Citrus, one of the world’s most important crops, is facing significant challenges due to drought events. Previous studies have demonstrated that tetraploid rootstocks may exhibit greater tolerance to abiotic stresses than their diploid counterparts. The effects of combining a tetraploid rootstock with a triploid scion under water deficit conditions have not been thoroughly explored. A water deficit experiment was conducted under controlled pot conditions using four citrus scion/rootstock combinations: diploid and tetraploid Swingle citrumelo rootstocks grafted with diploid Mexican lime and triploid Persian lime. Physiological, biochemical, and transcriptomic analyses under controlled pot condition revealed that tetraploid rootstocks exhibited significantly improved performance under drought stress, with an even greater effect when the scion was the triploid Persian lime. In that condition, the improved resilience was associated with reduced water consumption, higher photosynthesis, increased stomatal conductance and transpiration under water stress conditions. Elevated abscisic acid levels and stronger antioxidant activity in polyploid rootstocks further contributed to the stress response. Transcriptomic data revealed distinct gene expression changes in roots and leaves, influenced by organ ploidy and rootstock-scion interactions. Taken together our results provide insights into drought adaptation mechanisms including osmotic adjustment, oxidative stress protection, sustained photosynthesis, antioxidant enzyme activity and enhanced synthesis of protective barriers. These findings underscore ploidy’s role at both rootstock and scion levels in shaping the plant’s response to water deficit, revealing useful interactions between rootstock and scion influencing drought resilience.

Increasing water limitation and soil salinisation resulting from climate change negatively impacts plant growth and productivity, posing a significant challenge to citrus production. This highlights the need to develop new citrus rootstocks that can tolerate both abiotic and biotic stress. Polyploidy is a major driver of plant evolution that often enhances resilience to abiotic stressors, including salinity. In this study, we evaluated for the first time the salt stress response of a citrandarin hybrid derived from a Cleopatra mandarin and a trifoliate orange at two ploidy levels: diploid (2x) and allotetraploid (4x). Plants exposed to salt stress were analysed at physiological, biochemical, ion, and transcriptomic levels in leaves and roots. Using multifactorial, multivariate, and network approaches, we deciphered the complexity of the multilevel response of both 2x and 4x hybrids. Regardless of stress, ploidy level accounted for differences in photosynthetic performance as well as in the transcriptional regulation of secondary metabolism and inorganic nutrients in roots. Under salt stress, both 2x and 4x displayed a robust salt-tolerant phenotype with no visible damage, while activating profound and coordinated physiological, biochemical, and transcriptional reprogramming. However, marked divergence in their adaptive strategies was identified when evaluating the ploidy × stress interaction. The 2x genotype relied mainly on enhanced leaf antioxidant metabolism, whereas the 4x exhibited stronger root-centred regulation involving ion partitioning, osmoprotection, aquaporin expression, and antioxidant pathways. Comparison between orthologues of each citrandarin parent further revealed a transcriptional bias towards Cleopatra mandarin, which was reinforced by tetraploidy under salt stress. Altogether, our results show that tetraploidy amplifies parental root regulatory programmes, providing mechanistic insights and candidate markers for the development of salt-tolerant citrus rootstocks.

Among citrus diseases, Huanglongbing (HLB) is recognized as the most destructive and economically damaging worldwide. It is mainly associated with 'Candidatus Liberibacter asiaticus' (CLas) being transmitted by Diaphorina citri. There are no curative treatments or commercial citrus varieties resistant to CLas. Wild Aurantioideae species have been widely screened and, recently, Oceanian genotypes graft- and sexually compatible with Citrus were identified as HLB-resistant; however, there is no information regarding their use as interstocks of commercial varieties yet. Under greenhouse conditions, six HLB-resistant genotypes were evaluated as interstocks between 'Valencia' sweet orange scion and 'Rangpur' lime rootstock, both susceptible to HLB, with 'Valencia' interstock as the control. Rootstocks were nucellar seedlings, and the scion was a commercial accession preimmunized with a mild CTV strain. Plants were assessed for CLas infection and titer in leaves, stem bark, and roots up to 12-24 months after graft-inoculation in the scion and compared to non-inoculated controls. Furthermore, molecular, anatomical, and biometric variables were investigated. As expected, the scion variety was colonized by CLas regardless of the genotype evaluated as interstock. Although bacteria were detected in the roots of most CLas-inoculated plants, CLas movement from the scion to the roots was blocked in 42% and 86% of composite plants when using a F1 hybrid of C. australis × C. inodora or an admixture hybrid of C. glauca, C. australis, and C. australasica as interstocks. Overall, CLas titers were similar in infected plant tissues among the evaluated genotypes, but titers were lower in interstock bark tissues compared to scion and rootstock ones. After one-two years of CLas + CTV infection (experiments I and II, respectively), the dry weight of the root system decreased by 50% in infected trees compared to control trees for most genotypes, and CLas + CTV infection was associated with changes in the sieve phloem and gene expression. These findings suggest that, despite CTV infection, interstocks derived from some hybrids of Australian citrus types have the potential to restrict the movement of CLas from the scion into the roots of infected citrus trees. Long-term evaluation of composite plants in field conditions is necessary to assess tree performance and, ultimately, the impact of CLas blockage by interstocking on HLB disease damage.

