Genomic variation in weedy and cultivated broomcorn millet accessions uncovers the genetic architecture of agronomic traits.

Large-scale genomic variations are fundamental resources for crop genetics and breeding. Here we sequenced 1,904 genomes of broomcorn millet to an average of 40× sequencing depth and constructed a comprehensive variation map of weedy and cultivated accessions. Being one of the oldest cultivated crops, broomcorn millet has extremely low nucleotide diversity and remarkably rapid decay of linkage disequilibrium. Genome-wide association studies identified 186 loci for 12 agronomic traits. Many causative candidate genes, such as PmGW8 for grain size and PmLG1 for panicle shape, showed strong selection signatures during domestication. Weedy accessions contained many beneficial variations for the grain traits that are largely lost in cultivated accessions. Weedy and cultivated broomcorn millet have adopted different loci controlling flowering time for regional adaptation in parallel. Our study uncovers the unique population genomic features of broomcorn millet and provides an agronomically important resource for cereal crops.

Genetic linkage map construction and QTL analysis for plant height in proso millet (Panicum miliaceum L.).

KEY MESSAGE: A genetic linkage map representing proso millet genome was constructed with SSR markers, and a major QTL corresponding to plant height was mapped on chromosome 14 of this map. Proso millet (Panicum miliaceum L.) has the lowest water requirements of all cultivated cereal crops. However, the lack of a genetic map and the paucity of genomic resources for this species have limited the utility of proso millet for detailed genetic studies and hampered genetic improvement programs. In this study, 97,317 simple sequence repeat (SSR) markers were developed based on the genome sequence of the proso millet landrace Longmi 4. Using some of these markers in conjunction with previously identified SSRs, an SSR-based linkage map for proso millet was successfully constructed using a large mapping population (316 F2 offspring). In total, 186 SSR markers were assigned to 18 linkage groups corresponding to the haploid chromosomes. The constructed map had a total length of 3033.42 centimorgan (cM) covering 78.17% of the assembled reference genome. The length of the 18 linkage groups ranged from 88.89 cM (Chr. 15) to 274.82 cM (Chr. 16), with an average size of 168.17 cM. To our knowledge, this is the first genetic linkage map for proso millet based on SSR markers. Plant height is one of the most important traits in crop improvement. A major QTL was repeatedly detected in different environments, explaining 8.70-24.50% of the plant height variations. A candidate gene affecting auxin biosynthesis and transport, and ROS homeostasis regulation was predicted. Thus, the linkage map and QTL analysis provided herein will promote the development of gene mining and molecular breeding in proso millet.

Leaf cuticular wax composition of a genetically diverse collection of lettuce (Lactuca sativa L.) cultivars evaluated under field conditions.

Cuticular waxes of plants impart tolerance to many forms of environmental stress and help shed dangerous human pathogens on edible plant parts. Although the chemical composition of waxes on a wide variety of important crops has been described, a detailed wax compositional analysis has yet to be reported for lettuce (Lactuca sativa L.), one of the most widely consumed vegetables. We present herein the leaf wax content and composition of 12 genetically diverse lettuce cultivars sampled across five time points during their vegetative growth phase in the field. Mean total leaf wax amounts across all cultivars varied little over 28 days of vegetative growth, except for a notable decrease in total waxes following a major precipitation event, presumably due to wax degradation from wind and rain. All lettuce cultivars were found to contain a unique wax composition highly enriched in 22- and 24-carbon length 1-alcohols (docosanol and tetracosanol, respectively). In our report, the dominance of these shorter chain length 1-alcohols as wax constituents represents a relatively rare phenotype in plants. The ecological significance of these dominant and relatively short 1-alcohols is still unknown. Although waxes have been a target for improvement of various crops, no such work has been reported for lettuce. This study lays the groundwork for future research that aims to integrate cuticular wax characteristics of field grown plants into the larger context of lettuce breeding and cultivar development.

Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet.

Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve cereal production and quality, and ensure food security. Here we present the genetic variations, population structure and diversity of a diverse worldwide collection of 516 broomcorn millet genomes. Population analysis indicated that the domesticated broomcorn millet originated from its wild progenitor in China. We then constructed a graph-based pangenome of broomcorn millet based on long-read de novo genome assemblies of 32 representative accessions. Our analysis revealed that the structural variations were highly associated with transposable elements, which influenced gene expression when located in the coding or regulatory regions. We also identified 139 loci associated with 31 key domestication and agronomic traits, including candidate genes and superior haplotypes, such as LG1, for panicle architecture. Thus, the study's findings provide foundational resources for developing genomics-assisted breeding programs in broomcorn millet.

High-Throughput Absolute Quantification Sequencing Reveals that a Combination of Leguminous Shrubs Is Effective in Driving Soil Bacterial Diversity During the Process of Desertification Reversal.

Desertification leads to the extreme fragility of ecosystems and seriously threatens ecosystem functioning in desert areas. The planting of xerophytes, especially leguminous shrubs, is an effective and common means to reverse desertification. Soil microorganisms play a crucial role in nutrient cycling and energy flow in ecosystems. However, the effects of introducing leguminous shrubs on soil microbial diversity and the relevant mechanisms are not clear. Here, we employed the high-throughput absolute quantification 16S rRNA sequencing method to analyze the diversity of soil bacteria in sand-fixing areas of mixed shrublands with three combinations of shrubs, i.e., C. korshinskii × Corethrodendron scoparium (CaKCoS), C. korshinskii × Calligonum mongolicum (CaKCaM), and C. scoparium × C. mongolicum (CoSCaM), in the south of the Mu Us Sandy Land, China. This area suffered from moving dunes 20 years ago, but after introducing these shrubs to fix the dunes, the ecosystem was restored. Additionally, the effects of soil physicochemical properties on soil bacterial composition and diversity were analyzed with redundancy analysis (RDA) and structural equation modeling (SEM). It was found that the Shannon index of soil bacteria in CaKCoS was significantly higher than that in CaKCaM and CoSCaM, and the abundance of the dominant phyla, including Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Thaumarchaeota, Armatimonadetes, candidate_division_WPS-1, and Nitrospirae, increased significantly in CaKCoS and CaKCaM compared to that in CoSCaM. RDA showed that the majority of soil properties, such as total nitrogen (TN), available potassium (AK), N:P ratio, soil moisture (SM), and available phosphorus (AP), were important soil environmental factors affecting the abundance of the dominant phyla, and RDA1 and RDA2 accounted for 56.66% and 2.35% of the total variation, respectively. SEM showed that the soil bacterial α-diversity was positively affected by the soil organic carbon (SOC), N:P ratio, and total phosphorus (TP). Moreover, CaKCoS had higher SM, total carbon (TC), total potassium (TK), and AP than CaKCaM and CoSCaM. Collectively, these results highlight a conceptual framework in which the combination of leguminous shrubs can effectively drive soil bacterial diversity by improving soil physicochemical properties and maintaining ecosystem functioning during desertification reversal.

Effects of housing environments on COVID-19 transmission and mental health revealed by COVID-19 Participant Experience data from the All of Us Research Program in the USA: a case-control study.

