The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine

The wild side of grape genomics

With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture's climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species' adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement.

DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages

Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.

The Genome of Vitis zhejiang-adstricta Strengthens the Protection and Utilization of the Endangered Ancient Grape Endemic to China

Vitis zhejiang-adstricta (V. zhejiang-adstricta) is one of the most important and endangered wild grapes. It is a national key protected wild, rare and endangered ancient grape endemic to China and used as a candidate material for resistance breeding owing to its excellent significant disease resistance. Here, we present a high-quality chromosome-level assembly of V. zhejiang-adstricta (IB-VB-01), comprising 506.66 Mb assembled into 19 pseudo-chromosomes. The contig N50 length is 3.91 Mb with 31,196 annotated protein-coding genes. Comparative genome and evolutionary analyses illustrated that V. zhejiang-adstricta has a specific position in the evolution of East Asian Vitis and shared a common ancestor with Vitis vinifera during the divergence of the two species about 10.42 (between 9.34 and 11.12) Mya. The expanded gene families compared with those in plants were related to disease resistance, and constructed gene families were related to plant growth and primary metabolism. With the analysis of gene family expansion and contraction, the evolution of environmental adaptability and especially the NBS-LRR gene family of V. zhejiang-adstricta was elucidated based on the pathways of resistance genes (R genes), unique genes and structural variations. The near-complete and accurate diploid V. zhejiang-adstricta reference genome obtained herein serves as an important complement to wild grape genomes and will provide valuable genomic resources for investigating the genomic architecture of V. zhejiang-adstricta as well as for improving disease resistance breeding strategies in grape.

Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics

Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.

Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.

Polyploidization and genomic selection integration for grapevine breeding: a perspective

Grapevines are economically important woody perennial crops widely cultivated for their fruits that are used for making wine, grape juice, raisins, and table grapes. However, grapevine production is constantly facing challenges due to climate change and the prevalence of pests and diseases, causing yield reduction, lower fruit quality, and financial losses. To ease the burden, continuous crop improvement to develop superior grape genotypes with desirable traits is imperative. Polyploidization has emerged as a promising tool to generate genotypes with novel genetic combinations that can confer desirable traits such as enhanced organ size, improved fruit quality, and increased resistance to both biotic and abiotic stresses. While previous studies have shown high polyploid induction rates in Vitis spp., rigorous screening of genotypes among the produced polyploids to identify those exhibiting desired traits remains a major bottleneck. In this perspective, we propose the integration of the genomic selection approach with omics data to predict genotypes with desirable traits among the vast unique individuals generated through polyploidization. This integrated approach can be a powerful tool for accelerating the breeding of grapevines to develop novel and improved grapevine varieties.

Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding

In woody perennial plants, quantitative genetics and association studies remain scarce for root-related traits, due to the time required to obtain mature plants and the complexity of phenotyping. In grapevine, a grafted cultivated plant, most of the rootstocks used are hybrids between American Vitis species (V. rupestris, V. riparia, and V. berlandieri). In this study, we used a wild population of an American Vitis species (V. berlandieri) to analyze the genetic architecture of the root-related traits of rootstocks in a grafted context. We studied a population consisting of 211 genotypes, with one to five replicates each (n = 846 individuals), plus four commercial rootstocks as control genotypes (110R, 5BB, Börner, and SO4). After two independent years of experimentation, the best linear unbiased estimates method revealed root-related traits with a moderate-to-high heritability (0.36-0.82) and coefficient of genetic variation (0.15-0.45). A genome-wide association study was performed with the BLINK model, leading to the detection of 11 QTL associated with four root-related traits (one QTL was associated with the total number of roots, four were associated with the number of small roots (< 1 mm in diameter), two were associated with the number of medium-sized roots (1 mm < diameter < 2 mm), and four were associated with mean diameter) accounting for up to 25.1% of the variance. Three genotypes were found to have better root-related trait performances than the commercial rootstocks and therefore constitute possible new candidates for use in grapevine rootstock breeding programs.

Genome-Wide Identification and Analysis of the Genes Encoding Q-Type C2H2 Zinc Finger Proteins in Grapevine

Q-type C2H2 zinc finger proteins (ZFPs), the largest family of transcription factors, have been extensively studied in plant genomes. However, the genes encoding this transcription factor family have not been explored in grapevine genomes. Therefore, in this study, we conducted a genome-wide identification of ZFP genes in three species of grapevine, namely Vitis vinifera, Vitis riparia, and Vitis amurensis, based on the sequence databases and phylogenetic and their conserved domains. We identified 52, 54, and 55 members of Q-type C2H2 ZFPs in V. vinifera, V. riparia, and V. amurensis, respectively. The physical and chemical properties of VvZFPs, VrZFPs, and VaZFPs were examined. The results showed that these proteins exhibited differences in the physical and chemical properties and that they all were hydrophobic proteins; the instability index showed that the four proteins were stable. The subcellular location of the ZFPs in the grapevine was predicted mainly in the nucleus. The phylogenetic tree analysis of the amino acid sequences of VvZFP, VaZFP, VrZFP, and AtZFP proteins showed that they were closely related and were divided into six subgroups. Chromosome mapping analysis showed that VvZFPs, VrZFPs, and VaZFPs were unevenly distributed on different chromosomes. The clustered gene analysis showed that the motif distribution was similar and the sequence of genes was highly conserved. Exon and intron structure analysis showed that 118 genes of ZFPs were intron deletion types, and the remaining genes had variable numbers of introns, ranging from 2 to 15. Cis-element analysis showed that the promoter of VvZFPs contained multiple cis-elements related to plant hormone response, stress resistance, and growth, among which the stress resistance elements were the predominant elements. Finally, the expression of VvZFP genes was determined using real-time quantitative PCR, which confirmed that the identified genes were involved in response to methyl jasmonate (MeJA), abscisic acid (ABA), salicylic acid (SA), and low-temperature (4 °C) stress. VvZFP10-GFP and VvZFP46-GFP fusion proteins were localized in the nucleus of tobacco cells, and VvZFP10 is the most responsive gene among all VvZFPs with the highest relative expression level to MeJA, ABA, SA and low-temperature (4 °C) stress. The present study provides a theoretical basis for exploring the mechanism of response to exogenous hormones and low-temperature tolerance in grapes and its molecular breeding in the future.

Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes

Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.

Hybrid Vitis Cultivars with American or Asian Ancestries Show Higher Tolerance towards Grapevine Trunk Diseases

Grape production worldwide is increasingly threatened by grapevine trunk diseases (GTDs). No grapevine cultivar is known to be entirely resistant to GTDs, but susceptibility varies greatly. To quantify these differences, four Hungarian grape germplasm collections containing 305 different cultivars were surveyed to determine the ratios of GTDs based on symptom expression and the proportion of plant loss within all GTD symptoms. The cultivars of monophyletic Vitis vinifera L. origin were amongst the most sensitive ones, and their sensitivity was significantly (p < 0.01) higher than that of the interspecific (hybrid) cultivars assessed, which are defined by the presence of Vitis species other than V. vinifera (e.g., V. labrusca L., V. rupestris Scheele, and V. amurensis Rupr.) in their pedigree. We conclude that the ancestral diversity of grapes confers a higher degree of resilience against GTDs.

The transcription factor VaNAC72-regulated expression of the VaCP17 gene from Chinese wild Vitis amurensis enhances cold tolerance in transgenic grape (V. vinifera)

Papain-like cysteine proteases (PLCP) play diverse roles in plant biology. In our previous studies, a VaCP17 gene from the cold-tolerant Vitis amurensis accession 'Shuangyou' was isolated and its role in cold tolerance was preliminarily verified in Arabidopsis. Here, we confirmed the function of VaCP17 in cold tolerance by stably overexpressing VaCP17 in the cold-sensitive Vitis vinifera cultivar 'Thompson Seedless' and transiently silencing VaCP17 in 'Shuangyou' leaves. The results showed that overexpression of VaCP17 improved the cold tolerance in 'Thompson Seedless' as manifested by reduced electrolyte leakage and malondialdehyde accumulation, chlorophyll homeostasis, increased antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) activitiy, and rapid up-regulation of stress-related genes (VvKIN2, VvRD29B, and VvNCED1) compared with wild-type line. Conversely, RNA interfere-mediated knockdown of VaCP17 in 'Shuangyou' leaves resulted in opposite physiological and biochemical responses and exacerbated leaves wilting compared with control. Subsequently, by yeast one-hybrid, dual-luciferase assays, and transient overexpression of VaNAC72 in 'Shuangyou' leaves, a VaCP17-interacting protein VaNAC72 was confirmed to promote the expression of VaCP17 under cold stress, which depends on abscisic acid, methyl jasmonate, and salicylic acid signaling. By yeast two-hybrids, bimolecular fluorescence complementation and luciferase complementation assays, it was found that VaNAC72 could form homodimers or heterodimers with VaCBF2. Furthermore, co-expression analysis confirmed that VaNAC72 works synergistically with VaCBF2 or VaCP17 to up-regulate the expression of VaCP17. In conclusion, the study revealed that the VaNAC72-VaCP17 module positively regulated cold tolerance in grapevine, and this knowledge is useful for further revealing the cold-tolerance mechanism of V. amurensis and grape molecular breeding.

Discovery and genome-guided mapping of REN12 from Vitis amurensis, conferring strong, rapid resistance to grapevine powdery mildew

Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis. Here, a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis 'PI 588631' that rapidly stopped over 97% of Erysiphe necator conidia, before or immediately after emergence of a secondary hypha from appressoria. This resistance was effective across multiple years of vineyard evaluation on leaves, stems, rachises, and fruit and against a diverse array of E. necator laboratory isolates. Using core genome rhAmpSeq markers, resistance mapped to a single dominant locus (here named REN12) on chromosome 13 near 22.8-27.0 Mb, irrespective of tissue type, explaining up to 86.9% of the phenotypic variation observed on leaves. Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region, from 25.15 to 25.93 Mb. RNASeq analysis indicated the allele-specific expression of four resistance genes (NLRs) from the resistant parent. REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented, and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms. While no virulent isolates were identified among the genetically diverse isolates and wild populations of E. necator tested here, NLR loci like REN12 are often race-specific. Thus, stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90% reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.

Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)

Walnut (Juglans) species are used as nut crops worldwide. Eastern black walnut (EBW, Juglans nigra), a diploid, horticultural important woody species is native to much of eastern North America. Although it is highly valued for its wood and nut, there are few resources for understanding EBW genetics. Here, we present a high-quality genome assembly of J. nigra based on Illumina, Pacbio, and Hi-C technologies. The genome size was 540.8 Mb, with a scaffold N50 size of 35.1 Mb, and 99.0% of the assembly was anchored to 16 chromosomes. Using this genome as a reference, the resequencing of 74 accessions revealed the effective population size of J. nigra declined during the glacial maximum. A single whole-genome duplication event was identified in the J. nigra genome. Large syntenic blocks among J. nigra, Juglans regia, and Juglans microcarpa predominated, but inversions of more than 600 kb were identified. By comparing the EBW genome with those of J. regia and J. microcarpa, we detected InDel sizes of 34.9 Mb in J. regia and 18.3 Mb in J. microcarpa, respectively. Transcriptomic analysis of differentially expressed genes identified five presumed NBS-LRR (NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT) genes were upregulated during the development of walnut husks and shells compared to developing embryos. We also identified candidate genes with essential roles in seed oil synthesis, including FAD (FATTY ACID DESATURASE) and OLE (OLEOSIN). Our work advances the understanding of fatty acid bioaccumulation and disease resistance in nut crops, and also provides an essential resource for conducting genomics-enabled breeding in walnut.

Variations of freezing tolerance and sugar concentrations of grape buds in response to foliar application of abscisic acid

The purpose of this study was to explore the mechanism of ABA-induced freezing tolerance increase in grapevines. The specific objectives were to evaluate the impact of ABA treatment on soluble sugar concentration in grape buds and determine the correlations between freezing tolerance and ABA-affected soluble sugar concentration. Vitis spp 'Chambourcin' and Vitis vinifera 'Cabernet franc' were treated with 400 and 600 mg/L ABA in the greenhouse and field. The freezing tolerance and soluble sugar concentration of grape buds were measured monthly during the dormant season in the field and at 2wk, 4wk, and 6wk after ABA application in the greenhouse. It was observed that fructose, glucose, and sucrose are the main soluble sugars that correlate with freezing tolerance of grape buds and the synthesis of these sugars can be enhanced by ABA treatment. This study also found that ABA application can promote raffinose accumulation, however, this sugar may play a more important role in the early acclimation stage. The preliminary results suggest that raffinose accumulated first in buds, then its decrease in mid-winter corresponded with the increase of smaller sugars, such as sucrose, fructose, and glucose, which in turn, corresponded with reaching maximum freezing tolerance. It is concluded that ABA is a cultural practice tool that can be used to enhance freezing tolerance of grapevines.

Advances in understanding cold tolerance in grapevine

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.

Miniature Noninvasive Sensor Based on Impedance-Change Detection in Branches for Measuring Branch Ice Content in Overwintering Woody Plants

Advancements in detection instruments have enabled the real-time acquisition of water information during plant growth; however, the real-time monitoring of freeze-thaw information during plant overwintering remains a challenge. Based on the relationship between the change in the water-ice ratio and branch impedance during freezing, a miniature noninvasive branch volume ice content (BVIC) sensor was developed for monitoring real-time changes in volumetric ice content and the ice freeze-thaw rate of woody plant branches during the overwintering period. The results of the performance analysis of the impedance measurement circuit show that the circuit has a lateral sensitivity range, measurement range, resolution, measurement accuracy, and power consumption of 0-35 mm, 0-100%, 0.05%, ±1.76%, and 0.25 W, respectively. The dynamic response time was 0.296 s. The maximum allowable error by the output voltage fluctuation, owing to the ambient temperature and humidity, was only ±0.635%, which meets the actual use requirements. The calibration curve fit coefficients were >0.98, indicating a significant correlation. The ice content of plant branches under cold stress was measured for indoor and field environments, and the sensors could effectively monitor changes in the branch ice content in plants exposed to cold stress. Additionally, they can differentiate between plants with different cold resistances, indicating the reliability of the BVIC sensor.

Comparative Transcriptome Analysis Reveals OsBGs and OsGSLs Influence Sugar Transport through Callose Metabolism under Heat Stress in Rice

Heat or high temperature stress have caused huge damage to many crops and have become the largest threat in terms of the future. Although a huge amount of research has been conducted to explore the mechanisms of heat tolerance and many achievements were accomplished, the mechanism by which how heat stress (HS) influences the yield is still unclear. In this study, RNA-seq analysis indicated that nine 1,3-β-glucanases (BGs) belonging to the carbohydrate metabolic pathway were expressed differently during heat treatment. Therefore, we identified the BGs and glucan-synthase-likes (GSLs) in three rice ecotypes and processed the analyses of gene gain and loss, phylogenetic relationship, duplication, and syntenic relationship. We found the possibility of an environmental adaption based on BGs and GSLs during evolution. Submicrostructure and dry matter distribution analysis confirmed that HS might block the endoplasmic sugar transport pathway by increasing callose synthesis, which may lead to decreased yield and quality in rice production. This study provides a new clue regarding rice yield and quality under HS and provides guidance to rice cultivation and heat tolerance breeding.

