Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e. multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.

The large diversity of grapevine cultivars includes genotypes more tolerant to water deficit than others. Widely distributed cultivars, like Merlot, are more sensitive to water deprivation than local cultivars like Callet, which are more adapted to water deficit due to their Mediterranean origin. Despite their tolerance, adaptation to water deficit influenced by grafting in rootstocks like 110 Richter is key to facing drought in vineyards, defining the scion-rootstock relationship. To understand these differences, we explored transcriptomic, metabolic, hormonal and physiological responses under three levels of water deficit (mild, high, and extreme), using 110 Richter as the rootstock in both cultivars. Results revealed that sensitivity to abscisic acid (ABA) is essential for water deficit tolerance in the aerial part, guiding root responses. Callet/110 Richter activates more gene expression patterns in response to ABA, reducing water loss compared to Merlot/110 Richter in both aerial and root parts. This modulation in Callet/110 Richter involves regulating metabolic pathways to increase cell turgor, reducing photosynthesis, and producing molecules like polyphenols or flavonoids to respond to oxidative stress. In contrast, Merlot/110 Richter shows a lack of specific response, especially in the roots, indicating less resilience to water stress. Therefore, selecting genotypes more sensitive to ABA and their interaction with rootstocks is key for managing vineyards in future climate change scenarios.

Despite the transformative power of gene editing for crop improvement, its widespread application across species and varieties is limited by the transformation bottleneck that exists for many crops. The genetic transformation of plants is hindered by a general reliance on in vitro regeneration through plant tissue culture. Tissue culture requires empirically determined conditions and aseptic techniques, and cannot easily be translated to recalcitrant species and genotypes. Both Agrobacterium-mediated and alternative transformation protocols are limited by a dependency on in vitro regeneration, which also limits their use by non-experts and hinders research into non-model species such as those of possible novel biopharmaceutical or nutraceutical use, as well as novel ornamental varieties. Hence, there is significant interest in developing tissue culture-independent plant transformation and gene editing approaches that can circumvent the bottlenecks associated with in vitro plant regeneration recalcitrance. Compared to tissue culture-based transformations, tissue culture-independent approaches offer advantages such as avoidance of somaclonal variation effects, with more streamlined and expeditious methodological processes. The ease of use, dependability, and accessibility of tissue culture-independent procedures can make them attractive to non-experts, outperforming classic tissue culture-dependent systems. This review explores the diversity of tissue culture-independent transformation approaches and compares them to traditional tissue culture-dependent transformation strategies. We highlight their simplicity and provide examples of recent successful transformations accomplished using these systems. Our review also addresses current limitations and explores future perspectives, highlighting the significance of these techniques for advancing plant research and crop improvement.

Grasses, including turf and forage, cover most of the earth’s surface; predominantly important for land, water, livestock feed, soil, and water conservation, as well as carbon sequestration. Improved production and quality of grasses by modern molecular breeding is gaining more research attention. Recent advances in genome-editing technologies are helping to revolutionize plant breeding and also offering smart and efficient acceleration on grass improvement. Here, we reviewed all recent researches using (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing tools to enhance the growth and quality of forage and turf grasses. Furthermore, we highlighted emerging approaches aimed at advancing grass breeding program. We assessed the CRISPR-Cas effectiveness, discussed the challenges associated with its application, and explored future perspectives primarily focusing on turf and forage grasses. Despite the promising potential of genome editing in grasses, its current efficiency remains limited due to several bottlenecks, such as the absence of comprehensive reference genomes, the lack of efficient gene delivery tools, unavailability of suitable vector and delivery for grass species, high polyploidization, and multiple homoeoalleles, etc. Despite these challenges, the CRISPR-Cas system holds great potential to fully harness its benefits in grass breeding and genetics, aiming to improve and sustain the quantity and quality of turf and forage grasses.

The CRISPR-Cas-based gene targeting (GT) method has enabled precise modifications of genomic DNA ranging from single base to several kilobase scales through homologous recombination (HR). In plant somatic cells, canonical non-homologous end-joining (cNHEJ) is the predominant mechanism for repairing double-stranded breaks (DSBs), thus limiting the HR-mediated GT. In this study, we implemented an approach to shift the repair pathway preference toward HR by using a dominant-negative ku80 mutant protein (KUDN) to disrupt the initiation of cNHEJ. The employment of KUDN conferred a 1.71- to 3.55-fold improvement in GT efficiency at the callus stage. When we screened transformants, there was a more remarkable increase in GT efficiency, ranging from 1.62- to 9.84-fold, at two specific tomato loci, SlHKT1;2 and SlEPSPS1. With practical levels of efficiency, this enhanced KUDN-based GT tool successfully facilitated a 9-bp addition at an additional locus, SlCAB13. These findings provide another promising method for more efficient and precise plant breeding.