OBJECTIVES: To examine the association between housing types and COVID-19 infection (or mental health) during the early stages of the pandemic by using the large-scale individual-level All of Us Research Program COVID-19 Participant Experience (COPE) survey data. We hypothesise that housing types with a shared component are associated with elevated COVID-19 infection and subsequent mental health conditions. DESIGN: A retrospective case-control study. SETTING: Secondary analysis of online surveys conducted in the USA. PARTICIPANTS: 62 664 participant responses to COPE from May to July 2020. PRIMARY AND SECONDARY OUTCOME MEASURES: Primary outcome measure is the self-reported COVID-19 status, and the secondary outcome measures are anxiety or stress. Both measures were applied for matched cases and controls of the same race, sex, age group and survey version. RESULTS: A multiple logistic regression analysis revealed that housing types with a shared component are significantly associated with COVID-19 infection (OR=1.19, 95% CI 1.1 to 1.3; p=2×10-4), anxiety (OR=1.26, 95% CI 1.1 to 1.4; p=1.1×10-6) and stress (OR=1.29, 95% CI 1.2 to 1.4; p=4.3×10-10) as compared with free-standing houses, after adjusting for confounding factors. Further, frequent optional shopping or outing trips, another indicator of the built environment, are also associated with COVID-19 infection (OR=1.36, 95% CI 1.1 to 1.8; p=0.02), but not associated with elevated mental health conditions. Confounding factors are controlled in the analysis such as ethnicity, age, social distancing behaviour and house occupancy. CONCLUSION: Our study demonstrates that houses with a shared component tend to have an increased risk of COVID-19 transmission, which consequently leads to high levels of anxiety and stress for their dwellers. The study also suggests the necessity to improve the quality of the built environment such as residential housing and its surroundings through planning, design and management, ensuring a more resilient society that can cope with future pandemics.

Exploring the SiCCT Gene Family and Its Role in Heading Date in Foxtail Millet.

CCT transcription factors are involved in the regulation of photoperiod and abiotic stress in Arabidopsis and rice. It is not clear that how CCT gene family expand and regulate heading date in foxtail millet. In this study, we conducted a systematic analysis of the CCT gene family in foxtail millet. Thirty-nine CCT genes were identified and divided into four subfamilies based on functional motifs. Analysis showed that dispersed duplication played a predominant role in the expansion of CCT genes during evolution. Nucleotide diversity analysis suggested that genes in CONSTANS (COL)-like, CCT MOTIF FAMILY (CMF)-like, and pseudoresponse response regulator (PRR)-like subfamilies were subjected to selection. Fifteen CCT genes were colocalized with previous heading date quantitative trait loci (QTL) and genome-wide association analysis (GWAS) signals. Transgenic plants were then employed to confirm that overexpression of the CCT gene SiPRR37 delayed the heading date and increased plant height. Our study first investigated the characterization and expansion of the CCT family in foxtail millet and demonstrated the role of SiPRR37. These results lay a significant foundation for further research on the function of CCT genes and provide a cue for the regulation of heading date.

Epithelial cell responses to rhinovirus identify an early-life-onset asthma phenotype in adults.

BACKGROUND: The study of pathogenic mechanisms in adult asthma is often marred by a lack of precise information about the natural history of the disease. Children who have persistent wheezing (PW) during the first 6 years of life and whose symptoms start before age 3 years (PW+) are much more likely to have wheezing illnesses due to rhinovirus (RV) in infancy and to have asthma into adult life than are those who do not have PW (PW-). OBJECTIVE: Our aim was to determine whether nasal epithelial cells from PW+ asthmatic adults as compared with cells from PW- asthmatic adults show distinct biomechanistic processes activated by RV exposure. METHODS: Air-liquid interface cultures derived from nasal epithelial cells of 36-year old participants with active asthma with and without a history of PW in childhood (10 PW+ participants and 20 PW- participants) from the Tucson Children's Respiratory Study were challenged with a human RV-A strain (RV-A16) or control, and their RNA was sequenced. RESULTS: A total of 35 differentially expressed genes involved in extracellular remodeling and angiogenesis distinguished the PW+ group from the PW- group at baseline and after RV-A stimulation. Notably, 22 transcriptomic pathways showed PW-by-RV interactions; the pathways were invariably overactivated in PW+ patients, and were involved in Toll-like receptor- and cytokine-mediated responses, remodeling, and angiogenic processes. CONCLUSIONS: Asthmatic adults with a history of persistent wheeze in the first 6 years of life have specific biomolecular alterations in response to RV-A that are not present in patients without such a history. Targeting these mechanisms may slow the progression of asthma in these patients.