Oceanian citrus species, including wild taxa native to Australia and Papua New Guinea, form a genetically distinct clade within the Citrus L. (1753) genus. These species remain largely underexplored, despite their adaptation to diverse environments and relevance for citrus improvement. To support their use in breeding and evolutionary studies, we generated a high-quality, Chromosome-scale genome assembly of an Australian finger lime accession (SRA 1002), a natural interspecific hybrid. The genome was assembled using long-read sequencing, optical mapping, and a high-density genetic map, resulting in nine pseudomolecules covering over 97% of the genome. Using this reference, we analyzed whole-genome resequencing data from 132 accessions representing the diversity of Asian and Oceanian citrus. Variant calling across the dataset produced a high-resolution catalogue of single nucleotide polymorphisms (SNPs) and derived database of SNP fully discriminant of 20 Citrus species (DSNPs), enabling detailed exploration of inter- and intra-specific diversity. The data reveal a strong population structure within the group with clear heterozygosity variation between ancestral species and admixed accessions, reflecting their complex evolutionary history and hybridization patterns. This study provides the first integrated genomic framework for Oceanian citrus diversity, offering essential tools for downstream applications in citrus breeding, conservation, and evolutionary genomics. The resources generated lay the groundwork for future association studies and the targeted introgression of beneficial traits into cultivated citrus.

Fruits are increasingly recognized as an important part of a healthy diet. Fruit crops represent a wide range of woody perennial species grown in orchards. Water availability is a primary environmental factor limiting fruit crop growth and productivity. Erratic rainfall patterns and increased temperatures due to climate change are likely to increase the duration of droughts. This review aims to highlight the different mechanisms by which fruit crops respond to water stress deficits. Emphasis is placed on physiological, genetic and epigenetic determinants of stress response in fruit crops. These findings can contribute to a deeper understanding of the underlying effects of drought. We also describe new research opportunities made possible by the increasing availability of population-level genomic data from the field, including genome-wide association studies (GWAS) and high-throughput phenotyping.

Fruits and vegetables play a crucial role in addressing food security challenges posed by the growing global population. Citrus fruits are among the most widely cultivated crops worldwide; however, their production is steadily declining due to climate change. Among the various biotic and abiotic stresses affecting citrus production, water scarcity caused by climate change stands out as a significant issue. Interestingly, the rhizosphere of citrus plants is home to beneficial fungi known as arbuscular mycorrhizal fungi (AMF). AMF have been shown to enhance the growth and development of host plants. They also improve the plants’ tolerance to various stresses and enhance soil structure. This study aimed to evaluate the response of two different citrus rootstocks—Rangpur lime and Carrizo citrange—when subjected to three mycorrhizal treatments, namely, AMF+ (inoculated with AMF), AMF- (treated with fungicide to eliminate AMF), and a control (naturally occurring AMF), under conditions of water deficit. The results indicated that the AMF+ treatment had a significant positive effect on both rootstock genotypes compared to the AMF- treatment. Physiological attributes such as photosynthesis, stomatal conductance, transpiration, non-photochemical quenching, and both dark and light quantum yield exhibited significantly smaller declines under water deficit conditions in AMF+ plants compared to those in the AMF- and control groups. Conversely, stress indicators—such as malondialdehyde (MDA) and hydrogen peroxide (H2O2)—increased significantly in the AMF- treatment compared to AMF+. Additionally, the increase in antioxidative enzymes (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APx) and osmotic adjustment (proline (PRO)) was more pronounced in the AMF+ treatment in the leaves and roots of both citrus rootstocks. In conclusion, the findings suggest that the presence and application of AMF in citrus roots may enhance the plants’ ability to cope with water scarcity more effectively.