The pathogen Colletotrichum gloeosporioides causes anthracnose, a serious threat to tea trees around the world, particularly in warm and humid regions. RNA-Seq data have previously indicated NAC transcription factors are involved in anthracnose resistance, but underlying mechanisms remain unclear. The BiFC, Split-LUC, and Co-IP assays validated the interaction between CsbHLH62 and CsNAC17 identified through yeast two-hybrid (Y2H) screening. CsNAC17 or CsbHLH62 overexpression enhanced anthracnose resistance, as well as enhanced levels of H₂O₂, hypersensitivity, and cell death in Nicotiana benthamiana. The NBS-LRR gene CsRPM1 is regulated by CsNAC17 by binding directly to its promoter (i.e. CACG, CATGTG), while CsbHLH62 facilitates CsNAC17’s binding and increases transcriptional activity of CsRPM1. Additionally, transient silencing of CsNAC17 and CsbHLH62 in tea plant leaves using the virus-induced gene silencing (VIGS) system resulted in decreased resistance to anthracnose. Conversely, transient overexpression of CsNAC17 and CsbHLH62 in tea leaves significantly enhanced the resistance against anthracnose. Based on these results, it appears that CsbHLH62 facilitates the activity of CsNAC17 on CsRPM1, contributing to increased anthracnose resistance.

Cold stress seriously affects plant growth and development. The ubiquitination system plays an important role by degrading and modifying substrates at the protein level. In this study, the U-box type ubiquitin ligase VviPUB19 gene was induced by low temperature (4°C) in grapevine. In Arabidopsis thaliana, the pub19 mutant, a homologous mutation of VviPUB19, exhibited enhanced cold tolerance, and the resistance phenotype of the mutant could be attenuated by VviPUB19. VviPUB19-overexpressing grape lines exhibited lower cold tolerance. Furthermore, it was revealed that VviPUB19 interacted with the cold-related transcription factors VviICE1, 2, and 3 and VviCBF1 and 2, and was involved in the degradation of them. This is the first time that an E3 ligase (VviPUB19) that interacts with CBFs and affects its protein stability has been identified. It was also shown that VviICE1, 2, and 3 positively regulated VviPUB19 promoter activity. Therefore, our results suggest that VviPUB19 reduces grape cold tolerance via participating in the CBF-dependent pathway.

Black wolfberry (Lycium ruthenicum Murr.) is an important plant for ecological preservation. In addition, its fruits are rich in anthocyanins and have important edible and medicinal value. However, a high-quality chromosome-level genome for this species is not yet available, and the regulatory mechanisms involved in the biosynthesis of anthocyanins are unclear. In this study, haploid material was used to assemble a high-quality chromosome-level reference genome of Lycium ruthenicum, resulting in a genome size of 2272 Mb with contig N50 of 92.64 Mb, and 38 993 annotated gene models. In addition, the evolution of this genome and large-scale variations compared with the Ningxia wolfberry Lycium barbarum were determined. Importantly, homology annotation identified 86 genes involved in the regulatory pathway of anthocyanin biosynthesis, five of which [LrCHS1 (evm.TU.Chr05.295), LrCHS2 (evm.TU.Chr09.488), LrAOMT (evm.TU.Chr09.809), LrF3’5’H (evm.TU.Chr06.177), and LrAN2.1 (evm.TU.Chr05.2618)] were screened by differential expression analysis and correlation analysis using a combination of transcriptome and metabolome testing. Overexpression of these genes could significantly up- or downregulate anthocyanin-related metabolites. These results will help accelerate the functional genomic research of L. ruthenicum, and the elucidation of the genes involved in anthocyanin synthesis will be beneficial for breeding new varieties and further exploring its ecological conservation potential.

