Fruit acidity significantly influences fruit flavor, but the specific impact of soil pH on fruit acidity remains unclear. This study investigated the effects of various soil pH levels on fruit acidity and citric acid (CA) metabolism in lemon (Citrus limon L.). High soil pH (pH 8) decreased total soluble solids concentrations in lemon fruits, while low soil pH (pH 4) increased titratable acid and CA concentrations. Although low soil pH reduced the synthesis of CA due to the decreased citrate synthase and phosphoenolpyruvate carboxylase activities, the elevated fruit acidity under low soil pH conditions is not directly related to CA synthesis. Instead, low soil pH was found to suppress the activity of cytosolic aconitase (Cyt-ACO), an iron-dependent enzyme, indicating a potential role for CA degradation inhibition in low soil pH-induced CA accumulation. Furthermore, low soil pH significantly reduced cytosolic iron (Cyt-Fe) concentration, which was positively correlated with Cyt-ACO activity. In conclusion, low soil pH contributes to increasing fruit acidity in lemon, partially by inhibiting CA degradation due to the reduced Cyt-Fe concentrations. Our work unravels the influence of soil pH on CA accumulation and provides important clues for modulating CA levels through microelement fertilization in citrus.

In pears, the presence of stone cells adversely affects fruit quality. Pectin methylesterase (PME) plays various roles in plant biology, including lignin biosynthesis. However, only a limited fraction has been functionally characterized, and the distribution and function of PME in many Rosaceae trees remain unexplored. In this study, we identified 396 putative PME family candidate genes, with 81 in Pyrus bretschneideri, 92 in Malus domestica, 62 in Fragaria vesca, 65 in Prunus mume, 15 in Pyrus communis, and 81 in Pyrus pyrifolia. Leveraging insights from model plants, we categorized PME family genes into four groups. Additionally, the evolution of the PME gene family was shaped by various gene duplication events, primarily dispersed duplication, influenced by purifying selection. A specific gene, Pbr031522.1, designated PbPME35, emerged as a candidate associated with lignin biosynthesis in pear fruits, supported by RNA-seq data. The role of PbPME35 in repressing lignification was validated through its overexpression in pear callus and Arabidopsis. Overall, our findings highlight the ability of PbPME35 to reduce lignin content in pear fruit by downregulating the expression levels of lignin biosynthesis genes. These findings provide new insights into the characteristics of PME genes and their role in regulating lignification in pear fruits.

Low temperature is a major environmental factor that limits the growth, yield, and geographical distribution of Cavendish and Dajiao bananas ( Musa spp.). Dajiao bananas exhibit a significantly higher cold tolerance than the Cavendish cultivar. However, the underlying mechanisms involved in cold tolerance regulation in Dajiao plants have not been determined. In this study, we investigated the mechanisms underlying the differences in cold tolerance at the cellular level between the cold-sensitive Cavendish and cold-tolerant Dajiao banana types through comparative metabolomics and transcriptomics analyses in calli exposed to cold treatment under dark conditions. A higher accumulation of lipids was observed in Dajiao calli cells compared to Cavendish cells under cold stress. After cold treatment, 4,626 and 5,516 differentially expressed genes (DEGs) were identified in Cavendish and Dajiao banana cells, respectively. By integrating the transcriptomic and metabolomic datasets, we discovered that the linoleic acid and α-linoleic acid metabolism and the Abscisic acid (ABA)-independent Mitogen-activated protein kinase (MAPK) cascade-Inducer of CBF expression 1 (ICE1) signal transduction pathway (including Mitogen-activated protein kinase kinase kinase 1 [ MEKK1], MAPK5, ICE1, and Cold-regulated 47 [ COR47]) played crucial roles in the cold tolerance of Dajiao bananas. Our study provides new insights into cold response regulation and novel cold tolerance mechanisms, providing valuable leads and targets for the genetic improvement of cold tolerance in bananas.