Catalytic ozonation oxidation of ketoprofen by peanut shell-based biochar: effects of the pyrolysis temperatures.

A series of peanut shell (HS)-based biochar were prepared at different pyrolysis temperatures and subsequently used as the effective ozonation catalysts for ketoprofen (KET) degradation in aqueous solution. The physicochemical properties and morphology of the obtained biochar were analysed by ICP, TG, XRD, FT-IR, SEM, TEM, BET and etc. characterizations. The results demonstrated that the pyrolysis temperature played an important role on the structure and morphology of HS-based biochar. As the pyrolysis temperature increased, the cellulose and hemicellulose of HS gradually decomposed, resulting in the loss of biochar mass, improvement of the surface roughness, the increase of specific surface area, and the formation of new functional groups. The HS-based biochar pyrolyzed at 600°C (HS600) achieved the fast KET degradation rate with the pseudo-first-order rate constant of 0.922 min-1 and the low adsorption rate of 1.3% in O3/HS600 process. Meanwhile, the effects of the HS600 dosage, initial KET concentration, temperature, water matrix, and solution pH on KET degradation were systematically evaluated. Besides, the HS600 displayed great stability and reusability towards KET degradation during multiple cycling experiments. Moreover, the single oxygen, superoxide radical and hydroxyl radical were involved in O3/HS600 process and the mechanisms for the improvement of KET degradation were also elucidated. It could be speculated that the enhancement of the catalytic ozonation by HS-based biochar was probably attributed to the increased active sites and the intense chemical bonds, and delocalized π electron.

Experimental study on the effect of Si and P ion content in SiO2 exposure environment on the degree of pulmonary fibrosis.

BACKGROUND: Silicosis is a public health issue in developing countries for long and cannot be completely cured. OBJECTIVE: To study the changes of ion content with TNF-α and TGF-ß expression in alveolar lavage fluid (BALF) at different time points in rats exposed to silica and to investigate their correlation with pulmonary fibrosis. METHODS: 42 rats were randomly divided into control group (n = 12) and exposure group (n = 30). Tissues of right lower lungs were collected and fixed for further Hematoxylin-eosin (HE) and Masson staining. We collected the BALF to examine the inflammatory cytokines of TNF-α and TGF-ß and measured the ion contents in BALF. RESULTS: The increase of TNF-α level was earlier than TGF-ß. The content of silica in BALF was significantly increased after exposure and reached the maximum at 7th day, similar to the curve of cytokine TGF-ß level. However, phosphorus ions increased quickly after gradual decline of silicon ion and roughly proportional to the curve of degree of fibrosis. CONCLUSIONS: Crystalline silica exposure can cause changes in TGF-ß and TNF-α in BALF and accompanied with fibrosis and ions content variation. The abnormal expression of phosphorus ion may have significance in the occurrence and development of silicosis.

The complete chloroplast genome sequence of Pennisetum flaccidum (Poaceae).

Pennisetum flaccidum Grisebach is a typical high-quality forage and adrought-tolerant grass. In this study, we firstly reported the complete chloroplast (cp) genome of P. flaccidum, which was 138,336 bp in length, including a pair of inverted repeats (IR: 22,293 bp), a large single copy (LSC: 81,329 bp), and a small single copy (SSC: 12,421 bp) region. A total of 131 genes were annotated, containing seven rRNA genes, 38 tRNA genes, and 86 protein-coding genes. The GC content of the cp genome was 38.63%. The maximum-likelihood (ML) phylogenetic tree indicated that P. flaccidum was closely related to P. cetaceum in Poaceae.

Estimation of Vibration Characteristics of a Space Manipulator From Air Bearing Supported Test Data.