Flowering Chinese cabbage is a type of leafy vegetable that belongs to the Brassica genus. Originally native to South China, it is now widely cultivated and consumed across the globe, particularly in Asian countries. The recent cultivation and regional expansion of flowering Chinese cabbage provides a valuable opportunity to elucidate the genomic basis underlying environmental adaptation and desired traits during a short-term artificial selection process. Here, we investigate the genetic variation, population structure, and diversity of a diverse germplasm collection of 403 flowering Chinese cabbage accessions. Our investigation seeks to elucidate the genomic basis that guides the selection of adaptability, yield, and pivotal agronomic traits. We further investigated breeding improvement associated with stem development by integrating transcriptome data. Genome-wide association analysis identified 642 loci and corresponding candidate genes associated with 11 essential agronomic traits, including plant architecture and yield. Furthermore, we uncovered a significant disparity in the allele frequency distribution of nonsynonymous mutations in these candidate genes throughout the improvement stages. Our results shed light on the genetic basis of improvement and crucial agronomic traits in flowering Chinese cabbage, offering invaluable resources for upcoming genomics-assisted breeding endeavors.

Skin color is one of the major traits of fruit appearance quality in pear (Pyrus) that affects the fruit commodity value. Russet skin protects pear fruits from environmental stresses and its formation process is closely linked to lignin accumulation. However, the molecular regulatory networks underlying russet skin formation in pear fruits involve complex secondary metabolic pathways and remain elusive. Here, we explored the regulatory mechanisms underlying lignin accumulation in pear skin based on transcriptome sequencing, co-expression network analysis, and gene expression profiling. We identified a WRKY transcription factor gene, PbWRKY24, that regulates russet skin formation in pear fruits. The relative expression of PbWRKY24 in russet pear skin was significantly correlated with lignin content. We then verified the function of PbWRKY24 in lignin accumulation via genetic transformation. DNA affinity purification sequencing revealed that PbWRKY24 directly binds to the promoter of a lignin biosynthesis gene, PbPRX4. This binding was confirmed by yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays. Overexpression of PbPRX4 in pear skin stimulated lignin accumulation and consequently promoted russet skin formation. This study provides a glimpse into the intricate lignin biosynthesis mechanisms during russet skin formation in pear fruits, which is of practical significance to pear breeding for fruit quality.

Next-generation sequencing has fueled significant advancement in plant breeding tools, such as genome-wide association studies and single-nucleotide polymorphism (SNP) analysis. In this dynamic landscape, plant databases housing SNP markers have evolved into hubs facilitating breeding initiatives and genomic research. PrunusMap, accessible at https://prunusmap.eead.csic.es is an open-source Web application tailored for the Prunus community. Featuring a user-friendly interface, PrunusMap empowers users to seamlessly align and locate markers across multiple genome versions of Prunus species and cultivars, supporting different queries and formats. Beyond locating marker positions, it provides a comprehensive list of annotated nearby genes and proteins. This streamlined process, driven by four intuitive features ‘Find markers’, ‘Align sequences’, ‘Align proteins’, and ‘Locate by position’, significantly reduces workload and boosts efficiency, particularly for users with limited bioinformatics expertise. Moreover, PrunusMap’s versatility is underscored by its commitment to incorporate additional Prunus genome sequences, annotations, and markers upon user request.

The genus Brassica includes six species and over 15 types of vegetables that are widely cultivated and consumed globally. This group of vegetables is rich in bioactive compounds, including glucosinolates, vitamins (such as vitamin C, folate, tocopherol, and phylloquinone), carotenoids, phenols, and minerals, which are crucial for enriching diets and maintaining human health. However, the full extent of these phytonutrients and their significant health benefits remain to be fully elucidated. This review highlights the nutrient compositions and health advantages of Brassica vegetables and discusses the impacts of various processing methods on their nutritional value. Additionally, we discuss potential strategies for enhancing the nutrition of Brassica crops through agronomic biofortification, conventional breeding, and biotechnological or metabolic engineering approaches. This review lays the foundation for the nutritional improvement of Brassica crops.

