Strong seedling vigor is imperative to achieve stable seedling establishment and enhance the competitiveness against weeds in rice direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor in rice, but few genes for SL have been cloned so far. In the previous study, we identified two tightly linked and stably expressed QTLs for SL, qSL-1f and qSL-1d by genome-wide association study, and cloned the causal gene (LOC_Os01g68500) underlying qSL-1f. In the present study, we identify LOC_Os01g66100 (i.e. the semidwarf gene SD1), a well-known gene controlling plant height (PH) at the adult-plant stage, as the causal gene underlying qSL-1d through gene-based haplotype analysis and knockout transgenic verification. By measuring the phenotypes (SL and PH) of various haplotypes of the two genes and their knockout lines, we found SD1 and LOC_ Os01g68500 controlled both SL and PH, and worked in the same direction, which provided the directly genetic evidence for a positive correlation between SL and PH combined with the analysis of SL and PH in the diverse natural population. Moreover, the knockout transgenic experiments suggested that SD1 had a greater effect on PH compared with LOC_ Os01g68500, but no significant difference in the effect on SL. Further investigation of the pyramiding effects of SD1 and LOC_Os01g68500 based on their haplotype combinations suggested that SD1 may play a dominant role in controlling SL and PH when the two genes coexist. In this study, the effect of SD1 on SL at the seedling stage is validated. In total, two causal genes, SD1 and LOC_ Os01g68500, for SL are cloned in our studies, which controlled both SL and PH, and the suitable haplotypes of SD1 and LOC_ Os01g68500 are beneficial to achieve the desired SL and PH in different rice breeding objectives. These results provide a new clue to develop rice varieties for direct seeding and provide new genetic resources for molecular breeding of rice with suitable PH and strong seedling vigor.

Ketogenic diet alleviates ß-cell dedifferentiation but aggravates hepatic lipid accumulation in db/db mice.

OBJECTIVE: The aim of this study was to explore the effect of the ketogenic diet (KD) on ß-cell dedifferentiation and hepatic lipid accumulation in db/db mice. METHODS: After a 3-wk habituation, male db/db mice ages 8 wk were assigned into one of three groups: normal diet (ND), KD, and 75% calorie restriction (CR) group. Free access to a standard diet, a KD, and 75% of a standard diet, respectively, were given to each group. Additionally, sex-matched 8-wk-old C57BL/6 mice were used to construct a control (C) group. After a 4-wk dietary intervention, mouse body weight, fasting blood glucose (FBG), blood lipids, fasting insulin (FINS), glucose tolerance, and ß-hydroxybutyric acid level were measured. The morphologies of the islet and liver were observed by hematoxylin and eosin staining. Positive expressions of ß-cell-specific transcription factors in mouse islets were determined by double immunofluorescence staining. The size and number of lipid droplets in mouse liver were examined by Oil Red O staining. Real-time quantitative reverse transcription polymerase chain reaction detected relative levels of adipogenesis-associated and lipolysis-associated genes in mouse liver. Additionally, expressions of CD36 protein in the mouse liver were determined by immunohistochemical staining and Western blot. RESULTS: After a 4-wk dietary intervention, FBG, FINS, and glucose area under the curve in the KD group became significantly lower than in the ND group (all P < 0.05). Regular morphology of mouse islets was observed in the KD group, with an increased number of islet cells. The KD significantly reversed the decrease in ß-cell number, disarrangement of ß-cells, decline of ß/α-cell ratio, and downregulation of ß-cell-specific transcription factors in db/db mice. Serum levels of triacylglycerol, total cholesterol, and low-density lipoprotein cholesterol were comparable between the ND and KD groups. In contrast, serum triacylglycerol levels were significantly lower in the CR group than in the ND group (P < 0.05). Vacuolar degeneration and lipid accumulation in the liver were more prominent in the KD group than in the ND and CR groups. The mRNA levels of Pparα and Acox1 in the KD group were lower than those in the ND group, although no significant differences were detected. Relative levels of Cd36 and inflammatory genes in the mouse liver were significantly higher in the KD group than in the ND group (all P < 0.05). CONCLUSION: The KD significantly reduced FBG and FINS and improved glucose tolerance in db/db mice by upregulating ß-cell-specific transcription factors and reversing ß-cell dedifferentiation. However, the KD also induced hepatic lipid accumulation and aggravated inflammatory response in the liver of db/db mice.

Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.).

KEY MESSAGE: Genome-wide association mapping revealed a novel QTL for shoot length across multiple environments. Its causal gene, LOC_Os01g68500, was identified firstly through gene-based haplotype analysis, gene expression and knockout transgenic verification. Strong seedling vigor is an important breeding target for rice varieties used in direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor characterized by rapid growth of seedling, which enhance seedling emergence. Therefore, mining genes for SL and conducting molecular breeding help to develop varieties for direct seeding. However, few QTLs for SL have been fine mapped or cloned so far. In this study, a genome-wide association study of SL was performed in a diverse rice collection consisting of 391 accessions in two years, using phenotypes generated by different cultivation methods according to the production practice, and a total of twenty-four QTLs for SL were identified. Among them, the novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole population and indica subpopulation. Through gene-based haplotype analysis of the annotated genes within the putative region of qSL-1f, and validated by gene expression and knockout transgenic experiments, LOC_Os01g68500 (i.e., Os01g0913100 in RAP-DB) was identified as the causal gene for SL, which has a single-base variation (C-to-A transversion) in its CDS region, resulting in the significant difference in SL of rice. LOC_Os01g68500 encodes a DUF538 (Domain of unknown function) containing protein, and the function of DUF538 protein gene on rice seedling growth is firstly reported in this study. These results provide a new clue for exploring the molecular mechanism regulating SL, and promising gene source for the molecular breeding in rice.

The 14-3-3 protein OsGF14f interacts with OsbZIP23 and enhances its activity to confer osmotic stress tolerance in rice.

Drought, which can induce osmotic stress, is the leading environmental constraint on crop productivity. Plants in both agricultural and natural settings have developed various mechanisms to cope with drought stress. The identification of genes associated with drought stress tolerance and understanding the underlying regulatory mechanisms are prerequisites for developing molecular manipulation strategies to address this issue. Here, we reported that the G-BOX FACTOR 14-3-3f (14-3-3 protein OsGF14f) positively modulates osmotic stress tolerance in rice (Oryza sativa). OsGF14f transgenic lines had no obvious change in crucial agronomic traits including yield and plant height. OsGF14f is transcriptionally induced by PEG treatment, and in rice, overexpression or knockout of this gene leads to enhanced or weakened osmotic stress tolerance, respectively. Furthermore, OsGF14f positively regulates abscisic acid (ABA) responses by interacting with the core ABA-responsive transcription factor BASIC LEUCINE ZIPPER 23 (OsbZIP23) to enhance its transcriptional regulation activity toward downstream target genes. Further genetic analysis showed that OsGF14f is required for the full function of OsbZIP23 in rice osmotic response, and OsGF14f-mediated osmotic stress tolerance partially depends on OsbZIP23. Interestingly, OsGF14f is a direct target gene of OsbZIP23. Taken together, our findings reveal a genetic and molecular framework by which the OsGF14f-OsbZIP23 complex modulates rice osmotic response, providing targets for developing drought-tolerant crops.

Genome-wide association mapping and gene expression analysis reveal candidate genes for grain chalkiness in rice.

Grain chalkiness is the main factor determining the market value of rice. Reducing chalkiness is an important breeding goal for genetic improvement of high quality rice. Identification of QTLs or genes controlling chalkiness is the prerequisite for molecular breeding in rice. Here, we conducted a genome-wide association study to identify QTLs associated with grain chalkiness including percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC) in 450 rice accessions consisting of 300 indica and 150 japonica rice in two environments. A total of 34 QTLs were identified, including 14 QTLs for PGWC and 20 QTLs for DEC. Among them, seven QTLs were commonly identified in two environments, and eight QTLs were simultaneously related to two traits. Based on the haplotype analysis, LD decay analysis, RNA-sequencing, qRT-PCR confirmation and haplotype comparisons, four genes (LOC_Os10g36170, LOC_Os10g36260, LOC_Os10g36340 and LOC_Os10g36610) were considered as the candidate genes for qDEC-10c1w,2wj , which could be identified in both environments and had the most significant p-value among the newly identified QTLs. These results provided new insight into the genetic basis of grain chalkiness and gene resources for improving quality by molecular breeding in rice.