VabHLH137 promotes proanthocyanidin and anthocyanin biosynthesis and enhances resistance to Colletotrichum gloeosporioides in grapevine

Proanthocyanidins (PAs) and anthocyanins are involved in the response of plants to various environmental stresses. However, the mechanism behind defense-induced PA biosynthetic regulation is still not completely elucidated, also in grapevine. This study performed a transcriptome sequencing analysis of grape berries infected with Colletotrichum gloeosporioides to highlight the induction of the VabHLH137 factor from the basic helix-loop-helix (bHLH) XII subfamily by the fungus, which appeared to be significantly co-expressed with PA-related genes. The functional analysis of VabHLH137 overexpression and knockdown in transgenic grape calli showed that it positively regulated PA and anthocyanin biosynthesis. Moreover, VabHLH137 overexpression in the grape calli significantly increased resistance to C. gloeosporioides. A yeast one-hybrid and electrophoretic mobility shift assay revealed that VabHLH137 directly bound to the VaLAR2 promoter, enhancing its activity and interacting with VaMYBPAR, a transcriptional activator of PA biosynthesis. Furthermore, transient experiments showed that although the VabHLH137 + VaMYBPAR complex activated VaLAR2 expression, it failed to further enhance VaLAR2 expression compared to VaMYBPAR alone. The findings indicated that VabHLH137 enhanced PA biosynthesis by activating of VaLAR2 expression, providing new insight into the transcriptional regulation of defense-induced PA biosynthesis in grapevine.

Review: Status and prospects of association mapping in grapevine

Thanks to current advances in sequencing technologies, novel bioinformatics tools, and efficient modeling solutions, association mapping has become a widely accepted approach to unravel the link between genotype and phenotype diversity in numerous crops. In grapevine, this strategy has been used in the last decades to understand the genetic basis of traits of agronomic interest (fruit quality, crop yield, biotic and abiotic resistance), of special relevance nowadays to improve crop resilience to cope with future climate scenarios. Genome-wide association studies have identified many putative causative loci for different traits, some of them overlapping well-known causal genes identified by conventional quantitative trait loci studies in biparental progenies, and/or validated by functional approaches. In addition, candidate-gene association studies have been useful to pinpoint the causal mutation underlying phenotypic variation for several traits of high interest in breeding programs (like berry color, seedlessness, and muscat flavor), information that has been used to develop highly informative and useful markers already in use in marker-assisted selection processes. Thus, association mapping has proved to represent a valuable step towards high quality and sustainable grape production. This review summarizes current applications of association mapping in grapevine research and discusses future prospects in view of current viticulture challenges.

Chromosome-scale genomics, metabolomics, and transcriptomics provide insight into the synthesis and regulation of phenols in Vitis adenoclada grapes

Vitis adenoclada is a wild grape unique to China. It exhibits well resistance to heat, humidity, fungal disease, drought, and soil infertility. Here, we report the high-quality, chromosome-level genome assembly of GH6 (V. adenoclada). The 498.27 Mb genome contained 221.78 Mb of transposable elements, 28,660 protein-coding genes, and 481.44 Mb of sequences associated with 19 chromosomes. GH6 shares a common ancestor with PN40024 (Vitis vinifera) from approximately 4.26-9.01 million years ago, whose divergence occurred later than Vitis rotundifolia and Vitis riparia. Widely-targeted metabolome and transcriptome analysis revealed that the profiles and metabolism of phenolic compounds in V. adenoclada varieties significantly were differed from other grape varieties. Specifically, V. adenoclada varieties were rich in phenolic acids and flavonols, whereas the flavan-3-ol and anthocyanin content was lower compared with other varieties that have V. vinifera consanguinity in this study. In addition, ferulic acid and stilbenes content were associated with higher expressions of COMT and STSs in V. adenoclada varieties. Furthermore, MYB2, MYB73-1, and MYB73-2 were presumably responsible for the high expression level of COMT in V. adenoclada berries. MYB12 (MYBF1) was positively correlated with PAL, CHS, FLS and UFGT.Meanwhile, MYB4 and MYBC2-L1 may inhibit the synthesis of flavan-3-ols and anthocyanins in two V. adenoclada varieties (YN2 and GH6). The publication of the V. adenoclada grape genome provides a molecular foundation for further revealing its flavor and quality characteristics, is also important for identifying favorable genes of the East Asian species for future breeding.

The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis

Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.

Hormone biosynthesis and metabolism members of 2OGD superfamily are involved in berry development and respond to MeJA and ABA treatment of Vitis vinifera L

BACKGROUND

Hormones play an indispensable role during fruit ripening, nine clades in 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily are responsible for the hormone biosynthesis and metabolism, but less information is known about them.

RESULTS

A total of 163 Vv2OGD superfamily members were identified from grape genome, which were mainly expanded by local (tandem and proximal) duplication. Phylogenetic analysis of 2OGD members in grape and Arabidopsis indicates 37 members in Vv2OGD superfamily are related to hormone biosynthesis and metabolism process (Vv2OGD-H), which could be divided into 9 clades, gibberellin (GA) 3-oxidase (GA3ox), GA 20-oxidase (GA20ox), carbon-19 GA 2-oxidase (C₁₉-GA2ox), carbon-20 GA 2-oxidase (C₂₀-GA2ox), 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), dioxygenase for auxin oxidation (DAO), lateral branching oxidoreductas (LBO), downy mildew resistant 6 and DMR6-like oxygenase (DMR6/DLO) and jasmonate-induced oxygenase (JOX). Sixteen of these 37 Vv2OGD-Hs are expressed in grape berry, in which the expression patterns of VvGA2oxs, VvDAOs and VvJOXs shows a correlation with the change patterns of GAs, indole-3-acetic acid (IAA) and jasmonates (JAs), indicating the involvement of these genes in grape berry development by regulating corresponding hormones. Twelve Vv2OGD-Hs respond to methyl JA (MeJA) treatment, of which eight may lead to the inhibition of the ripening process by the crosstalk of JAs-salicylic acids (SAs), JAs-GAs and JAs-JAs, while seven Vv2OGD-Hs respond to ABA treatment may be responsible for the promotion of ripening process by the interplay of abscisic acid (ABA)-strigolactones (SLs), ABA-SAs, ABA-GAs, ABA-JAs. Especially, VvLBO1 reach an expression peak near véraison and up-regulate about four times after ABA treatment, which implies SLs and ABA-SLs crosstalk may be related to the onset of berry ripening in grape.