Tuber dormancy and sprouting are significant for potato cultivation, storage, and processing. Although the substantial role of microRNAs (miRNAs) in some biological processes has been recognized, the critical role of miRNA in breaking potato tuber dormancy is not well understood to date. In this investigation, we expand research on miRNA-mediated gene regulation in tuber dormancy release. In this work, 204 known and 192 novel miRNAs were identified. One hundred thirty-six differentially expressed miRNAs (DE-miRNAs) were also screened out, of which 56 DE-miRNAs were regulated by temperature during tuber dormancy release. Additionally, degradome sequencing revealed that 821 target genes for 202 miRNAs were discovered. Among them, 63 target genes and 48 miRNAs were predicted to be involved in plant hormone signaling pathways. This study used degradome sequencing, tobacco cotransformation system, and β-glucuronidase (GUS) staining technology to confirm that stu-miR319c can target StTCP26 and StTCP27 and effectively suppress their expression. The transgenic approach exhibited that stu-miR319c overexpressed tubers sprouted in advance, while silent expression of stu-miR319c showed delayed sprouting. Treatment of wild-type tubers with exogenous MeJA revealed that 1 mg/L MeJA significantly broke dormancy and enhanced potato sprouting ability. Furthermore, transgenic tubers revealed variance in jasmonic acid (JA) content and relative expression of genes associated with the JA synthesis pathway, including StAOC, StLOX2, and StLOX4, suggesting that the miR319c may participate in the JA pathway to regulate tuber dormancy release. In summary, our research offers evidence that miRNA regulates potato dormancy release and supports the idea that stu-miR319c is a unique epigenetic regulator for dormancy-sprouting transition in potatoes.

Grape is an important fruit crop, and its production faces significant threat from diseases, resulting in substantial economic loss. Wild grape relatives are valuable resources for the restoration of disease-resistance loci. However, available resistance loci in wild grape genomes remain largely unexplored. In this study, we assembled two phased genomes, including a high-resistant Chinese wild grape, Vitis davidii Föex, and a susceptible cultivar, Vitis vinifera L. cv. ‘Manicure Finger’. We detected a total of 36 688 structural variations (SVs), with the genes associated with heterozygous SVs showing an enrichment in allele-specific expression (ASE). Furthermore, we identified eight subgroups of R genes and found that 74.2% of R genes overlap with transposable elements (TEs). Among R genes, NBS-type genes exhibit higher expression profiles in the wild grape genome compared with those in the grape cultivar. Additionally, five specific NBS-type R gene clusters were identified in the wild grape genome that are absent in the cultivar. Through genetic mapping, we identified four quantitative trait loci (QTLs) associated with grape white rot resistance based on the V. davidii genome, within which six NBS-type R genes exhibit differential expression between wild and cultivated grapes. Overall, our study revealed the landscape of resistance genes in grape genomes, providing valuable genetic resources for further breeding programs.

Banana breeding is hampered by the very low fertility of domesticated bananas and the lack of knowledge about the genetic determinism of agronomic traits. We analysed a breeding population of 2723 triploid hybrids resulting from crosses between diploid and tetraploid Musa acuminata parents, which was evaluated over three successive crop cycles for 24 traits relating to yield components and plant, bunch, and fruit architectures. A subset of 1129 individuals was genotyped by sequencing, revealing 205 612 single-nucleotide polymorphisms (SNPs). Most parents were heterozygous for one or several large reciprocal chromosomal translocations, which are known to impact recombination and chromosomal segregation. We applied two linear mixed models to detect associations between markers and traits: (i) a standard model with a kinship calculated using all SNPs and (ii) a model with chromosome-specific kinships that aims at recovering statistical power at alleles carried by long non-recombined haplotypic segments. For 23 of the 24 traits, we identified one to five significant quantitative trait loci (QTLs) for which the origin of favourable alleles could often be determined amongst the main ancestral contributors to banana cultivars. Several QTLs, located in the rearranged regions, were only detected using the second model. The resulting QTL landscape represents an important resource to support breeding programmes. The proposed strategy for recovering power at SNPs carried by long non-recombined rearranged haplotypic segments is an important methodological advance for future association studies in banana and other species affected by chromosomal rearrangements.