Space manipulators have attracted much attention due to their implications in on-orbit servicing in recent years. Air bearing based support equipment is widely used for ground test to offset the effect of gravity. However, an air bearing support introduces a new problem caused by additional inertial and mass properties. Additional mass and inertial load will influence the dynamics behavior, especially stiffness information and vibration response of the whole ground test system. In this paper, a set of procedures are presented to remove the influence of air bearings and identify the true equivalent joint stiffness and damping from the test data of a motor-braked space manipulator with an air bearing support. First, inertia parameters are identified. Then, the equivalent joint stiffness and damping are determined by using a genetic algorithm (GA) method. Finally, true vibration characteristics of the manipulator are estimated by removing the additional inertia caused by the air bearings. Moreover, simulations and experiments are carried out to validate the presented procedures.

Comparison and impact of COVID-19 for patients with cancer: a survival analysis of fatality rate controlling for age, sex and cancer type.

OBJECTIVES: Prior research has reported an increased risk of fatality for patients with cancer, but most studies investigated the risk by comparing cancer to non-cancer patients among COVID-19 infections, where cancer might have contributed to the increased risk. This study is to understand COVID-19's imposed HR of fatality while controlling for covariates, such as age, sex, metastasis status and cancer type. METHODS: We conducted survival analyses of 4606 cancer patients with COVID-19 test results from 16 March to 11 October 2020 in UK Biobank and estimated the overall HR of fatality with and without COVID-19 infection. We also examined the HRs of 13 specific cancer types with at least 100 patients using a stratified analysis. RESULTS: COVID-19 resulted in an overall HR of 7.76 (95% CI 5.78 to 10.40, p<10-10) by following 4606 patients with cancer for 21 days after the tests. The HR varied among cancer type, with over a 10-fold increase in fatality rate (false discovery rate ≤0.02) for melanoma, haematological malignancies, uterine cancer and kidney cancer. Although COVID-19 imposed a higher risk for localised versus distant metastasis cancers, those of distant metastases yielded higher overall fatality rates due to their multiplicative effects. DISCUSSION: The results confirmed prior reports for the increased risk of fatality for patients with COVID-19 plus hematological malignancies and demonstrated similar findings of COVID-19 on melanoma, uterine, and kidney cancers. CONCLUSION: The results highlight the heightened risk that COVID-19 imposes on localised and haematological cancer patients and the necessity to vaccinate uninfected patients with cancer promptly, particularly for the cancer types most influenced by COVID-19. Results also suggest the importance of timely care for patients with localised cancer, whether they are infected by COVID-19 or not.

High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet.

KEY MESSAGE: Based on the high-density variation map, we identified genome-level evidence for local adaptation and demonstrated that Siprr37 with transposon insertion contributes to the fitness of foxtail millet in the northeastern ecoregion. Adaptation is a robust way through which plants are able to overcome environmental constraints. The mechanisms of adaptation in heterogeneous natural environments are largely unknown. Deciphering the genomic basis of local adaptation will contribute to further improvement in domesticated plants. To this end, we describe a high-depth (19.4 ×) haplotype map of 3.02 million single nucleotide polymorphisms in foxtail millet (Setaria italica) from whole-genome resequencing of 312 accessions. In the genome-wide scan, we identified a set of improvement signals (including the homologous gene of OsIPA1, a key gene controlling ideal plant architecture) related to the geographical adaptation to four ecoregions in China. In particular, based on the genome-wide association analysis results, we identified the contribution of a pseudo-response regulator gene, SiPRR37, to heading date adaptation in foxtail millet. We observed the expression changes of SiPRR37 resulted from a key Tc1-Mariner transposon insertion in the first intron. Positive selection analyses revealed that SiPRR37 mainly contributed to the adaptation of northeastern ecoregions. Taken together, foxtail millet adapted to the northeastern region by regulating the function of SiPRR37, which sheds lights on genome-level evidence for adaptive geographical divergence. Besides, our data provide a nearly complete catalog of genomic variation aiding the identification of functionally important variants.