Bufei Yishen Formula Inhibits the Cell Senescence in COPD by Up-Regulating the ZNF263 and Klotho Expression.

Background: Bufei Yishen formula (BYF) is an effective prescription for the clinical treatment of chronic obstructive pulmonary disease (COPD). However, the molecular mechanism by which it exerts its pharmacological effects remains to be explored. Methods: The human bronchial cell line BEAS-2B was treated with cigarette smoke extract (CSE). Cellular senescence markers were detected by Western blot and ELISA. Potential transcription factor of klotho was predicted using JASPAR and USCS databases. Results: CSE induced cellular senescence with intracellular accumulation of cellular senescence biomarkers (p16, p21 and p27) and increased secretion of senescence-related secretory phenotypic (SASP) factors (IL-6, IL-8, and CCL3). In contrast, BYF treatment inhibited CSE-induced cellular senescence. CSE suppressed the transcription, expression and secretion of klotho, whereas BYF treatment rescued its transcription, expression and secretion. CSE downregulated the protein level of ZNF263, whereas BYF treatment rescued the expression of ZNF263. Furthermore, ZNF263-overexpressing BEAS-2B cells could inhibit CSE-induced cellular senescence and SASP factor secretion by upregulating the expression of klotho. Conclusion: This study revealed a novel pharmacological mechanism by which BYF alleviates clinical symptoms of COPD patients, and regulating ZNF263 and klotho expression may be beneficial to the treatment and prevention of COPD.

Overexpression of OsGF14C enhances salinity tolerance but reduces blast resistance in rice.

High-salinity and blast disease are two major stresses that cause dramatic yield loss in rice production. GF14 (14-3-3) genes have been reported to play important role in biotic and abiotic stresses in plants. However, the roles of OsGF14C remain unknown. To understand the functions and regulatory mechanisms of OsGF14C in regulating salinity tolerance and blast resistance in rice, we have conducted OsGF14C-overexpressing transgenic experiments in the present study. Our results showed that overexpression of OsGF14C enhanced salinity tolerance but reduced blast resistance in rice. The enhanced salinity tolerance is related to the reduction of methylglyoxal and Na+ uptake instead of exclusion or compartmentation and the negative role of OsGF14C in blast resistance is associated with the suppression of OsGF14E, OsGF14F and PR genes. Our results together with the results from the previous studies suggest that the lipoxygenase gene LOX2 which is regulated by OsGF14C may play roles in coordinating salinity tolerance and blast resistance in rice. The current study for the first time revealed the possible roles of OsGF14C in regulating salinity tolerance and blast resistance in rice, and laid down a foundation for further functional study and crosstalk regulation between salinity and blast resistance in rice.

A pangenome analysis pipeline provides insights into functional gene identification in rice.

BACKGROUND: A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking. RESULTS: To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants' position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic diversity. We characterize a new locus (qPH8-1) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS). CONCLUSIONS: Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.

Guanxinping ameliorates atherosclerosis via MAPK/NF-κB signaling pathway in ApoE-/- mice.

BACKGROUND: Atherosclerosis (AS), one of the leading causes of deaths and disabilities, is a kind of vascular disease of lipid disorders and chronic inflammation. Guanxinping (GXP) has been administrated in the treatment of AS for nearly 20 years with satisfying clinical response. This study aimed to explore its underlying mechanisms of anti-atherosclerotic effect in AS. METHODS: Male ApoE-/- mice were randomized into five groups and fed with either standard diet (control group, CON) or high-fat diet (HFD) for 12 weeks. HFD mice were further divided randomly and either fed continually with HFD as a model group, or atorvastatin (ATO), or low-dose GXP (LGXP), or high-dose GXP (HGXP). After 12 weeks, the body weight, serum triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-c), and low-density lipoprotein cholesterol (LDL-c) were detected. Moreover, serum inflammation cytokines including tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and interleukin-1ß (IL-1ß) concentrations were measured. The structure of aortic tissues was examined by hematoxylin-eosin staining. The mRNA expression of TNF-α, IL-6, and IL-1ß were assessed by qPCR. The protein expressions of ICAM-1, VCAM-1, MCP-1, IL-6, IL-1ß, p38MAPK, ERK1/2, JNK, IκB-α, and NF-κBp65 in the aorta were also detected. RESULTS: GXP treatment reduced serum TG, TC, and LDL-c levels in ApoE-/- mice. Moreover, GXP reduced lipid accumulation in the aorta of ApoE-/- mice, induced by HFD. Furthermore, GXP ameliorated the aorta morphological damage and reduced the serum TNF-α, IL-6, and IL-1ß levels. GXP also attenuated the protein expression of ICAM-1, VCAM-1, MCP-1, IL-6, IL-1ß, p38MAPK, ERK1/2, JNK, and NF-κBp65, whereas it increased the IκBα level in aortic tissues of ApoE-/- mice. CONCLUSIONS: Our results show that GXP could ameliorate atherosclerosis, which is mediated by inhibition of the MAPK/NF-κB signaling pathway in ApoE-/- mice. This study provides evidence that GXP might be a promising drug for the treatment of AS.