Golden Camellia refers to a group of species in the genus Camellia that display yellow petals. The secondary metabolites in these petals hold ornamental significance and potential health benefits. However, the biosynthetic mechanisms governing the synthesis of these metabolites in golden petals remain elusive, and the exploitation of their bioactive components is not fully realized. This research involved the collection and analysis of 23 species of golden Camellia, leading to the discovery that flavonols, particularly quercetin 3-O-glucoside and quercetin 7-O-glucoside, are the primary contributors to the golden flower pigmentation. Integrative transcriptomics and coexpression network analyses pinpointed CnFLS1 as a crucial gene in the biosynthetic pathway, which, in conjunction with CnCHS, CnF3’H, and CnUFGT, orchestrates the specific pathway for flower color development. The enzyme assays revealed a high affinity and catalytic efficiency of CnFLS1 for DHQ, and transient expression of CnFLS1 in tobacco was shown to enhance the biosynthesis of quercetin flavonols, highlighting the pathway specificity in golden Camellia. Moreover, strategic transformations of cultivated tomatoes with various biosynthetic genes yielded transgenic lines exhibiting yellow fruit and quercetin-enriched flesh. These modified lines not only contained distinct flavonol components characteristic of golden Camellia but also demonstrated markedly improved antioxidant capabilities and enhanced resistance. The outcomes of this study not only elucidate the metabolic processes underlying the pigmentation of golden Camellia flowers but also provide a foundation for the development of novel tomato breeds through synthetic biology.

Cultivated strawberry (Fragaria x ananassa) is a globally important fruit crop that shows promise as a candidate for various methods of controlled environment production. However, a better understanding of the mechanisms of the regulation of flowering is needed, as more frequent or consistent flowering would be advantageous in controlled production. It is well understood that flowering in F. x ananassa responds to both photoperiod and temperature; however, the mechanism behind this response is not fully understood, particularly in perpetually flowering cultivars. While some genes of interest have been identified, a more complete model has not been established. This is largely due to the complexity of the octoploid genome and a lack of current knowledge on the mechanism of temperature response in both seasonal- and perpetual-flowering F. x ananassa. A starting point for developing a better model of flowering response in cultivated strawberries lies in the simpler Fragaria vesca, which indicates an FvCO-FvFT1-FvSOC1-FvTFL1 module for control of seasonal flowering and a lack of functional FvTFL1 responsible for perpetual flowering. However, there are some key differences when discussing F. x ananassa’s perpetual flowering characteristics. Recent studies have helped to elucidate some of these differences, allowing for a putative model of seasonal flowering in F. x ananassa, as well as indicating where further questions need to be asked regarding perpetually flowering cultivars.

Sweet cherry is very appreciated by consumers because of its attractive appearance and taste, which is determined by the balanced sweet-sour flavor. In this work, the genetics of soluble solid content (SSC), titratable acidity (TA), sugars, and organic acids was investigated in sweet cherry to facilitate breeding improvement for fruit quality. The fruits of five sweet cherry populations (N = 372), three F₁ and two F₂, were sampled over two years to evaluate SSC, TA, and the content of individual sugars (glucose, fructose, sorbitol, and sucrose) and organic acids (malic, quinic, oxalic, citric, and shikimic) by ultra-performance liquid chromatography. Glucose, followed by fructose, was the most abundant sugar, while malic acid was the predominant acid. Sorbitol and malic acid were the most stable compounds between years, and had the highest heritability, being also the best correlated to SSC and TA, respectively, revealing their relevance for breeding. Significantly positive correlations were observed among sugars and SSC, and acids and TA, but high interannual variability between years was observed for all traits. Quantitative trait loci (QTL) mapping for SSC, sugars, TA, and organic acids was performed using a multi-family approach with FlexQTL™. Twenty QTLs were detected consistently during the two phenotyped years, and several relevant regions with overlapping QTLs for sugars and acids were also identified. The results confirmed major stable SSC and TA QTLs on the linkage groups 4 and 6, respectively. Within the main LG4 SSC QTL region, where maturity and fruit development time QTLs have been previously detected, three stable sugar (glucose, sorbitol, and sucrose) and two acid (quinic, shikimic) QTLs were also identified, suggesting a pleiotropic effect of ripening date on the content of these compounds. The major malic acid QTL overlapped with TA QTL on LG6; thus, TA QTL mapping on LG6 may correspond to malic acid QTLs. Haplotype analyses of major SSC and sugars QTL on LG4, and TA and malic acid on LG6 revealed haplotypes of breeding interest. Several candidate genes previously identified in other Prunus fruit species, like peach, were found to collocate with the QTLs detected herein. This work reports QTLs regions and haplotypes of sugar and acid content in a Prunus nonclimacteric stone fruit for the first time.