CONCLUSIONS

This study provides valuable clues and new insights for the mechanism research of Vv2OGD-Hs in hormones regulation during the grape berry development.

Adaptation to a new environment with pre-adaptive genomic features - Evidence from woody plants colonizing the land-sea interface

Adaptation to new environments is a key evolutionary process which presumably involves complex genomic changes. Mangroves, a collection of approximately 80 woody plants that have independently invaded intertidal zones >20 times, are ideal for studying this process. We assembled near-chromosome-scale genomes of three Xylocarpus species as well as an outgroup species using single-molecule real-time sequencing. Phylogenomic analysis reveals two separate lineages, one with the mangrove Xylocarpus granatum and the other comprising a mangrove Xylocarpus moluccensis and a terrestrial Xylocarpus rumphii. In conjunction with previous studies, we identified several genomic features associated with mangroves: (i) signals of positive selection in genes related to salt tolerance and root development; (ii) genome-wide elevated ratios of non-synonymous to synonymous substitution relative to terrestrial relatives; and (iii) active elimination of long terminal repeats. These features are found in the terrestrial X. rumphii in addition to the two mangroves. These genomic features, not being strictly mangrove-specific, are hence considered pre-adaptive. We infer that the coastal but non-intertidal habitat of X. rumphii may have predisposed the common ancestor to invasion of true mangrove habitats. Other features including the preferential retention of duplicated genes and intolerance to pseudogenization are not found in X. rumphii and are likely true adaptive features in mangroves. In conclusion, by studying adaptive shift and partial shifts among closely related species, we set up a framework to study genomic features that are acquired at different stages of the pre-adaptation and adaptation to new environments.

Diversification of Vascular Occlusions and Crystal Deposits in the Xylem Sap Flow of Five Tunisian Grapevines

Xylem vessels are essential pivotal organs in bulk hydraulic flow through the whole woody plant. However, environmental constraints generate disagreements in xylem structures, which are characterized by air emboli and occlusions formations, compromising water conductivity in grapevines. The aim of this work was to explore xylem morphology dynamics through the xylem sap flow of five Tunisian grapevine cultivars during the natural bleeding sap periods of 2019, 2021, and 2022. In fact, Sakasly, Khamri, Hencha, Razegui1, and Razegui2 rain-fed grapevine cultivars revealed differential responses towards xylem sap movement. The results demonstrated that the xylem sap flow was significantly more abundant in 2019 than 2021 and 2022 bleeding sap campaigns. A variation was revealed between the cultivars regarding the xylem sap flow. In fact, Sakasly gave the best xylem flow during the three campaigns. Razegui1 and Razegui2 registered approximately similar xylem sap flow, while Hencha and Khamri present the lowest sap fluxes during the three campaigns. Moreover, several vascular occlusions forms were identified from stem cross sections using environmental scanning electron microscopy (ESEM), including tyloses, gels, starch, and gum deposits. The highest occlusion number was observed in Sakasly, Razegui1, and Razegui2 cultivars. Among different biogenic calcium shapes, several were observed for the first time in grapevine, including multi-faceted druse, cubic, crystalline sand, styloids, spherical, or drop-like structures. Considering their lower flow and totally blocked vessels, both Hencha and Khamri confirmed their susceptibility to environmental constraints. However, Sakasly, Razegui1, and Razegui2 cultivars presented higher tolerance according to their sap flow and xylem morphology.

Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq

Background

In cold regions, low temperature is the main limiting factor affecting grape production. As an important breeding resource, V. amurensis Rupr. has played a crucial role in the discovery of genes which confer cold resistance in grapes. Thus far, many cold-resistance genes have been reported based on the study of V. amurensis. In order to identify more candidate genes related to cold resistance in V. amurensis, QTL mapping and RNA-seq was conducted based on the hybrid population and different cold-resistance cultivars in this study.

Results

In this study, highly cold-resistant grape cultivar ‘Shuangyou’ (SY) which belongs to V. amurensis, and cold-sensitive cultivar ‘Red Globe’ (RG) which belongs to Vitis vinifera L. were used to identify cold resistance genes. Cold-resistance quantitative trait locus (QTL) mapping was performed based on genetic population construction through interspecific crossing of ‘Shuangyou’ and ‘Red Globe’. Additionally, transcriptome analysis was conducted for the dormant buds of these two cultivars at different periods. Based on transcriptome analysis and QTL mapping, many new structural genes and transcription factors which relate to V. amurensis cold resistance were discovered, including CORs (VaCOR413IM), GSTs (VaGST-APIC, VaGST-PARB, VaGSTF9 and VaGSTF13), ARFs (VaIAA27 and VaSAUR71), ERFs (VaAIL1), MYBs (VaMYBR2, VaMYBLL and VaMYB3R-1) and bHLHs (VaICE1 and VabHLH30).