During harvesting, storage, transportation, and processing, potato ( Solanum tuberosum L .) tubers undergo greening after exposure to light, leading to the accumulation of toxic glycoside alkaloids, resulting in quality deterioration and economic losses. However, the underlying mechanisms are unclear. This study compared the transcriptome and proteome differences among four potato cultivars during the light-induced greening process, identifying 3,751 unique proteins (high confidence; ≥91.7%). The levels of enzymes involved in steroidal glycoalkaloid biosynthesis varied among the cultivars. In addition, coexpression network analysis of the transcriptomic data identified the transcription factor MYB113 (Soltu.DM.10G020780.1) as a potential positive regulator of steroidal glycoalkaloid biosynthesis. The dual-luciferase assay revealed that StMYB113 could bind to the promoters of steroidal glycoalkaloid biosynthesis-related genes and activate them. The transgenic lines overexpressing Solanum tuberosum L. Myb domain protein ( StMYB113) exhibited greater mRNA abundance of these genes and elevated levels of steroidal glycoalkaloids. This study provided a theoretical basis for exploring the impact of light on the synthesis of solanine in potatoes.

Flower color and scent, crucial qualitative characteristics of ornamental plants, display extensive variation. These distinct pigments and scents play a key role in attracting specific pollinators. While previous research primarily delved into the synthetic regulatory mechanisms of individual traits and their respective attraction to insects, recent studies unveil an interconnectedness between flower color and scent through transcriptional regulatory networks. Moreover, evidence suggests that both color and scent actively contribute to insect attraction. This review summarizes the co-regulation and synthesis of pigments and scents, highlighting their pivotal roles in pollinator attraction. The insights provided will serve as valuable references for applications in metabolic engineering, novel variety breeding, and insect and pest detection and management.

Rose ( Rosa) is a prominent ornamental plant that holds substantial economic and social significance. Roses originating from different regions exhibit intricate phenotypic and genetic characteristics, but the majority of rose genetic resources are poorly characterized. In this study, 192 genotypes of the genus Rosa were examined using 33 phenotypic traits and 10 pairs of SSR markers. Compared to wild species, both old garden and modern roses exhibited a significant level of diversity, with flower color having the highest degree of diversity and style morphology having the lowest degree of diversity. This phenomenon may be attributed to the limited utilization of wild roses due to their simpler ornamental traits and the frequent phenotypic and molecular infiltration between old garden roses and modern roses. Following a inaugural comprehensive evaluation employing principal component analysis, R. chinensis ‘Zihongxiang’, R. hybrida ‘Burgundy Iceberg’, R. hybrida ‘Conrad F. Meyer’, R. rugosa ‘Gaohong’ and R. floribunda ‘Sheherazad’ were selected as core germplasm resources for future breeding. Moreover, three tetraploid roses, namely R. hybrida ‘Midnight Blue’, R. floribunda ‘Sheherazad’, and R. hybrida ‘Couture Rose Tilia’, with significant differences in both phenotypic and molecular profiles were selected and reciprocally intercrossed. Ultimately, two populations were obtained exhibiting significant variation in flower size, annual stem color, stem pickle density, and leaf number. Furthermore, our results indicated that the traits of flower diameter, flower height, petal width, and petal number may potentially be controlled by two major-effect loci. In conclusion, this study provides novel insights into the evolutionary patterns of Rosa germplasm resources. It paves the way for identifying core genotypes that carry distinct ornamental characteristics and possess immense value for breeding novel varieties in the future.

Sequencing strategies have continually advanced, with high-throughput sequencing (HTS) technologies emerging as pivotal tools in plant phylogenomics. As a standard form of target capture sequencing, hybridization target enrichment sequencing (Hyb-seq) is innovative and flexible, and then HTS strategy is widely adopted in phylogenomics. The universal Angiosperms353 probe sets (Angiosperms353) are instrumental in Hyb-seq and have been witnessed increased application in recent years. This review integrates numerous publications and empirical datasets to comprehensively assess the potential applications of Angiosperms353. Through evaluations using 18-taxa and 343-taxa genomic datasets, this review explores potential factors influencing Angiosperms353 gene capture. The RNA-seq strategy yielded the highest number of Angiosperms353 genes, followed by whole-genome sequencing and genome skimming. Increased sequencing depth enhanced gene capture yields, and no evident bias was observed across all tested angiosperm groups. In the genomics era with extensive HTS data, this review provides comprehensive guidelines for the practical application of Angiosperms353, promoting resource recycling and maximizing genomic data sharing and utilization.