The vector-borne disease huanglongbing (HLB) causes severe economic losses to citrus production worldwide with no available cure. Herein, we applied virus-induced gene silencing technology to engineer citrus that preferentially attracted and specifically killed Diaphorina citri, the vector associated with HLB. We engineered the infectious citrus tristeza virus (CTV-T36) clone to carry three truncated genes. The triple construct (CTV-tAwd-tWnt-tPDS) produces small interfering RNAs (siRNAs) against phytoene desaturase, PDS, to yield a phenotype with visual, olfactory, and gustatory cues that preferentially attracted D. citri. In addition, siRNAs targeted two genes related to flight in D. citri, abnormal wing disc (DcAwd) and wingless (DcWnt), that caused wing malformations and decreased survival in psyllids that fed on plants inoculated with the engineered virus. During two successive generations, D. citri reared on CTV-tAwd-tWnt-tPDS-inoculated plants exhibited higher mortality across life stages as well as reduced fecundity and fertility as compared with those reared on noninfected plants or CTV-wt-inoculated plants. Furthermore, CTV-tAwd-tWnt-tPDS-inoculated plants shortened the lifespan of D. citri by more than 20 days. Morphological abnormalities were noted in those adults that did successfully emerge on plants inoculated with CTV-tAwd-tWnt-tPDS, including cocked wings with a bowl-shaped depression and/or a convex shape. Phloem sap from CTV-tAwd-tWnt-tPDS-inoculated plants decreased the survival of D. citri adults, confirming that siRNAs were present in the sap of these plants. Collectively, we provide proof of concept for a novel variant of the attract-and-kill method where the cultivated crop is potentially transformed into a hyper-attractive population and transmission sink for a phytopathogen vector.

Blackcurrant (Ribes nigrum L., family Grossulariaceae) is a perennial shrub that is widely cultivated for its edible berries. These are rich in antioxidants, vitamin C, and anthocyanins, making them a valuable ingredient in the food and beverage industry. However, prolonged periods of drought during the fruiting season lead to drought stress, which has serious ecological and agricultural implications, inhibiting blackcurrant growth and reducing yields. To facilitate the analysis of underlying molecular processes, we present the first high-quality chromosome-scale and partially haplotype-resolved assembly of the blackcurrant genome (cv. Rosenthals Langtraubige), also the first in the family Grossulariaceae. We used this genomic reference to analyze the transcriptomic response of blackcurrant leaves and roots to drought stress, revealing differentially expressed genes with diverse functions, including those encoding the transcription factors bZIP, bHLH, MYB, and WRKY, and tyrosine kinase-like kinases such as PERK and DUF26. Gene expression was correlated with the abundance of primary metabolites, revealing 14 with significant differences between stressed leaves and controls indicating a metabolic response to drought stress. Amino acids such as proline were more abundant under stress conditions, whereas organic acids were depleted. The genomic and transcriptomic data from this study can be used to develop more robust blackcurrant cultivars that thrive under drought stress conditions.

Leaf trichome formation is a very important agronomic trait as it confers resistance to biotic and abiotic stresses, but the causal genes involved in this process in Brassica juncea remain largely unexplored. In this study, we first characterized the haplotypes of BjB02.GL1 among different inbred lines with leaf trichomes or glabrous leaves. A comparative analysis of the number and density of leaf trichomes between the two mustard inbred lines was then performed. BSA analysis of leaves with trichomes and glabrous pools from the F2 segregating population mapped the candidate genes on Chr.A06 and Chr.B02. Two candidate genes, BjA06.GL1 and BjB02.GL1, were subsequently cloned. After sequence alignment of the BjGL1 genes, both single-nucleotide polymorphisms (SNPs) and indel were identified in the BjA06.GL1 and BjB02.GL1 genes. And quantitative real-time polymerase chain reaction (qRT-PCR) analysis further confirmed that both the BjA06.GL1 and BjB02.GL1 genes were more highly expressed in leaves with trichomes than in glabrous leaves. As the leaf size increased, the leaf trichome density decreased. Gene editing of both BjA06.GL1 and BjB02.GL1 changed the leaf trichome to a glabrous leaf phenotype in mustard. In addition, plants with leaf trichomes presented greater resistance to aphids. Taken together, our results revealed that both BjA06.GL1 and BjB02.GL1 positively regulate leaf trichome formation and help increase aphid resistance in mustard. This study provides valuable resources and helps to elucidate the molecular mechanism of leaf trichome formation in B. juncea.