Conclusions

This discovery of candidate cold-resistance genes will provide an important theoretical reference for grape cold-resistance mechanisms, research, and cold-resistant grape cultivar breeding in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08788-y.

The genome of Prunus humilis provides new insights to drought adaption and population diversity

Prunus humilis (2n = 2x = 16) is a dwarf shrub fruit tree native to China and distributed widely in the cold and arid northern region. In this study, we obtained the whole genome sequences of P. humilis by combining Illumina, PacBio and HiC sequencing technologies. This genome was 254.38 Mb long and encodes 28,301 putative proteins. Phylogenetic analysis indicated that P. humilis shares the same ancestor with Prunus mume and Prunus armeniaca at ∼ 29.03 Mya. Gene expansion analysis implied that the expansion of WAX-related and LEA genes might be associated with high drought tolerance of P. humilis and LTR maybe one of the driver factors for the drought adaption by increase the copy number of LEAs. Population diversity analysis among 20 P. humilis accessions found that the genetic diversity of P. humilis populations was limited, only 1.40% base pairs were different with each other, and more wild resources need to be collected and utilized in the breeding and improvement. This study provides new insights to the drought adaption and population diversity of P. humilis that could be used as a potential model plant for horticultural research.

Temperature-phase transcriptomics reveals that hormones and sugars in the phloem of grape participate in tolerance during cold acclimation

Most of the upregulated genes contributed to the accumulation of soluble sugars and ABA in the phloem of 'Vitis amurensis' compared to 'Merlot' during cold acclimation. Extreme cold is one of the dominant abiotic factors affecting grape yield and quality. However, the changes in sugars, phytohormones, and gene expression in the branch phloem of different tolerant grape varieties during cold acclimation remain elusive. The data supported that with decreasing temperature, the contents of fructose, sucrose, and ABA in the phloem of Vitis amurensis (cold-tolerant, T) and 'Merlot' (cold-sensitive, S) increased during cold acclimation, and these indicators were higher in T than in S. Furthermore, the activities of sucrose synthetase, sucrose phosphate synthetase, and acid invertase peaked in the early phase of cold acclimation (approximately 5 °C) compared to other phases (approximately 28 °C, 0 °C, - 5 °C and - 10 °C). Moreover, the RNA sequencing results helped identify a total of 11,343 differentially expressed genes in the phloem of T and S, among which 4912 were upregulated and 6431 were downregulated. In the abscisic acid pathway, CRTISO, PSPY1-1, CYCP707A4-2, PYL4-1, PYL4-2, P2C08, SAPK2, TARAB1, and DBF3 were more highly expressed in T than in S. In the starch and sucrose metabolism pathway, HXK1, PGMP, GLGL1, SUS6, VCINV, BGL11, SSY1, GPS, BAM1 and BAM3 were also more highly expressed in T than in S. Moreover, the genes related to oxidative phosphorylation, such as NDHF, ND4, ND1, NAD7, NAD2, ATPB, YMF19, ATP9, PMA1 and AHA8, were upregulated in T. These results will be beneficial for understanding the potential differences in tolerance across two different cold-tolerant grapes with respect to sugar metabolism and gene expression.

The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis

The lacquer tree (Toxicodendron vernicifluum (Stokes) F.A. Barkley) is an important tree with economic, industrial, and medicinal values. Here, we generated the reference genome of T. vernicifluum at the chromosome level with 491.93 Mb in size, in which 98.26% of the assembled contigs were anchored onto 15 pseudochromosomes with the scaffold N50 of 32.97 Mb. Comparative genomic analysis revealed the gene families related to urushiol biosynthesis were expanded, contributing to the ecological fitness and biological adaptability of the lacquer tree. We combined multi-omics data to identify genes that encode key enzymes in the T. vernicifluum urushiol and lignin biosynthetic pathways. Furthermore, the unique active metabolites, such as butin and fisetin, in cultivar lacquers were identified by metabolism profiling. Our work would provide crucial insights into metabolite synthesis such as urushiol and lignin, meanwhile offer a basis for further exploration of the cultivation and breeding of T. vernicifluum and other Anacardiaceae members.

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We provide the first chromosome-level genome for Toxicodendron vernicifluum

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We explore the phylogenetic position of lacquer tree

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We identify genes involved in the urushiol and lignin biosynthetic pathways

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Analysis of the unique active metabolites in cultivar lacquers by LC-MS/MS is reported

Bringing more players into play: Leveraging stress in genome wide association studies

In order to meet the demand of the burgeoning human population as well as to adapt crops to the enhanced abiotic and biotic stress caused by the global climatic change, breeders focus on identifying valuable genes to improve both crop stress tolerance and crop quality. Recently, with the development of next-generation sequencing methods, millions of high quality single-nucleotide polymorphisms (SNPs) have been made available and genome-wide association studies (GWAS) are widely used in crop improvement studies to identify the associations between genetic variants of genomes and relevant crop agronomic traits. Here, we review classic cases of use of GWAS to identify genetic variants associated with valuable traits such as geographic adaptation, crop quality and metabolites. We discuss the power of stress GWAS to identify further associations including those with genes that are not, or only lowly, expressed during optimal growth conditions. Finally, we emphasize recent demonstrations of the efficiency and accuracy of time-resolved dynamic stress GWAS and GWAS based on genomic gene expression and structural variations, which can be applied to resolve more comprehensively the genetic regulation mechanisms of complex traits.