Comparison of macular structural and vascular changes in neuromyelitis optica spectrum disorder and primary open angle glaucoma: a cross-sectional study.

AIMS: To compare macular structure and vasculature between neuromyelitis optica spectrum disorder (NMOSD) and primary open angle glaucoma (POAG) using optical coherence tomography angiography. METHODS: NMOSD patients (n=124) with/without a history of optic neuritis (ON) (NMO+ON: 113 eyes; NMO-ON: 95 eyes), glaucomatous patients (n=102) with early/advanced glaucoma (G-E: 74 eyes; G-A: 50 eyes) and healthy controls (n=62; 90 eyes) were imaged. The main outcome measures were macular ganglion cell-inner plexiform layer (GC-IPL) thickness, vessel density (VD) and perfusion density (PD) in the superficial capillary plexus, and diagnostic capabilities of the parameters as calculated by area under the curve (AUC). RESULTS: Significant losses in GC-IPL, VD and PD were detected in both patients with NMOSD and POAG. With matched losses in the peripapillary retinal nerve fibre layer, NMOSD group showed significant thinning of GC-IPL in the nasal-superior quadrant, whereas in POAG group, significant thinning was observed in the inferior and temporal-inferior quadrants. GC-IPL thinning was more prominent in the superior, nasal-superior and nasal-inferior quadrants in NMO+ON eyes. In G-A eyes, significant GC-IPL thinning was seen in the temporal-inferior quadrant. The specific structural parameters combining VD and foveal avascular zone (FAZ) indices showed the best diagnostic accuracies. The FAZ area in eyes with NMOSD was significantly smaller than the eyes of healthy controls and POAG. CONCLUSION: NMOSD and POAG have specific patterns of macular structural and vascular changes associated with pathophysiology. Our results indicate that FAZ could be a sensitive biomarker of macular changes in NMOSD.

U-shaped association between plasma sphingosine-1-phosphate levels and mortality in patients with chronic systolic heart failure: a prospective cohort study.

BACKGROUND: The endogenous lipid molecule sphingosine-1-phosphate (S1P) has received attention in the cardiovascular field due to its significant cardioprotective effects, as revealed in animal studies. The purpose of our study was to identify the distribution characteristics of S1P in systolic heart failure patients and the prognostic value of S1P for long-term prognosis. METHODS: We recruited 210 chronic systolic heart failure patients from June 2014 to December 2015. Meanwhile 54 healthy people in the same area were selected as controls. Plasma S1P was measured by liquid chromatography-tandem mass spectrometry. Patients were grouped according to the baseline S1P level quartiles, and restricted cubic spline plots described the association between S1P and all-cause death. Cox proportional hazard analysis was used to determine the relationship between category of S1P and all-cause death. RESULTS: Compared with the control group, the plasma S1P in chronic heart failure patients demonstrated a higher mean level (1.269 µmol/L vs 1.122 µmol/L, P = 0.006) and a larger standard deviation (0.441 vs 0.316, P = 0.022). Based on multivariable Cox regression with restricted cubic spline analysis, a non-linear and U-shaped association between S1P levels and the risk of all-cause death was observed. After a follow-up period of 31.7 ± 10.3 months, the second quartile (0.967-1.192 µml/L) with largely normal S1P levels had the lowest all-cause mortality and either an increase (adjusted HR = 2.368, 95%CI 1.006-5.572, P = 0.048) or a decrease (adjusted HR = 0.041, 95%CI 0.002-0.808, P = 0.036) predicted a worse prognosis. The survival curves showed that patients in the lowest quartile and highest quartile were at a higher risk of death. CONCLUSIONS: Plasma S1P levels in systolic heart failure patients are related to the long-term all-cause mortality with a U-shaped correlation. TRIAL REGISTRATION: CHiCTR, ChiCTR-ONC-14004463. Registered 20 March 2014.

miR-21 promotes growth, invasion and migration of lung cancer cells by AKT/P-AKT/cleaved-caspase 3/MMP-2/MMP-9 signaling pathway.