Wildtype fruit of cultivated strawberry (Fragaria × ananassa) are typically soft and highly perishable when fully ripe. The development of firm-fruited cultivars by phenotypic selection has greatly increased shelf-life, decreased postharvest perishability, and driven the expansion of strawberry production worldwide. Hypotheses for the firm-fruited phenotype include mutations affecting the expression of genes encoding polygalacturonases (PGs) that soften fruit by degrading cell wall pectins. Here we show that loss-of-function mutations in the fruit softening gene POLYGALACTURONASE1 (FaPG1; PG1-6A1) double fruit firmness in strawberry. PG1-6A1 was one of three tandemly duplicated PG genes found to be in linkage disequilibrium (LD) with a quantitative trait locus (QTL) affecting fruit firmness on chromosome 6A. PG1-6A1 was strongly expressed in soft-fruited (wildtype) homozygotes and weakly expressed in firm-fruited (mutant) homozygotes. Genome-wide association, quantitative trait transcript, DNA sequence, and expression-QTL analyses identified genetic variants in LD with PG1-6A1 that were positively correlated with fruit firmness and negatively correlated with PG1-6A1 expression. An Enhancer/Suppressor-mutator (En/Spm) transposable element insertion was discovered upstream of PG1-6A1 in mutant homozygotes that we hypothesize transcriptionally downegulates the expression of PG1-6A1. The PG1-6A1 locus was incompletely dominant and explained 26-76% of the genetic variance for fruit firmness among phenotypically diverse individuals. Additional loci are hypothesized to underlie the missing heritability. Highly accurate codominant genotyping assays were developed for modifying fruit firmness by marker-assisted selection of the En/Spm insertion and single nucleotide polymorphisms associated with the PG1-6A1 locus.

Peach is one of the most economically valuable fruit trees. Haploid peach trees occur spontaneously at very low frequencies and they are usually highly sterile. Therefore, the haploid with partial fertility is an extremely rare germplasm, which is highly valuable to genetic research and breeding programs. In this study, we investigated the cytological mechanism underlying the fertility of a peach haploid mutant ‘9-D’ derived from a spontaneous mutation. Cytologic evaluation and flow cytometry analysis demonstrated that ‘9-D’ is a pure haploid. Scanning electron microscope analysis revealed a considerable proportion of abnormal pollen grains in ‘9-D’. Pollen viability assay by Alexander staining showed that 50.4% of pollen grains from ‘9-D’ were viable. However, the pollen germination assay showed that only 7.6% of the pollen grains could germinate normally. Investigation of the chromosomal behavior of pollen mother cells at different stages of meiosis showed that pollen mother cells of ‘9-D’ lacked the process between anaphase I and prophase II of meiosis. Various types of sporophyte morphology were observed in haploid pollen mother cells at the tetrad stage. Measurement of the diameter of pollen grains indicated the presence of pollen with 2x ploidy in ‘9-D’. The offspring of ‘9-D’ were predominantly triploid or triploid aneuploid. The triploid offspring were more likely derived from the 2x male gametophyte combined with the haploid female gametophyte, which may explain the reason why ‘9-D’ has fertility. This study not only expands our understanding of haploid fertility mechanisms, but is also useful for ploid breeding programs in peach.

Theanine is a crucial indicator of tea quality, and its significance is closely tied to the economic value of tea. There have been many reports on the regulation mechanism of theanine synthesis and accumulation, but the mechanism by which gibberellin regulates theanine synthesis in tea plants is poorly understood. Previous studies have shown that the content of theanine experiences significant changes in the growth stages of tea shoots, displaying a strong correlation with gibberellin. This study confirmed that gibberellin significantly promoted the expression of the major gene of theanine synthesis, known as CsTSI. Additionally, the study identified CsWRKY71 as a transcription factor that mediated the regulation by gibberellin of theanine synthesis in tea plants. CsWRKY71 was localized in the nucleus and had a typical WRKY domain. It was a member of subclass IIC and its expression was significantly suppressed following exogenous GA₃ treatment. Further assays, such as the electrophoretic mobility shift assay, dual luciferase and asODN (antisense oligodeoxynucleotide) interference, demonstrated that CsWRKY71 significantly interacted with the promoter of CsTSI, which inhibited theanine synthesis by binding to the cis-acting element (C/T)TGAC(T/C) of the CsTSI promoter. Overall, the addition of exogenous gibberellin alleviated the inhibition of CsTSI by down-regulating the expression of CsWRKY71, ultimately facilitating the rapid biosynthesis of theanine. This study elucidated the molecular mechanism of CsWRKY71-mediated gibberellin regulation of theanine synthesis in tea plant. The findings not only enhance our understanding of the regulatory processes involved in theanine synthesis in tea plants, but also provide important references for maintaining the characteristics of high theanine in the tea plant.