OsFLZ2 interacts with OsMADS51 to fine-tune rice flowering time.

Flowering time is an important agronomic trait affecting crop yield. FCS-LIKE ZINC FINGER (FLZ) proteins are plant-specific regulatory proteins that are involved in multiple biological processes. However, their roles in plant flowering time control have not been clarified. Here, we report that OsFLZ2 is a negative regulator of rice flowering time. OsFLZ2 delays flowering by repressing the expression of key floral integrator genes. Biochemical assays showed OsFLZ2 physically interacts with OsMADS51, a flowering activator under short-day (SD) conditions. Both OsFLZ2 and OsMADS51 are highly expressed in rice leaves before floral transition under natural SD conditions, and their proteins are colocalized in the nucleus. Co-expression of OsFLZ2 can destabilize OsMADS51 and weaken its transcriptional activation of the downstream target gene Early heading date 1 (Ehd1). Taken together, these results indicate that OsFLZ2 can interfere with the function of OsMADS51 to fine-tune rice flowering time.

Transcriptome and Metabolome Analyses Reveal New Insights into the Regulatory Mechanism of Head Milled Rice Rate.

The head milled rice rate (HMRR) is the most important trait of milling quality, which affects the final yield and quality of rice. However, few genes related to HMRR have been identified and the regulatory mechanism of HMRR remains elusive. In this study, we performed a comparative analysis integrating the transcriptome sequencing of developing seeds at the grain-filling stage and a metabolome analysis of brown rice between two groups of accessions with contrasting performances in HMRR. A total of 768 differentially expressed genes (DEGs) were identified between the transcriptome profiles of low-HMRR and high-HMRR accessions. In comparison to the high-HMRR accessions, 655 DEGs were up-regulated in the low-HMRR accessions, which was 4.79 folds higher than the number of down-regulated genes. These up-regulated DEGs were enriched in various metabolic and biosynthetic processes, oxidation reduction, phosphorylation, ion transport and ATP-related processes. However, the 113 down-regulated DEGs in the low-HMRR accessions were concentrated in carbohydrate metabolic processes, cell-death-related processes and defense response. Among the 30 differential metabolites, 20 and 10 metabolites were down-/up-regulated, respectively, in the accessions with low HMRR. In addition, 10 differential metabolites, including five metabolites of the shikimate pathway and five metabolites of the pyruvate pathway, were integrated into two separate pathways, starting from sucrose. Our global analysis of HMRR provides an invaluable resource for a better understanding of the molecular mechanism underlying the genetic regulation of HMRR.

Segmental aneuploidies with 1 Mb resolution in human preimplantation blastocysts.