VaAPRT3 Gene is Associated With Sex Determination in Vitis amurensis

In the past decade, progress has been made in sex determination mechanism in Vitis. However, genes responsible for sexual differentiation and its mechanism in V. amurensis remain unknown. Here, we identify a sex determination candidate gene coding adenine phosphoribosyl transferase 3 (VaAPRT3) in V. amurensis. Cloning and sequencing of the VaAPRT3 gene allowed us to develop a molecular marker able to discriminate female individuals from males or hermaphrodites based on a 22-bp InDel. Gene expression and endogenous cytokinin content analysis revealed that the VaAPRT3 gene is involved in sex determination or, to be precise, in female organ differentiation, through regulating cytokinin metabolism in V. amurensis. This study enlarged the understanding of sex determination mechanism in the genus Vitis, and the sex marker could be used as a helpful tool for sexual identification in breeding programs as well as in investigation and collection of V. amurensis germplasms.

Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation

BACKGROUND

Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks.

RESULTS

By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce's disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors.

CONCLUSIONS

Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.

Full-length transcriptome profiling reveals insight into the cold response of two kiwifruit genotypes (A. arguta) with contrasting freezing tolerances

BACKGROUND

Kiwifruit (Actinidia Lindl.) is considered an important fruit species worldwide. Due to its temperate origin, this species is highly vulnerable to freezing injury while under low-temperature stress. To obtain further knowledge of the mechanism underlying freezing tolerance, we carried out a hybrid transcriptome analysis of two A. arguta (Actinidi arguta) genotypes, KL and RB, whose freezing tolerance is high and low, respectively. Both genotypes were subjected to - 25 °C for 0 h, 1 h, and 4 h.

RESULTS

SMRT (single-molecule real-time) RNA-seq data were assembled using the de novo method, producing 24,306 unigenes with an N50 value of 1834 bp. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs showed that they were involved in the 'starch and sucrose metabolism', the 'mitogen-activated protein kinase (MAPK) signaling pathway', the 'phosphatidylinositol signaling system', the 'inositol phosphate metabolism', and the 'plant hormone signal transduction'. In particular, for 'starch and sucrose metabolism', we identified 3 key genes involved in cellulose degradation, trehalose synthesis, and starch degradation processes. Moreover, the activities of beta-GC (beta-glucosidase), TPS (trehalose-6-phosphate synthase), and BAM (beta-amylase), encoded by the abovementioned 3 key genes, were enhanced by cold stress. Three transcription factors (TFs) belonging to the AP2/ERF, bHLH (basic helix-loop-helix), and MYB families were involved in the low-temperature response. Furthermore, weighted gene coexpression network analysis (WGCNA) indicated that beta-GC, TPS5, and BAM3.1 were the key genes involved in the cold response and were highly coexpressed together with the CBF3, MYC2, and MYB44 genes.

CONCLUSIONS

Cold stress led various changes in kiwifruit, the 'phosphatidylinositol signaling system', 'inositol phosphate metabolism', 'MAPK signaling pathway', 'plant hormone signal transduction', and 'starch and sucrose metabolism' processes were significantly affected by low temperature. Moreover, starch and sucrose metabolism may be the key pathway for tolerant kiwifruit to resist low temperature damages. These results increase our understanding of the complex mechanisms involved in the freezing tolerance of kiwifruit under cold stress and reveal a series of candidate genes for use in breeding new cultivars with enhanced freezing tolerance.

The Influence of the Grapevine Bacterial and Fungal Endophytes on Biomass Accumulation and Stilbene Production by the In Vitro Cultivated Cells of Vitis amurensis Rupr

Plant endophytes are known to alter the profile of secondary metabolites in plant hosts. In this study, we identified the main bacterial and fungal representatives of the wild grape Vitis amurensis Rupr. microbiome and investigated a cocultivation effect of the 14 endophytes and the V. amurensis cell suspension on biomass accumulation and stilbene biosynthesis. The cocultivation of the V. amurensis cell culture with the bacteria Agrobacterium sp., Bacillus sp., and Curtobacterium sp. for 2 weeks did not significantly affect the accumulation of cell culture fresh biomass. However, it was significantly inhibited by the bacteria Erwinia sp., Pantoea sp., Pseudomonas sp., and Xanthomonas sp. and fungi Alternaria sp., Biscogniauxia sp., Cladosporium sp., Didymella sp. 2, and Fusarium sp. Cocultivation of the grapevine cell suspension with the fungi Didymella sp. 1 and Trichoderma sp. resulted in cell death. The addition of endophytic bacteria increased the total stilbene content by 2.2–5.3 times, while the addition of endophytic fungi was more effective in inducing stilbene accumulation by 2.6–16.3 times. The highest content of stilbenes in the grapevine cells cocultured with endophytic fungi was 13.63 and 13.76 mg/g of the cell dry weight (DW) after cultivation with Biscogniauxia sp. and Didymella sp. 2, respectively. The highest content of stilbenes in the grapevine cells cocultured with endophytic bacteria was 4.49 mg/g DW after cultivation with Xanthomonas sp. The increase in stilbene production was due to a significant activation of phenylalanine ammonia lyase (PAL) and stilbene synthase (STS) gene expression. We also analyzed the sensitivity of the selected endophytes to eight antibiotics, fluconazole, and trans-resveratrol. The endophytic bacteria were sensitive to gentamicin and kanamycin, while all selected fungal strains were resistant to fluconazole with the exception of Cladosporium sp. All endophytes were tolerant of trans-resveratrol. This study showed that grape endophytes stimulate the production of stilbenes in grape cell suspension, which could further contribute to the generation of a new stimulator of stilbene biosynthesis in grapevine or grape cell cultures.