OBJECTIVE: This study aimed to demonstrate the effects of miR-21 on the growth, migration, and invasion of lung cancer cells A549 in vitro and the possible mechanism. METHODS: In vitro cell migration and invasion potential were determined by Transwell chamber assays. FACS was used to assess the effect of miR-21 on A549 cell cycle and apoptosis. 4-6 week-old female mice were utilized to establish a lung cancer model. The pathologic biopsy was processed by H&E staining. The expression of the proteins PTEN, RECK and Caspase 3 were detected through immunohistochemy and tumor cell apoptosis was measured by TUNEL. RESULTS: Transwell chamber assays showed that the cells going through the membrane increased significantly compared to the negative control (P<0.05). The tumor volume resulting from miR-21 mimics was significantly greater than in normal mice. Serum ELISA showed that the protein expression levels of MMP-2 and MMP-9 in miR-21 overexpression group were increased significantly. In addition, H&E staining results showed that in miR-21 overexpression tissue, invasion is more severe and immunohistochemical results proved that the miR-21 overexpression group had high expression of Caspase 3 protein but the expression of PTEN and RECK were decreased. TUNEL experiments show that increased the expression of miR-21 can inhibit the apoptosis of tumor cells. CONCLUSION: MicroRNA-21 promotes the proliferation of lung cancer cells and inhibits the apoptosis of lung cancer cells by the AKT/P-AKT/cleaved-caspase 3/MMP-2/MMP-9 signaling pathway.

On fusion methods for knowledge discovery from multi-omics datasets.

Recent years have witnessed the tendency of measuring a biological sample on multiple omics scales for a comprehensive understanding of how biological activities on varying levels are perturbed by genetic variants, environments, and their interactions. This new trend raises substantial challenges to data integration and fusion, of which the latter is a specific type of integration that applies a uniform method in a scalable manner, to solve biological problems which the multi-omics measurements target. Fusion-based analysis has advanced rapidly in the past decade, thanks to application drivers and theoretical breakthroughs in mathematics, statistics, and computer science. We will briefly address these methods from methodological and mathematical perspectives and categorize them into three types of approaches: data fusion (a narrowed definition as compared to the general data fusion concept), model fusion, and mixed fusion. We will demonstrate at least one typical example in each specific category to exemplify the characteristics, principles, and applications of the methods in general, as well as discuss the gaps and potential issues for future studies.

Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress.

BACKGROUND: Broomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly understood. The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family that is involved in the regulation of tissue development and abiotic stress. To date, NAC transcription factors have not been systematically researched in broomcorn millet. RESULTS: In the present study, a total of 180 NAC (PmNAC) genes were identified from the broomcorn millet genome and named uniformly according to their chromosomal distribution. Phylogenetic analysis demonstrated that the PmNACs clustered into 12 subgroups, including the broomcorn millet-specific subgroup Pm_NAC. Gene structure and protein motif analyses indicated that closely clustered PmNAC genes were relatively conserved within each subgroup, while genome mapping analysis revealed that the PmNAC genes were unevenly distributed on broomcorn millet chromosomes. Transcriptome analysis revealed that the PmNAC genes differed greatly in expression in various tissues and under different drought stress durations. The expression of 10 selected genes under drought stress was analyzed using quantitative real-time PCR. CONCLUSION: In this study, 180 NAC genes were identified in broomcorn millet, and their phylogenetic relationships, gene structures, protein motifs, chromosomal distribution, duplication, expression patterns in different tissues, and responses to drought stress were studied. These results will be useful for the further study of the functional characteristics of PmNAC genes, particularly with regards to drought resistance.