PURPOSE: This study aimed to investigate the spectrum and characteristics of segmental aneuploidies (SAs) of <10 megabase (Mb) length in human preimplantation blastocysts. METHODS: Preimplantation genetic testing for aneuploidy was performed in 15,411 blastocysts from 5171 patients using a validated 1 Mb resolution platform. The characteristics and spectrum of SAs, including the incidence, sizes, type, inheritance pattern, clinical significance, and embryo distribution, were studied. RESULTS: In total, 6.4% of the 15,411 blastocysts carried SAs of >10 Mb, 4.9% of embryos had SAs ranging between 1 to 10 Mb, and 84.3% of 1 to 10 Mb SAs were <5 Mb in size. Inheritance pattern analysis indicated that approximately 63.8% of 1 to 10 Mb SAs were inherited and were predominantly 1 to 3 Mb in size. Furthermore, 18.4% of inherited SAs and 51.9% de novo 1 to 10 Mb SAs were pathogenic or likely pathogenic (P/LP). Different from whole-chromosome aneuploidies, reanalysis indicated that 50% of the de novo 1 to 10 Mb SAs and 70% of the >10 Mb SAs arose from mitotic errors. CONCLUSION: Based on the established platform, 1 to 10 Mb SAs are common in blastocysts and include a subset of P/LP SAs. Inheritance pattern analysis and clinical interpretation based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines contributed to determine the P/LP SAs.

[Effect of Winter Cover Cropping on Soil Greenhouse Gas Emissions in a Dryland Spring Maize Field on the Loess Plateau of China].

A field experiment was carried out to study the effects of winter cover cropping on soil greenhouse gas emissions in dryland maize. Four cover crop treatments, namely oat, lentil, a mixture of oat and lentil, and no cover crops (CK), were included during the winter fallow period. Greenhouse gas emission fluxes from soil were measured using the static chamber-gas chromatograph technique. The results showed that:both soil CO2 and N2O were emitted, but the soil acted as a sink for CH4. Compared with the that in CK, oat and lentil had no effect on the cumulative amount of soil CO2 emissions during the winter fallow period and increased the cumulative amount of soil CO2 emissions by 7.77% and 25.7% (P<0.05) in the spring maize growing period, respectively; the mixture increased the cumulative amount of soil CO2 emissions by 19.1% and 14.5% (P<0.05) during the winter fallow and spring maize growing periods. In the winter fallow and spring maize periods, compared with that in CK, oat declined the cumulative amount of soil N2O emissions by 11.6% and 14.7% (P<0.05), and lentil increased the cumulative amount of soil N2O emissions by 31.9% and 14.9% (P<0.05), respectively. Compared to that in the CK, the mixture declined the cumulative amount of soil N2O emissions by 19.2% (P<0.05) in the winter fallow period but had no effect in the spring maize period. Compared with the CK, oat, lentil, and their mixture resulted in a declined cumulative amount of soil CH4 uptake by 37.9%, 23.6%, and 29.6% (P<0.05) in the winter fallow period and by 19.4%, 33.5%, and 31.5% (P<0.05) in the spring maize growing period, respectively. Compared with the CK, oat had no effect on global warming potential (GWP), maize yield, and greenhouse gas intensity (GHGI). Lentil and the mixture increased GWP, and lentil showed a greater increase in GWP than that of the mixture. Compared with the CK, lentil and the mixture increased maize yield by 20.3% and 15.4% (P<0.05), respectively, and had no effect on GHGI. The findings from this study show that the lentil and oat mixture can significantly increase maize yield and decrease GHGI.

Mining candidate genes for rice cadmium accumulation in the shoot through a genome-wide association study and transcriptomic analysis.

High cadmium (Cd) accumulation in rice is a serious threat to human health. The genetic mechanism of Cd accumulation in rice is highly complicated. To identify the low Cd accumulation in rice germplasm, investigate the genetic mechanism underlying Cd accumulation, and mine the elite genes of significant importance for rice breeding of low Cd accumulation varieties, we performed a genome-wide association study (GWAS) for rice Cd concentration in the shoot. The rice accessions were 315 diverse indica rice accessions selected from the 1568 rice accessions with 700,000 SNPs. Within the high rate of linkage disequilibrium (LD) decay, eight QTLs related to rice Cd accumulation were identified. Transcriptomic analysis showed there were 799 differentially expressed genes (DEGs) in the root and 857 DEGs in the shoot, which are probably considered to be the cause of the significant difference in Cd accumulation between high and low Cd accumulation varieties. In qCd11-1, we detected a crucial candidate gene, LOC_Os11g11050, which encodes an initiation factor, expressed differently in the root between the high and low Cd accumulation varieties. Furthermore, under Cd treatment, the expression levels of LOC_Os11g11050 significantly decreased in both the high and low Cd accumulation varieties. Sequence comparison and qRT-PCR revealed that there were indel sequences and base substitutions in the promoter region of LOC_Os11g11050 correlated with the LOC_Os11g11050 expression level, as well as the phenotype of Cd concentration differences in shoot between the high and low Cd accumulation accessions. LOC_Os11g11050 might play important roles in Cd accumulation. The results of our study provide valuable resources for low Cd accumulation in indica varieties and the candidate functional gene, as well as molecular mechanisms for Cd accumulation in indica rice. The genetic architecture underlying Cd accumulation in indica can be used for further applying the low Cd gene existing in indica for decreasing Cd accumulation in rice.

Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice.

High seedling vigor can improve the ability to compete against weeds and flooding at the seedling stage and is essential for the direct seeding of rice. Early shoot length is an important performance index in seedling vigor evaluation. However, information on the identity of rice germplasm with high seedling vigor, and the genetic basis of seedling vigor are not well understood. In this study, we have conducted a genome-wide association study using 302 international diverse rice accessions from the Rice Diversity Panel 2. Six quantitative trait loci (QTLs) were found to associate with shoot length (SL). The locus qSL2 was further analyzed for candidate gene characterization. We identified OsCPS1, which encodes CDP synthase and functions in GA (Gibberellins) biosynthesis in rice, exhibits differential expression between long and short SL accessions. Using the Nipponbare genome sequence as the reference, we identified a 36 bp deletion in the 5' UTR of OsCPS1 in long SL accessions, which is absent in short SL accessions. GA content analysis showed that the levels of bioactive GA1 and GA4 are considerably higher in long SL accessions than in short SL accessions. Genome-wide gene expression analysis indicated the expression of some photosynthesis genes is higher in long SL accessions than in short SL accessions. In contrast, genes involved in ABA (Abscisic Acid)-activated signal pathway showed lower expression in long SL accessions. Population analysis across wild rice, indica and japonica, suggested that OsCPS1 may be under selection in japonica during domestication. The results suggest that OsCPS1 is a candidate gene underlying qSL2. These data provide a promising source for candidate genetic variation associated with seedling vigor, with practical applications in rice breeding.

Overexpression of OsGF14f Enhances Quantitative Leaf Blast and Bacterial Blight Resistance in Rice.

Although it is known that rice 14-3-3 family genes are involved in various defense responses, the functions of OsGF14f in response to diseases have not been reported. Here, we showed that the transcription of OsGF14f was significantly induced by leaf blast infection, and the overexpression of OsGF14f quantitatively enhanced resistance to leaf blast and bacterial blight in rice. Further analysis showed that the expression levels of salicylic acid (SA) pathway-associated genes (PAL1, NH1, PR1a and PR10) in the OsGF14f-overexpressing plants, were higher than those in wild-type plants after inoculation with the blast isolate (Magnaporthe oryzae Barr). In addition, the expression level of OsGF14f was significantly induced after SA treatment, and higher endogenous SA levels were observed in the OsGF14f-overexpressing plants compared with that in wild-type plants, especially after blast challenge. Taken together, these results suggest that OsGF14f positively regulates leaf blast and bacterial blight resistance in rice via the SA-dependent signaling pathway.

Short-term moderate caloric restriction in a high-fat diet alleviates obesity via AMPK/SIRT1 signaling in white adipocytes and liver.