Comparative Metabolomic and Transcriptomic Studies Reveal Key Metabolism Pathways Contributing to Freezing Tolerance Under Cold Stress in Kiwifruit

Cold stress poses a serious treat to cultivated kiwifruit since this plant generally has a weak ability to tolerate freezing tolerance temperatures. Surprisingly, however, the underlying mechanism of kiwifruit's freezing tolerance remains largely unexplored and unknown, especially regarding the key pathways involved in conferring this key tolerance trait. Here, we studied the metabolome and transcriptome profiles of the freezing-tolerant genotype KL (Actinidia arguta) and freezing-sensitive genotype RB (A. arguta), to identify the main pathways and important metabolites related to their freezing tolerance. A total of 565 metabolites were detected by a wide-targeting metabolomics method. Under (-25°C) cold stress, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway annotations showed that the flavonoid metabolic pathways were specifically upregulated in KL, which increased its ability to scavenge for reactive oxygen species (ROS). The transcriptome changes identified in KL were accompanied by the specific upregulation of a codeinone reductase gene, a chalcone isomerase gene, and an anthocyanin 5-aromatic acyltransferase gene. Nucleotides metabolism and phenolic acids metabolism pathways were specifically upregulated in RB, which indicated that RB had a higher energy metabolism and weaker dormancy ability. Since the LPCs (LysoPC), LPEs (LysoPE) and free fatty acids were accumulated simultaneously in both genotypes, these could serve as biomarkers of cold-induced frost damages. These key metabolism components evidently participated in the regulation of freezing tolerance of both kiwifruit genotypes. In conclusion, the results of this study demonstrated the inherent differences in the composition and activity of metabolites between KL and RB under cold stress conditions.

The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing

For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.

Biodiversity of endophytic bacteria and fungi of wild grapes Vitis amurensis Rupr

The diversity of endophytic bacteria and fungi of V. amurensis grape plants growing in the suburbs of Vladivostok in the summer and autumn periods of 2018-2020 was analyzed. About 600 strains of bacteria and 160 strains of fungi were inoculated from peripherally sterilized leaves and stems of V. amurensis. Isolated bacteria were representatives of 36 genera: Actinobacterium, Acinetobacter, Agrobacterium, Arthrobacter, Bacillus, Buttiauxella, Curtobacterium, Duganella, Erwinia, Enterobacter, Frigoribacterium, Frondihabitans, Klebsiella, Leclercia, Lelliottia, Methylobacterium, Microbacterium, Mucilaginibacter, Luteibacter, Lysinimonas, Pantoea, Paenibacillus, Parageobacillus, Pedobacter, Phyllobacterium, Plantibacter, Pseudomonas, Pullulanibacillus, Raoultella, Rhizobium, Sphingomonas, Staphylococcus, Stenotrophomonas, Streptomyces, Serratia, Xanthomonas. The largest number of strains were representatives of the genera Erwinia, Pantoae and Pseudomonas. Endophytic grape fungi were represented by 25 genera: Alternaria, Annulohypoxylon, Aureobasidium, Biscogniauxia, Cladosporium, Colletotrichum, Coniochaeta, Coprinellus, Davidiellaceae, Didymella, Discosia, Epicoccum, Fusarium, Hypoxylon, Neosetophoma, Nemania, Neurospora, Nigrospora, Paraphoma, Penicillium, Pestalotiopsis, Pestalosphaeria, Phoma, Trichoderma, Xylaria. The largest number of representatives were of the genus Didymella, Cladosporium and Colletotrichum.

Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications

Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source of genetic variation. Thlaspi arvense, a close relative of the model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plant adaptation in extreme environments. However, how the retrotransposons affect the T. arvense genome evolution and adaptation is largely unknown. We report a high-quality chromosome-scale genome assembly of T. arvense with a scaffold N50 of 59.10 Mb. Long terminal repeat retrotransposons (LTR-RTs) account for 56.94% of the genome assembly, and the Gypsy superfamily is the most abundant TEs. The amplification of LTR-RTs in the last six million years primarily contributed to the genome size expansion in T. arvense. We identified 351 retrogenes and 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those retrogenes and genes flanked by LTRs have a higher percentage of significantly expanded orthogroups (SEOs), and these SEOs possess more recent tandem duplicated genes. All present results indicate that RNA-based gene duplication (retroduplication) accelerated the subsequent tandem duplication of homologous genes resulting in family expansions, and these expanded gene families were implicated in plant growth, development, and stress responses, which were one of the pivotal factors for T. arvense's adaptation to the harsh environment in the QTP regions. In conclusion, the high-quality assembly of the T. arvense genome provides insights into the retroduplication mediated mechanism of plant adaptation to extreme environments.