Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose pathway in tomato.

Tomato (Solanum lycopersicum) is one of the highest-value vegetable crops worldwide. Understanding the genetic regulation of primary metabolite levels can inform efforts aimed toward improving the nutrition of commercial tomato cultivars, while maintaining key traits such as yield and stress tolerance. We identified 388 suggestive association loci (including 126 significant loci) for 92 metabolic traits including nutrition and flavor-related loci by genome-wide association study from 302 accessions in two different environments. Among them, an ascorbate quantitative trait locus TFA9 (TOMATO FRUIT ASCORBATEON CHROMOSOME 9) co-localized with SlbHLH59, which promotes high ascorbate accumulation by directly binding to the promoter of structural genes involved in the D-mannose/L-galactose pathway. The causal mutation of TFA9 is an 8-bp InDel, named InDel_8, located in the promoter region of SlbHLH59 and spanned a 5'UTR Py-rich stretch motif affecting its expression. Phylogenetic analysis revealed that differentially expressed SlbHLH59 alleles were selected during tomato domestication. Our results provide a dramatic illustration of how ascorbate biosynthesis can be regulated and was selected during the domestication of tomato. Furthermore, the findings provide novel genetic insights into natural variation of metabolites in tomato fruit, and will promote efficient utilization of metabolite traits in tomato improvement.

Rapid quantification of goat milk adulteration with cow milk using Raman spectroscopy and chemometrics.

As goat milk has a higher economic value compared to cow milk, the phenomenon of adulterating goat milk with cow milk appears in the market. In this study, the potential of Raman spectroscopy along with chemometrics was investigated for the authentication and quantitation of liquid goat milk adulterated with cow milk. First, the results of principal component analysis (PCA) showed that there were differences between the Raman spectra of cow and goat milk, which made quantitative experiments possible. For quantification, three different brands of cow milk and goat milk were selected randomly and adulterated goat milk with cow milk at the proportion of 5-95%. 342 samples were used for the construction of the partial least squares regression (PLSR) model with 80% for the calibration set and 20% for the prediction set. The PLSR model showed excellent performance in quantifying the level of adulteration, for the prediction set, with a coefficient of determination (R2) of 0.9781, root mean square error (RMSE) of 3.82%, and a ratio of prediction to deviation (RPD) of 6.8. The results demonstrated the potential of Raman spectroscopy as a rapid, low cost and non-destructive analytical tool for detecting adulteration in goat milk.

Rapid quantification of the adulteration of pomegranate juices by Raman spectroscopy and chemometrics.

The juice drink industry has repeatedly been exposed to adulteration. Unscrupulous producers, for example, use cheap juice for substitution in the pursuit of more significant economic benefits, which presents a tremendous challenge for the control of the quality of drinks. The objective of this study was to apply Raman spectroscopy combined with chemometrics to rapidly quantify the adulteration concentration of apple juice or grape juice in pomegranate juice. Two supervised learning algorithms: partial least squares regression (PLSR) and support vector machine regression (SVR) were used to analyze the Raman spectra of 114 samples. The coefficient of determination (R2), root mean square error (RMSE), and residual prediction deviation (RPD) of the prediction set when using PLSR and SVR to predict the adulterated concentration of apple juice in pomegranate juice were 0.9357 and 0.9465, 6.446% and 5.974%, 3.945 and 4.322, respectively. The R2, RMSE, and RPD of the prediction set when using PLSR and SVR to predict the adulteration concentration of grape juice in pomegranate juice were 0.9501 and 0.9502, 6.334% and 5.571%, and 4.475 and 4.481, respectively. It was concluded that Raman spectroscopy combined with chemometrics has excellent potential for application as a rapid quantitative method to detect adulterated concentrations of pomegranate juice.

SlGH3.15, a member of the GH3 gene family, regulates lateral root development and gravitropism response by modulating auxin homeostasis in tomato.

Multiple Gretchen Hagen 3 (GH3) genes have been implicated in a range of processes in plant growth and development through their roles in maintaining hormonal homeostasis. However, there has only been limited study on the functions of GH3 genes in tomato (Solanum lycopersicum). In this work, we investigated the important function of SlGH3.15, a member of the GH3 gene family in tomato. Overexpression of SlGH3.15 led to severe dwarfism in both the above- and below-ground sections of the plant, accompanied by a substantial decrease in free IAA content and reduction in the expression of SlGH3.9, a paralog of SlGH3.15. Exogenous supply of IAA negatively affected the elongation of the primary root and partially restored the gravitropism defects in SlGH3.15-overexpression lines. While no phenotypic change was observed in the SlGH3.15 RNAi lines, double knockout lines of SlGH3.15 and SlGH3.9 were less sensitive to treatments with the auxin polar transport inhibitor. Overall, these findings revealed important roles of SlGH3.15 in IAA homeostasis and as a negative regulator of free IAA accumulation and lateral root formation in tomato.

Case Report: Metagenomic Next-Generation Sequencing Clinches the Diagnosis of Acute Q Fever and Verified by Indirect Immunofluorescence Assay.

Q fever is a zoonotic infectious disease caused by Coxiella burnetii. The clinical symptoms of acute Q fever are usually atypical, and routine serological tests of C. burnetii are not readily available, making the diagnosis of Q fever a challenge. In this case, we report a male patient who had repeated fevers and was administered empirical anti-infective treatment, but the effect was poor. After conducting relevant laboratory and imagological examinations, the etiology has not yet been confirmed. Subsequently, metagenomic next-generation sequencing (mNGS) identified the sequence reads of C. burnetii from the patient's peripheral blood within 48 h, and then the diagnosis of acute Q fever was established. Moreover, the serological test of indirect immunofluorescence assay (IFA) of the C. burnetii antibody was further performed in the Centers for Disease Control, certifying the result of mNGS. The patient was ultimately treated with doxycycline and recovered well. mNGS is an unbiased and comprehensive method in infrequent or culture-negative pathogen identification. To our knowledge, this is the first case of acute Q fever identified by mNGS and confirmed by IFA in Taizhou, China. A further large-scale prospective clinical cohort study is worth carrying out to compare the diagnostic efficiency of mNGS with traditional serological methods and PCR in acute Q fever.

Genome-Wide Identification and Molecular Characterization of the Growth-Regulating Factors-Interacting Factor Gene Family in Tomato.

Growth-regulating factors-interacting factor (GIF) proteins play crucial roles in the regulation of plant growth and development. However, the molecular mechanism of GIF proteins in tomato is poorly understood. Here, four SlGIF genes (named SlGRF1a, SlGIF1b, SlGIF2, and SlGIF3) were identified from the tomato genome and clustered into two major clades by phylogenetic analysis. The gene structure and motif pattern analyses showed similar exon/intron patterns and motif organizations in all the SlGIFs. We identified 33 cis-acting regulatory elements (CAREs) in the promoter regions of the SlGIFs. The expression profiling revealed the four GIFs are expressed in various tissues and stages of fruit development and induced by phytohormones (IAA and GA). The subcellular localization assays showed all four GIFs were located in nucleus. The yeast two-hybrid assay indicated various growth-regulating factors (SlGRFs) proteins interacted with the four SlGIF proteins. However, SlGRF4 was a common interactor with the SlGIF proteins. Moreover, a higher co-expression relationship was shown between three SlGIF genes and five SlGRF genes. The protein association network analysis found a chromodomain helicase DNA-binding protein (CHD) and an actin-like protein to be associated with the four SlGIF proteins. Overall, these results will improve our understanding of the potential functions of GIF genes and act as a base for further functional studies on GIFs in tomato growth and development.