IntroductionCitrus is an important fruit crop for human health. The sensitivity of citrus trees to a wide range of abiotic stresses is a major challenge for their overall growth and productivity. Among these abiotic stresses, salinity results in a significant loss of global citrus yield. In order to find straightforward and sustainable solutions for the future and to ensure citrus productivity, it is of paramount importance to decipher the mechanisms responsible for salinity stress tolerance. Thisstudy aimed to investigate how ploidy levels influence salt stress tolerance in citrus by comparing the transcriptomic responses of diploid and tetraploid genotypes. In a previous article we investigated the physiological and biochemical response of four genotypes with different ploidy levels: diploid trifoliate orange (Poncirus trifoliata [L.] Raf.) (PO2x) and Cleopatra mandarin (Citrus reshni Hort. Ex Tan.) (CL2x) and their respective tetraploids (PO4x, CL4x).MethodsIn this study, we useda multifactorial gene selection and gene clustering approach to finely dissect the influence of ploidy level on the salt stress response of each genotype. Following transcriptome sequencing, differentially expressed genes (DEGs) were identified in response to salt stress in leaves and roots of the different citrus genotypes.Result and discussionGene expression profiles and functional characterization of genes involved in the response to salt stress, as a function of ploidy level and the interaction between stress response and ploidy level, have enabled us to highlight the mechanisms involved in the varieties tested. Saltstress induced overexpression of carbohydrate biosynthesis and cell wall remodelling- related genes specifically in CL4x Ploidy level enhanced oxidative stress response in PO and ion management capacity in both genotypes. Results further highlighted that under stress conditions, only the CL4x genotype up- regulated genes involved in sugar biosynthesis, transport management, cell wall remodelling, hormone signalling, enzyme regulation and antioxidant metabolism. These findings provide crucial insights that could inform breeding strategies for developing salt-tolerant citrus varieties.

IntroductionUseful germplasm for citrus breeding includes all sexually compatible species of the former genera Citrus, Clymenia, Eremocitrus, Fortunella, Microcitrus, Oxanthera, and Poncirus, now merged in the single Citrus genus. An improved knowledge on the synteny/collinearity between the genome of these different species, and on their recombination landscapes, is essential to optimize interspecific breeding schemes.MethodWe have performed a large comparative genetic mapping study including several main clades of the Citrus genus. It concerns five species (C. maxima, C. medica, C. reticulata, C. trifoliata and C. glauca), two horticultural groups resulting from interspecific admixture (clementine and lemon) and two recent interspecific hybrids (C. australis x C. australasica and C. maxima x C. reticulata). The nine individual genetic maps were established from GBS data of 1,216 hybrids.Results and discussionThe number of SNPs mapped for each parent varies from 760 for C. medica to 4,436 for the C. maxima x C. reticulata hybrid, with an average of 2,162.3 markers by map. Their comparison with C. clementina v1.0 assembly and inter-map comparisons revealed a high synteny and collinearity between the nine genetic maps. Non-Mendelian segregation was frequent and specific for each parental combination. The recombination landscape was similar for the nine mapped parents, and large genomic regions with very low recombination were identified. A consensus genetic map was successfully established. It encompasses 10,756 loci, including 7,915 gene-based markers and 2,841 non-genic SNPs. The anchoring of the consensus map on 15 published citrus chromosome-scale genome assemblies revealed a high synteny and collinearity for the most recent assemblies, whereas discrepancies were observed for some older ones. Large structural variations do not seem to have played a major role in the differentiation of the main species of the Citrus genus. The consensus genetic map is a useful tool to check the accuracy of genome assemblies, identify large structural variation and focus on analyzing potential relationships with phenotypic variations. It should also be a reference framework to integrate the positions of QTLs and useful genes identified in different analyses.