Traditionally, the root system has been regarded as the primary component influencing citrus tolerance. Aerial tissues also play a crucial role in abiotic stress tolerance, as they are responsible for vital physiological processes, such as photosynthesis and transpiration. In addition, these tissues are directly exposed to various stress conditions, including extreme temperatures (heat and cold), high light irradiation, and ultraviolet (UV) exposure. In the current climate change scenario, optimizing both citrus rootstocks and grafted scions is crucial to ensure fruit quality and crop yield. Various approaches have been used to investigate the significance of aerial tissues, including in vitro systems, isolated aerial tissue growth, reciprocal grafting, and girdling. This review highlights recent research on the role of aerial tissues in citrus plants under various abiotic stress conditions. Studying and optimizing the genotypes used as scions in grafted citrus plants under abiotic stress conditions is crucial and may contribute to the development of new crop management strategies and breeding programs. Furthermore, this knowledge could be extended to other crops, enabling the development of more resilient and productive agricultural systems.

The WUSCHEL-related homeobox ( WOX) transcription factors (TFs) belong to the homeodomain (HD) family. WOX TFs are involved in various regulatory pathways related to plant growth and development. In addition to their recognized role in various development processes, many reports suggest that they play a key role in abiotic stress perception in plants. However, their underlying molecular mechanisms have rarely been studied in horticultural crops. WOXs govern the transcription of the target genes through specific binding to the cis-regulatory elements present in their promoters. Additionally, they associate with other factors to form a specific pathway regulating numerous abiotic stress responses. Here, we review the recent advances in the multifaceted functions of WOXs in the complex, developmental, and abiotic stress-sensing networks, with particular emphasis on regulating the related genes and other TFs. In addition, we suggest that WOXs are essential components of the gene regulatory networks involved in the response of plants to abiotic stress tolerance and aim to provide a reference for future research.

Theanine (Thea) is a unique metabolite in tea plants, but its physiological functions remain elusive. A low soil pH increases cadmium (Cd) availability, affecting the quality of tea plant products. In this study, we found that Thea reversed the Cd-induced reduction in free amino acid (FAA) and caffeine (CAF) in the young tea leaves, as well as the down-regulation in the expression of nitrate transporters CsNRT1.2 and CsNRT2.5, and genes responsible for the nitrogen (N) assimilation. We demonstrated that Thea could alleviate Cd-induced oxidative stresses and enhance photosynthesis. Moreover, an ATP-binding cassette (ABC) transporter, CsABCG11.2, could uptake distinct Cd substrates and the five major amino acids in tea plants. Heterologous expression of CsABCG11.2 in yeast indicated a competitive absorption between Cd and Thea in a concentration-dependent pattern. CsABCG11.2-overexpressing Arabidopsis plants exhibited increased sensitivity to Cd due to enhanced Cd concentration, accumulation in the shoots, and reduction in the primary root length. Exogenous application of Thea at environmentally regular levels attenuated the adverse effects of Cd-induced growth inhibition and chlorosis in CsABCG11.2-overexpressing Arabidopsis plants. Knockdown of CsABCG11.2 tea plants significantly lowered Cd levels in young shoots. Our results suggest that Thea plays beneficial roles in alleviating Cd stress directly or indirectly by modulating CsABCG11.2-mediated Cd uptake and translocation within plants.

Tulips ( Tulipa gesneriana) are one of the most widely cultivated bulbous plants with substantial ornamental value. However, the lack of well-documented reference genomes has limited the research progress and molecular breeding of tulips. In the present study, a full-length transcriptome of a commercial tulip cultivar was obtained using single-molecule long-read sequencing (PacBio Iso-Seq). In total, 244,357 full-length transcripts were identified, which had an average length of 2,044 bp and an N50 value of 3,861; 67,350 of these were annotated to databases. An inaugural integrated analysis of the transcriptome and phytohormone profiles during flower opening and petal senescence was performed using Illumina RNA-seq, coupled with Mfuzz (an R pakage, http://mfuzz.sysbiolab.eu) and weighted gene coexpression network analysis (WGCNA). A total of 16 gene coexpression and six transcription factor (TF) modules were constructed. Additionally, 26 hormone analogs were comprehensively profiled. Finally, a prominently novel gene, Tulipa gesneriana Homeobox12-like ( TgHB12-like), which encodes an homeodomain–leucine zipper (HD-zip) TF, was identified as a pivotal regulator of petal senescence. Overall, this work facilitates the identification of hormones and TFs in plants related to flower opening and senescence in tulips. It also provides an important and valuable genetic basis for further research in them.

