Integrating a genome-wide association study with transcriptomic analysis to detect genes controlling grain drying rate in maize (Zea may, L.)

Key message Candidate genes on GDR were identified and drying molecular mechanism of grain was explored by integrating genome-wide association with transcriptomic analysis in maize. Abstract Grain drying rate (GDR) is a key determinant of grain moisture (GM) at harvest. Here, a genome-wide association study (GWAS) of 309 inbred maize lines was used to identify single nucleotide polymorphisms (SNPs) associated with drying rates of grain, cobs, and bracts. Out of 217,933 SNPs, seven significant SNPs were repeatedly identified in four environments (P\u3c 10-4). Based on genomic position of significant SNPs, six candidate genes were identified, and one of which (Zm00001d047468) was verified by transcriptomic data between inbred lines with high and low GDR, indicating stable and reliable correlation with GDR. To further detect more genes correlated with GDR and explore drying molecular mechanism of grain, expression profile of all GWAS-identified genes (4,941) detected from different environments, tissues and developmental stage were evaluated by transcriptomic data of six inbred lines with high or low GDR. Results revealed 162 genes exhibit up-regulated expression and another 123 down-regulated in three higher GDR inbred lines. Based on GO enrichment, 162 up-regulated genes were significantly enriched into grain primary metabolic process, nitrogen compound metabolic process and marcromolecule metabolic process (P\u3c 0.05), which indicated grain filling impose notably influence on GDR before and after physiological maturity. Our results lay foundation in accelerating development of higher GDR maize gerplasm through marker-assisted selection and clarifying genetic mechanism of GDR in maize

Genome-wide association study of maize resistance to Pythium aristosporum stalk rot

Stalk rot, a severe and widespread soil-borne disease in maize, globally reduces yield and quality. Recent documentation reveals that Pythium aristosporum has emerged as one of the dominant causal agents of maize stalk rot. However, a previous study of maize stalk rot disease resistance mechanisms and breeding had mainly focused on other pathogens, neglecting P. aristosporum. To mitigate crop loss, resistance breeding is the most economical and effective strategy against this disease. This study involved characterizing resistance in 295 inbred lines using the drilling inoculation method and genotyping them via sequencing. By combining with population structure, disease resistance phenotype, and genome-wide association study (GWAS), we identified 39 significant single-nucleotide polymorphisms (SNPs) associated with P. aristosporum stalk rot resistance by utilizing six statistical methods. Bioinformatics analysis of these SNPs revealed 69 potential resistance genes, among which Zm00001d051313 was finally evaluated for its roles in host defense response to P. aristosporum infection. Through virus-induced gene silencing (VIGS) verification and physiological index determination, we found that transient silencing of Zm00001d051313 promoted P. aristosporum infection, indicating a positive regulatory role of this gene in maize’s antifungal defense mechanism. Therefore, these findings will help advance our current understanding of the underlying mechanisms of maize defense to Pythium stalk rot

Prediction of Fracture Behavior of 6061 Aluminum Alloy Based on GTN Model

To determine the Gurson-Tvergaard-Needleman (GTN)damage model parameters of 6061 aluminum alloy after secondary heat treatment, the uniaxial tensile test was carried out on the aluminum alloy circular arc specimen, and the mechanical properties parameters and the load-displacement curve of aluminum alloy tube were obtained. With the help of the finite element reverse method, scanning electron microscope and a orthogonal test method, the GTN damage model parameters (f0, fN, fC, and fF) were calibrated, and their values were 0.004535, 0.04, 0.1, and 0.2135, respectively. Then the shear specimen and notch specimen were designed to verify the damage model, the results show that the obtained GTN damage model parameters can effectively predict the fracture failure of 6061 aluminum alloy after secondary heat treatment during the tensile process

First report on the QSAR modelling and multistep virtual screening of the inhibitors of nonstructural protein Nsp14 of SARS-CoV-2: Reducing unnecessary chemical synthesis and experimental tests

Corona Virus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a serious threat to human health and life safety. How to effectively prevent and treat COVID-19 is crucial. In this study, we used the inhibitors of nonstructural protein Nsp14 of SARS-CoV-2 to perform the quantitative structure activity relationship (QSAR) modelling for the first time. Based on different dataset division strategies, we selected partial least square (PLS) and multiple linear regression (MLR) methods to develop easily interpretable and reproducible QSAR models with 2D molecular descriptors. All models complied with the strict QSAR validation principles of OECD and internationally recognized validation metrics. The best model contained two molecular descriptors with the following statistical parameters: R2 = 0.7796, QLOO2= 0.7373, Rtest2 = 0.8539 and CCCtest = 0.9073. Obviously, the model exhibited good prediction performance and can be used for quickly predicting the inhibitory activity of unknown compounds against Nsp14. Mechanistic interpretation identified the detailed relationship between molecular structure information and inhibitory activity. The best QSAR model was used to predict the inhibitory activity of 263 true external compounds without experimental values against Nsp14, and the prediction reliability was analyzed and discussed. Molecular docking and ADMET analyses were conducted for compounds with higher similarity to the modelling compounds. Finally, two compounds were identified as potential candidate drugs of targeting Nsp14. The current work lays a solid theoretical foundation for the discovery of inhibitors targeting Nsp14, and has an important reference significance for the development of anti-COVID-19 drugs

Integrating a genome-wide association study with transcriptomic analysis to detect genes controlling grain drying rate in maize (Zea may, L.)