Citrus plants face various abiotic stresses like drought during their life span which significantly affect their active growth and development. Tetraploid (4x) plants are more adaptable to environmental constraints than diploid (2x) plants by inducing critical physiological and biochemical processes. In this study, tetraploid and their corresponding diploid sour orange rootstocks were subjected to drought stress for 12 days. Results revealed that drought stress significantly affected plant physiology by reducing photosynthesis rate, stomatal conductance, transpiration rate, and leaf colour, which was prominent in diploid plants compared to tetraploid plants. In diploid plants, phenotypic differences (i.e. wilting and rolling of leaves) were also significant. Diploids with more accumulation of malondialdehyde and hydrogen peroxide in their leaves and roots exhibited more oxidative damage. It was observed that tetraploid plants had higher activities of peroxidase and catalase enzymes, while lower superoxide dismutase was recorded in the leaves and roots of plants. Higher glycine betaine, proline, total soluble protein, total phenolic content, and antioxidant activities were also observed in the leaves and roots of tetraploids. Overall, results suggest that tetraploids in citrus can have better defence mechanisms that help them to sustain under water deficit scenarios.

Sexual breeding at the tetraploid level is a promising strategy for rootstock breeding in citrus. Due to the interspecific origin of most of the conventional diploid citrus rootstocks that produced the tetraploid germplasm, the optimization of this strategy requires better knowledge of the meiotic behavior of the tetraploid parents. This work used Genotyping By Sequencing (GBS) data from 103 tetraploid hybrids to study the meiotic behavior and generate a high-density recombination landscape for their tetraploid intergenic Swingle citrumelo and interspecific Volkamer lemon progenitors. A genetic association study was performed with root architecture traits. For citrumelo, high preferential chromosome pairing was revealed and led to an intermediate inheritance with a disomic tendency. Meiosis in Volkamer lemon was more complex than that of citrumelo, with mixed segregation patterns from disomy to tetrasomy. The preferential pairing resulted in low interspecific recombination levels and high interspecific heterozygosity transmission by the diploid gametes. This meiotic behavior affected the efficiency of Quantitative Trait Loci (QTL) detection. Nevertheless, it enabled a high transmission of disease and pest resistance candidate genes from P. trifoliata that are heterozygous in the citrumelo progenitor. The tetrazyg strategy, using doubled diploids of interspecific origin as parents, appears to be efficient in transferring the dominant traits selected at the parental level to the tetraploid progenies.

Citrus are classified as salt-sensitive crops. However, a large diversity has been observed regarding the trends of tolerance among citrus. In the present article, physiological and biochemical studies of salt stress tolerance were carried out according to the level of polyploidy of different citrus genotypes. We particularly investigated the impact of tetraploidy in trifoliate orange (Poncirus trifoliata (L.) Raf.) (PO4x) and Cleopatra mandarin (Citrus reshni Hort. Ex Tan.) (CL4x) on the tolerance to salt stress compared to their respective diploids (PO2x and CL2x). Physiological parameters such as gas exchange, ions contents in leaves and roots were analyzed. Roots and leaves samples were collected to measure polyphenol, malondialdehyde (MDA), ascorbate and H2O2 contents but also to measure the activities of enzymes involved in the detoxification of active oxygen species (ROS). Under control conditions, the interaction between genotype and ploidy allowed to discriminate different behavior in terms of photosynthetic and antioxidant capacities. These results were significantly altered when salt stress was applied when salt stress was applied. Contrary to the most sensitive genotype, that is to say the diploid trifoliate orange PO2x, PO4x was able to maintain photosynthetic activity under salt stress and had better antioxidant capacities. The same observation was made regarding the CL4x genotype known to be more tolerant to salt stress. Our results showed that tetraploidy may be a factor that could enhance salt stress tolerance in citrus.

Micronutrients are essential to plants, and enhancing their availability is one of the agronomic challenges to improving crop quality and yield. This study, under controlled greenhouse conditions, compares tomato plants’ responses to two different micronutrient EDTA-chelated formulations, one of them including a newly developed fulvate–lignosulfonate coating. Growth, yield, and several physiological parameters, including photosynthetic gas exchange, water-use efficiency, leaf nutrient content, leaf greenness and the effective quantum yield of photosystem II, were measured to compare their efficiency. The results showed that the new coated formulation significantly improved growth and most of the determined physiological parameters. At the end of the experiment, higher foliar levels of Fe (2.4-fold) and Mn (2.9-fold) were measured, revealing increased availability of lignofulfonate-complexed micronutrients compared to the traditional fertiliser. Moreover, the photosynthesis rate and stomatal conductance were 9- and 20-fold higher, respectively, than when using the standard fertiliser. In conclusion, the new coated fulvate–lignosulfonated fertiliser provided a more suitable source of micronutrients for tomato plant fertilisation, allowing for higher yields, which correlated with a generally improved physiological response.