Localised fruit thinning strategies must be investigated to improve precision crop load management in narrow-canopy, multileader apple trees. This study aimed to determine the effects of within-leader and tree total crop load on leaders’ and trunk’s growth, fruit set, yield, and fruit quality in ‘Ruby Matilda’ apples (marketed as Pink Lady) over three years. Different crop loads were imposed on two leaders (primary and secondary) of bi-axis trees. Leader and trunk relative growth rate, return fruit set, yield, and fruit quality parameters at harvest were measured. High within-leader crop loads led to a significant increase in yield and reductions in trunk growth, return fruit set, and deterioration of fruit quality parameters except for flesh firmness and starch index. Similar trends were observed in whole-tree relationships. High crop load in secondary leaders had moderate negative effects on trunk growth, yield, and fruit mass of primary leaders; it only marginally affected their return fruit set and had no significant effect (p>0.05) on their fruit quality. A crop load of 6.8 fruit no. cm ² of leader cross-sectional area was estimated to achieve a relatively consistent return fruit set within the same leader. At a whole-tree level, a similar crop load (6.9 fruit no. cm ² of trunk cross-sectional area) produced a consistent return fruit set despite its higher variability. These crop loads produced high yields (120 and 111 t ha ¹, respectively) and good quality fruit. Using individual leaders as management units is recommended to simplify operations and reduce variability.

This study presents the first annotated, haplotype-resolved, chromosome-scale genome of Lantana camara, a flowering shrub native to Central America and known for its dual role as an ornamental plant and an invasive species. Despite its widespread cultivation and ecological impact, the lack of a high-quality genome has hindered the investigation of traits of both ornamental and invasive. This research bridges the gap in genomic resources for L. camara, which is crucial for both ornamental breeding programs and invasive species management. Whole-genome and transcriptome sequencing were utilized to elucidate the genetic complexity of a diploid L. camara breeding line UF-T48. The genome was assembled de novo using HiFi and Hi-C reads, resulting in two phased genome assemblies with high Benchmarking Universal Single-Copy Orthologs (BUSCO) scores of 97.7%, indicating their quality. All 22 chromosomes were assembled with pseudochromosomes averaging 117 Mb. The assemblies revealed 29 telomeres and an extensive presence of repetitive sequences, primarily long terminal repeat transposable elements. The genome annotation identified 83,775 protein-coding genes, with 83% functionally annotated. In particular, the study mapped 42 anthocyanin and carotenoid candidate gene clusters and 12 herbicide target genes to the assembly, identifying 38 genes spread across the genome that are integral to flower color development and 53 genes for herbicide targeting in L. camara. This comprehensive genomic study not only enhances the understanding of L. camara’s genetic makeup but also sets a precedent for genomic research in the Verbenaceae family, offering a foundation for future studies in plant genetics, conservation, and breeding.

Chloroplast genomes, pivotal for understanding plant evolution, remain unexplored in Rutaceae, a family with key perennial crops like citrus. Leveraging next-generation sequencing data from 509 Rutaceae accessions across 15 species, we conducted a de novo assembly of 343 chloroplast genomes, unveiling a chloroplast variation map highlighting the heterogeneous evolution rates across genome regions. Notably, differences in chloroplast genome size primarily originate from large single-copy and small single-copy regions. Structural variants predominantly occurred in the single-copy region, with two insertions located at the single-copy and inverted repeat region boundary. Phylogenetic analysis, principal component analysis, and population genetic statistics confirmed the cohesive clustering of different Citrus species, reflecting evolutionary dynamics in Citrus diversification. Furthermore, a close chloroplast genetic affinity was revealed among Atalantia (previously regarded as primitive citrus), Clausena, and Murraya. Zanthoxylum formed a distinct group with heightened genetic diversity. Through expanding our analysis to include 34 published chloroplast genomes, we explored chloroplast gene selection, revealing divergent evolutionary trends in photosynthetic pathways. While Photosystem I and Photosystem II exhibited robust negative selection, indicating stability, the Nicotinamide adenine dinucleotide (NADH) dehydrogenase pathway demonstrated rapid evolution, which was indicative of environmental adaptation. Finally, we discussed the effects of gene length and GC content on chloroplast gene evolution. In conclusion, our study reveals the genetic characterization of chloroplast genomes during Rutaceae diversification, providing insights into the evolutionary history of this family.