Key message Candidate genes on GDR were identified and drying molecular mechanism of grain was explored by integrating genome-wide association with transcriptomic analysis in maize. Abstract Grain drying rate (GDR) is a key determinant of grain moisture (GM) at harvest. Here, a genome-wide association study (GWAS) of 309 inbred maize lines was used to identify single nucleotide polymorphisms (SNPs) associated with drying rates of grain, cobs, and bracts. Out of 217,933 SNPs, seven significant SNPs were repeatedly identified in four environments (PThis is a manuscript of an article published as Jia, Tengjiao, Lifeng Wang, Jingjing Li, Juan Ma, Yanyong Cao, Thomas Lübberstedt, and Huiyong Li. "Integrating a genome-wide association study with transcriptomic analysis to detect genes controlling grain drying rate in maize (Zea may, L.)." Theoretical and Applied Genetics (2019). doi: 10.1007/s00122-019-03492-0. Posted with permission.</p

Study of Trivalent Chromium Conversion Coating Formation at Solution—Metal Interface

The present study employed a tungsten pH microelectrode to study the formation of trivalent chromium conversion (TCC) coatings on Al, AA 2024-T3 aluminum alloy and AZ91D magnesium alloy in SurTec ChromitAL solutions. The tungsten microelectrode had a sensitivity of –60 mV/pH in the SurTec ChromitAL solutions. The peak and final pH values for pre-treated Al, AA 2024 alloy and AZ91D alloy were 4.9 and 3.5, 4.3 and 4.1, 4.7 and 3.5, respectively. The initial pH value is of great importance in influencing coating deposition-driven force and final coating thickness. In addition, the time to attain the peak values was 10, 100 and 20 s for Al, AA 2024 alloy and AZ91D alloy, respectively. The interfacial pH evolution is associated with the hydrolysis process of the weak acid nature of zirconium and chromium salts as the main components of TCC coating solutions. Raman spectra revealed the presence of chromium and zirconium oxides and sulphate in the solution deposits from in-house Cr/Zr and SurTec ChromitAL solutions

Table_1_Genome-wide association study of maize resistance to Pythium aristosporum stalk rot.xlsx

Stalk rot, a severe and widespread soil-borne disease in maize, globally reduces yield and quality. Recent documentation reveals that Pythium aristosporum has emerged as one of the dominant causal agents of maize stalk rot. However, a previous study of maize stalk rot disease resistance mechanisms and breeding had mainly focused on other pathogens, neglecting P. aristosporum. To mitigate crop loss, resistance breeding is the most economical and effective strategy against this disease. This study involved characterizing resistance in 295 inbred lines using the drilling inoculation method and genotyping them via sequencing. By combining with population structure, disease resistance phenotype, and genome-wide association study (GWAS), we identified 39 significant single-nucleotide polymorphisms (SNPs) associated with P. aristosporum stalk rot resistance by utilizing six statistical methods. Bioinformatics analysis of these SNPs revealed 69 potential resistance genes, among which Zm00001d051313 was finally evaluated for its roles in host defense response to P. aristosporum infection. Through virus-induced gene silencing (VIGS) verification and physiological index determination, we found that transient silencing of Zm00001d051313 promoted P. aristosporum infection, indicating a positive regulatory role of this gene in maize’s antifungal defense mechanism. Therefore, these findings will help advance our current understanding of the underlying mechanisms of maize defense to Pythium stalk rot.</p

DataSheet_1_Genome-wide association study of maize resistance to Pythium aristosporum stalk rot.pdf

Stalk rot, a severe and widespread soil-borne disease in maize, globally reduces yield and quality. Recent documentation reveals that Pythium aristosporum has emerged as one of the dominant causal agents of maize stalk rot. However, a previous study of maize stalk rot disease resistance mechanisms and breeding had mainly focused on other pathogens, neglecting P. aristosporum. To mitigate crop loss, resistance breeding is the most economical and effective strategy against this disease. This study involved characterizing resistance in 295 inbred lines using the drilling inoculation method and genotyping them via sequencing. By combining with population structure, disease resistance phenotype, and genome-wide association study (GWAS), we identified 39 significant single-nucleotide polymorphisms (SNPs) associated with P. aristosporum stalk rot resistance by utilizing six statistical methods. Bioinformatics analysis of these SNPs revealed 69 potential resistance genes, among which Zm00001d051313 was finally evaluated for its roles in host defense response to P. aristosporum infection. Through virus-induced gene silencing (VIGS) verification and physiological index determination, we found that transient silencing of Zm00001d051313 promoted P. aristosporum infection, indicating a positive regulatory role of this gene in maize’s antifungal defense mechanism. Therefore, these findings will help advance our current understanding of the underlying mechanisms of maize defense to Pythium stalk rot.</p