Background: Obesity is a growing problem for public health worldwide. Calorie restriction (CR) is a safety and effective life intervention to defend against obesity. Short-term moderate CR may be a more favorable strategy against this pathology. However, the mechanisms behind the effects of CR remain to be clarified. Increased energy expenditure in the liver and brown adipose tissue could potentially be manipulated to modulate and improve metabolism in obesity. Moreover, nicotinamide adenine dinucleotide (NAD)-dependent deacetylase sirtuin-1 (SIRT1) and AMP-activated protein kinase (AMPK) are well-characterized metabolic modulators. We aim to explore the anti-obesity effects of short-term moderate CR by improving energy metabolism via the SIRT1/AMPK pathway in white adipocytes and liver in a mouse model of obesity. Methods: Male C57BL/6 mice were randomized into two groups receiving either a standard or a high-fat diet (HFD) for 8 weeks to induce obesity. The HFD-induced obese mice were further randomized into two groups: HFD group or CR group (received 75% of the food eaten by HFD group). Their energy metabolism, white adipose tissue (WAT) contents, hepatic fat deposition, the expression of AMPK, SIRT1, peroxisome proliferators γ-activated receptor coactivator-1α (PGC-1α), nuclear factor kappa B (NF-κB), endothelial nitric oxide synthase (eNOS) in WAT, and hepatic tissues were determined. Results: After 4 weeks, body weight, total serum cholesterol, fasting blood glucose, and insulin levels were significantly lower in the CR group. Moreover, CR ameliorated hepatocyte steatosis, attenuated white adipogenesis, and increased energy expenditure and expressions of SIRT1, PGC-1α, and phosphorylated AMPK in subcutaneous WAT and the hepatic tissues. In addition, CR reduced the protein levels of NF-κB and increased the eNOS expression. Conclusion: Short-term moderate CR decreases obesity, increases the thermogenesis, and inhibits inflammation in a mouse model of obesity, probably via the activation of the AMPK/SIRT1 pathway in WAT and liver.

Effects of Fallow Management Practices on Soil Water, Crop Yield and Water Use Efficiency in Winter Wheat Monoculture System: A Meta-Analysis.

Winter wheat monoculture is a predominant cropping system for agricultural production in dry areas. However, fallow management effects on soil water conservation and crop yield and water use have been inconsistent among studies. We selected 137 studies and performed a meta-analysis to test the effects of tillage and mulching during the fallow period on precipitation storage efficiency (PSE), soil water storage at wheat planting (SWSp), crop yield, evapotranspiration (ET), and water use efficiency (WUE). Compared to conventional tillage (CT), conservation tillage during fallow period overall increased PSE, SWSp and wheat yield by 31.0, 6.4, and 7.9%, respectively, but did not affect ET and WUE. No tillage (NT) had a better performance on soil water conservation during fallow period but a similar effect on wheat yield and WUE compared to reduced tillage (RT) and subsoil tillage (ST). Compared to no mulching, fallow mulching practices overall increased PSE by 19.4%, but had a non-significant impact on SWSp, wheat yield, and ET. Compared to straw mulching, film mulching, and stubble mulching during fallow period, cover cropping as a biological mulching decreased SWSp, wheat yield, and WUE significantly. Wheat WUE was improved by straw mulching but not affected by film mulching and stubble mulching. Strong interactions between tillage method and mulching practices were found for most variables. NT with fallow mulching or with no mulching exhibited a greater impact on soil water conservation during fallow period compared to other combinations. The effects of tillage and mulching during fallow period on soil water conservation and wheat yield and water use also varied with soil and climatic conditions. Overall, NT in combination with straw mulching significantly increased SWSp, PSE, wheat yield, and WUE and can be the best fallow management practice for winter wheat production in varying edaphic and climatic conditions.

Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures.

Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. However, the genetic basis of PC in rice is still not well-understood. In this study, a genome-wide association study (GWAS) of PC was performed in a diverse rice collection consisting of 442 accessions using different phenotyping methods in two locations over 2 years. In the whole population consisting of white and colored pericarp rice, a total of 11 quantitative trait loci (QTLs) were identified using two phenotyping methods. Among these QTLs, nine were identified using the phenotypes represented by the presence and absence of pigmentation in pericarp, while 10 were identified using phenotypes of the degree of PC (DPC), in which eight are common QTLs identified using the two phenotyping methods. Using colored rice accessions and phenotypes based on DPC, four QTLs were identified, and they were totally different from the QTLs identified using the whole population, suggesting the masking effects of major genes on minor genes. Compared with the previous studies, 10 out of the 15 QTLs are first reported in this study. Based on the differential expression analysis of the predicted genes within the QTL region by both RNA-seq and real-time PCR (RT-PCR) and the gene functions in previous studies, LOC_Os01g49830, encoding a RAV transcription factor was considered as the candidate gene underlying qPC-1, a novel QTL with a large effect in this study. Our results provide a new insight into the genetic basis of PC in rice and contribute to developing the value-added rice with optimized flavonoid content through molecular breeding.