Sauce-flavor baijiu is a popular Chinese baijiu. To avoid adulteration and market cheating, this study aims to develop a new, reliable, and accurate traceability system for characterization of the geographical origins. Totally, 100 samples collected from seven regions in Guizhou Province of China are analyzed, involving 13 trace elements, 5 organic acids, and stable carbon isotope composition of acetic acid. Based on these data, a geographical classification model is established. The origin accuracy is found to reach as high as 83%, thus providing a useful technique for authentication of the sauce-flavor baijiu and contributing to the healthy development of the baijiu industry in China.

DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation, development, and evolution. However, the dynamics of cytonuclear interaction during crop domestication have still been rarely investigated. Here, we examine cytonuclear interactions during grapevine domestication using pan‐mitogenome, pan‐plastome, and haplotype‐resolved nuclear genomes, all assembled from long‐read sequences across 33 wild and domesticated grapevine accessions. Structural variation shaped the mitogenomic variation in gene contents, leading to duplications of three specific genes during grapevine domestication (one cox and two rpl genes). Extensive genomic signals of cytonuclear interactions were detected, including a total of 212–431 nuclear–mitochondrial segments (NUMTs) and 95–205 nuclear–plastid segments (NUPTs). These results showed that NUMTs were under strong selection and were more abundant in cultivated grapes, whereas NUPTs dominated in wild grapes, indicating the evolutionary trajectories of cytonuclear interactions during grape domestication. Through Genome‐Wide Association Study (GWAS), we identified 84 candidate genes associated with mitochondrial–nuclear genome interactions. Among these, the PFD1 gene acts as a signaling regulator, modulating specific signaling pathways regulated by the mitochondria. Interestingly, there are significantly more cytonuclear interaction genes near NUMTs than in other genomic regions, suggesting NUMT‐mediated interactions between the nuclear and mitochondrial genomes. Overall, our study provides evidence that NUMTs promote cytonuclear interaction during grapevine domestication, offering new insight into the impact of cytonuclear interactions on plant evolution, genetics, and breeding.

Munage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is renowned for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate the origin, private mutations and selection in Munage. Our analyses suggest that Munage likely shares a common ancestor with Eurasian grapes that originated in West Asia. Selective analysis between Munage clones and Eurasian grapes mapped genomic signals of selection in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. We also identified 283 somatic mutation sites between WM and RM, along with differential selection on genome and expressed genes. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine using this ancient cultivar as a gene donor.

Simultaneously verifying the original region of green and roasted coffee beans is very important for protecting legal interests of the stakeholder according to the chemical analyzing method. 131 green coffee bean samples are collected from six different original regions and pretreated with three degrees (green, middle, and dark roasted); five stable isotope ratios (δ¹³C, δ¹⁴N, δ¹⁸O, δ²H, and δ³²S) and twelve elemental contents (Al, Cr, Ni, Zn, Ba, Cu, Na, Mn, Fe, Ca, K, and Mg) of green, middle, and dark roasted coffee bean samples (131×3) were analyzed. Fractionation of stable isotopes and variation of elemental contents were evaluated, only isotope hydrogen (²H) significantly fractionated, and elemental concentrations increased with a certain rate during the roasting process. One-way analysis of variance (ANOVA) was used to compare the stable isotope ratios and elemental concentrations of all coffee bean samples from six different original regions. Random forest (RF) was employed to build a discriminating model for simultaneously verifying the original regions of green and roasted coffee bean samples; this model provided 100 accuracy. Inclusion of this mathematical model for simultaneously verifying the original region of green and roasted coffee beans had powerful distinguishing capability and which will not be influenced by fractionation of hydrogen (²H) and variation of element contents during the roasted process.

Developing a robust and reliable geographical origin discrimination model, unaffected by grape varieties, wine types, or the scale and distance of the wine‐growing area, is essential for the sustainable growth of China’s wine industry. A total of 967 wine samples were collected from 10 original regions in China, and 27 elemental profiles and two stable isotope ratios were determined by ICP‐MS and IRMS, respectively. PCA was used to evaluate the contributions of 29 regional markers in classifying the geographical regions of Chinese wine. Six chemometric methods were employed, including PCA, PLS‐DA, RF, ANN, SVM, and R‐Part, to verify the regions and subregions of Chinese wine. This study successfully proposed advanced simultaneous classification models for original regions and subregions of Chinese wine using multielements and stable ratios combined with random forest (100% accuracy) for the first time.

Introduction: Grape is of high economic value. Colletotrichum viniferum, a pathogen causing grape ripe rot and leaf spot, threatens grape production and quality.Methods: This study investigates the interplay between C. viniferum by Cytological study and transcriptome sequencing.Results: Different grapevine germplasms, V. vinifera cv. Thompson Seedless (TS), V. labrusca accession Beaumont (B) and V. piasezkii Liuba-8 (LB-8) were classified as highly sensitive, moderate resistant and resistant to C. viniferum, respectively. Cytological study analysis reveals distinct differences between susceptible and resistant grapes post-inoculation, including faster pathogen development, longer germination tubes, normal appressoria of C. viniferum and absence of white secretions in the susceptible host grapevine. To understand the pathogenic mechanisms of C. viniferum, transcriptome sequencing was performed on the susceptible grapevine “TS” identifying 236 differentially expressed C. viniferum genes. These included 56 effectors, 36 carbohydrate genes, 5 P450 genes, and 10 genes involved in secondary metabolism. Fungal effectors are known as pivotal pathogenic factors that modulate plant immunity and affect disease development. Agrobacterium-mediated transient transformation in Nicotiana benthamiana screened 10 effectors (CvA13877, CvA01508, CvA05621, CvA00229, CvA07043, CvA05569, CvA12648, CvA02698, CvA14071 and CvA10999) that inhibited INF1 (infestans 1, P. infestans PAMP elicitor) induced cell death and 2 effectors (CvA02641 and CvA11478) that induced cell death. Additionally, transcriptome analysis of “TS” in response to C. viniferum identified differentially expressed grape genes related to plant hormone signaling (TGA, PR1, ETR, and ERF1/2), resveratrol biosynthesis genes (STS), phenylpropanoid biosynthesis genes (PAL and COMT), photosynthetic antenna proteins (Lhca and Lhcb), transcription factors (WRKY, NAC, MYB, ERF, GATA, bHLH and SBP), ROS (reactive oxygen species) clearance genes (CAT, GSH, POD and SOD), and disease-related genes (LRR, RPS2 and GST).Discussion: This study highlights the potential functional diversity of C. viniferum effectors. Our findings lay a foundation for further research of infection mechanisms in Colletotrichum and identification of disease response targets in grape.