Citrus fruit quality is defined as the combination of physical and chemical traits; some of which may change during the ripening phase, e.g., acidity and sugar content. A clear understanding of their genetic control would be very helpful for marker-assisted breeding programs especially with regard to the juvenile phase and some reproductive features that hamper the selection of improved hybrids. A genetic study was thus performed on the heredity of quality traits and QTL detection based on segregation in a progeny generated from a cross between clementine cv “Commun” ( Citrus × reticulata cv clementine ) and mandarin cv “Willow leaf” ( C. reticulata Blanco). Parental and consensus genetic linkage maps were constructed using 645 SNP and SSR markers. These maps were represented by 10 linkage groups in clementine and 12 linkage groups in mandarin, representing 75% and 58% respectively of the previously published clementine reference map. A total of 16 traits, including fruit mass, equatorial diameter, juice percentage, total soluble solids, acidity, pH, glucose, fructose, sucrose, and citric and malic acid concentrations were evaluated at three maturation dates. High variations indicating transgressive segregation were found for all traits, with normal or close to normal distributions. QTL analysis performed using the multiple QTL model allowed the detection of 34 QTLs on the three maps. QTLs were distributed in different linkage groups and generally detected at only one date of the ripening phase. The percentage of total variation explained ranged from 12 to 37% per QTL. Major QTLs ( R 2 ≥ 30%) were detected for equatorial diameter, glucose, and fructose (expressed in percentage dry matter) on linkage groups 8 and 9. Co-localization of QTLs controlling correlated and uncorrelated traits were mainly found on linkage groups 2, 4, 8, and 9, particularly between fruit mass and acidity.

Currently, drought stress is a major issue for crop productivity, and future climate models predict a rise in frequency and severity of drought episodes. Polyploidy has been related to improved tolerance of plants to environmental stresses. In Citrus breeding programs, the use of triploidy is an effective way to produce seedless fruits, one of the greatest consumer expectations. The current study used physiological and biochemical parameters to assess the differential responses to moderate water deficit of 3x genotypes compared to 2x genotypes belonging to the same hybridization. Both parents, the mandarin Fortune and Ellendale tangor, were also included in the experimental design, while the 2x common clementine tree was used as reference. Water deficit affects leaf water status, as well as physiological and detoxification processes. Triploid genotypes showed a better ability to maintain water status through increased proline content and photosynthetic capacity. Moreover, less oxidative damage was associated with stronger antioxidant defenses in triploid genotypes. We also found that triploidy improved the recovery capacity after a water deficit episode.

Rootstocks are an important component for citrus adaptation to increasing biotic and abiotic stresses resulting from global climate change. There is a strong complementarity between Citrus species, which adapt to abiotic stresses, and Poncirus trifoliata and its intergeneric hybrids, which exhibit resistances or tolerances to major diseases and pests. Thus, symmetrical somatic hybridization between complementary diploid rootstocks of these two genera appears to be an efficient way to develop new tetraploid rootstocks in order to address the new challenges of the citrus industry. New intergeneric somatic hybrids were obtained by electrofusion between protoplasts of Citrus and P. trifoliata hybrids. Extensive characterization of the nuclear and cytoplasmic genomes was performed by genotyping-by-sequencing (GBS) analysis. This revealed diploid cybrids and nuclear somatic hybrids. Mitochondrial genomes were mostly inherited from the callus parent, but homologous recombination events were observed for one parental combination. Chloroplasts exhibited random uniparental inheritance. GBS revealed local chromosomal instabilities for all nuclear somatic hybrids and whole chromosome eliminations for two hybrids. However, at the whole genome level, symmetrical addition of the nuclear genomes of both parents was predominant and all somatic hybrids displayed at least one trifoliate orange haplotype throughout the genome.