Potassium (K) availability in plant cells is critical for maintaining plant productivity across many terrestrial ecosystems. Yet, there is no comprehensive assessment of the mechanisms by which plants respond to potassium application in such conditions, despite the global challenge of escalating osmotic stress. Herein, we conducted a meta-analysis using data from 2381 paired observations to investigate plant responses to potassium application across various morphological, physiological, and biochemical parameters under both osmotic and nonosmotic stress. Globally, our results showed the significant effectiveness of potassium application in promoting plant productivity (e.g. +12%~30% in total dry weight), elevating photosynthesis (+12%~30%), and alleviating osmotic damage (e.g. −19%~26% in malonaldehyde), particularly under osmotic stress. Moreover, we found evidence of interactive effects between osmotic stress and potassium on plant traits, which were more pronounced under drought than salt stress, and more evident in C₃ than C₄ plants. Our synthesis verifies a global potassium control over osmotic stress, and further offers valuable insights into its management and utilization in agriculture and restoration efforts.

Genomic prediction for multiple environments can aid the selection of genotypes suited to specific soil and climate conditions. Methodological advances allow effective integration of phenotypic, genomic (additive, nonadditive), and large-scale environmental (enviromic) data into multi-environmental genomic prediction models. These models can also account for genotype-by-environment interaction, utilize alternative relationship matrices (kernels), or substitute statistical approaches with deep learning. However, the application of multi-environmental genomic prediction in apple remained limited, likely due to the challenge of building multi-environmental datasets and structurally complex models. Here, we applied efficient statistical and deep learning models for multi-environmental genomic prediction of eleven apple traits with contrasting genetic architectures by integrating genomic- and enviromic-based model components. Incorporating genotype-by-environment interaction effects into statistical models improved predictive ability by up to 0.08 for nine traits compared to the benchmark model. This outcome, based on Gaussian and Deep kernels, shows these alternatives can effectively substitute the standard genomic best linear unbiased predictor (G-BLUP). Including nonadditive and enviromic-based effects resulted in a predictive ability very similar to the benchmark model. The deep learning approach achieved the highest predictive ability for three traits with oligogenic genetic architectures, outperforming the benchmark by up to 0.10. Our results demonstrate that the tested statistical models capture genotype-by-environment interactions particularly well, and the deep learning models efficiently integrate data from diverse sources. This study will foster the adoption of multi-environmental genomic prediction to select apple cultivars adapted to diverse environmental conditions, providing an opportunity to address climate change impacts.

Fruit softening directly impacts its storage life, transportability, and customer acceptance. Auxin plays a key role during fruit ripening, but the underlying mechanisms of how auxin regulates fruit softening remain unclear. In this study, we investigated the regulatory roles of auxin on berry cell wall degradation during grape (Vitis vinifera L.) softening. During grape berry development, berry firmness and auxin content both firstly increase and then decrease, and peaks occur 4-6 weeks after full blooming. Exogenous NAA (α-naphthalene acetic acid, a synthetic auxin) treatment inhibits berry softening by delaying propectin, cellulose, and hemicellulose degradation, which maintains cell wall integrity in the grape flesh. Weighted gene co-expression network analysis (WGCNA) showed that VvLBD13, correlated with VvARF19, could be a key gene in this delaying of berry softening, and is involved in auxin signal transduction and cell wall degradation metabolism. Overexpression and transient overexpression of VvLBD13 in tomato or in grape berry indicate that VvLBD13 accelerates hemicellulose degradation by binding the promoters of VvXTH10 (xyloglucan endotransglucosylase/hydrolase 10) and VvEXPLA1 (expansion-like A1), which results in rapid softening after veraison. Collectively, this research furnishes an exhaustive understanding of the auxin-driven regulatory mechanisms of grape berry softening.