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Review

Physiological and Molecular Insights into Citrus Rootstock–Scion Interactions: Compatibility, Signaling, and Impact on Growth, Fruit Quality and Stress Responses

by
Peng Wang
1,
Feng Liu
1,
Yueting Sun
1,
Xiao Liu
2 and
Longfei Jin
1,*
1
Institute of Citrus Research, Zhejiang Academy of Agricultural Sciences, Taizhou 318026, China
2
College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
*
Author to whom correspondence should be addressed.
Horticulturae 2025, 11(9), 1110; https://doi.org/10.3390/horticulturae11091110
Submission received: 23 July 2025 / Revised: 9 September 2025 / Accepted: 12 September 2025 / Published: 13 September 2025
(This article belongs to the Special Issue Recent Advances in Citrus Cultivation and Scion–Rootstock Interactions)
Versions Notes

Abstract

Grafting is a crucial horticultural propagation technique that plays a vital role in citrus production and research. Selecting compatible rootstock–scion combinations is essential for achieving high yields and superior fruit quality in citrus cultivation. This paper reviews recent advances in the physiological and molecular mechanisms involved in rootstock–scion interactions in citrus, with a focus on (1) commonly used rootstocks, (2) graft compatibility, (3) signal molecule transport at the graft union, and (4) the effects of rootstock–scion interactions on citrus growth, nutrient absorption, fruit quality, and responses to both biotic and abiotic stresses. Additionally, we prospected the future research direction and practical applications of rootstock–scion interactions.

1. Introduction

Grafting is a widely used technique in the production and research of horticultural crops, including fruits and vegetables [1]. The part below the union point is called the rootstock, and the part above the union point is called the scion. Grafting has a long history in horticultural cultivation [2]. As early as 1000 BC, the practice of grafting woody plants had already begun in China [2]. The grafting technique was recorded in Aristotle’s (384 BC–322 BC) monograph [3]. During the late stage of the Western Han Dynasty (33 BC–7 BC), the grafting technique for bottle gourds was recorded in Fan Sheng Zhi Shu [4]. In Sixie Jia’s monograph, Qi Min Yao Shu, from the Northern Wei Dynasty, pear grafting techniques were meticulously recorded, encompassing grafting time, rootstock selection, grafting methods, post-grafting management, and the impact of grafting on pear fruit quality [2]. Similarly, in the monograph Ju Lu authored by Yanzhi Han during the Northern Song Dynasty, the timeframe and methods of citrus grafting were systematically described.
Citrus ranks among the most economically and agriculturally important fruit crops globally. According to the statistics of the FAO (https://www.fao.org/faostat/en/#home, accessed on 6 June 2025), in 2023, citrus was cultivated in 169 countries and regions worldwide. The total planting area of citrus fruits worldwide was 10.55 million hectares, and the output was 169 million tons. As a perennial woody fruit tree, the juvenile period of citrus fruits is relatively long. The seed-propagated seedlings usually take 6 to 8 years to flower and bear fruit [5]. The grafted citrus seedlings generally begin to flower and bear fruit in the following growing season. During the long-term evolution of perennial fruit trees, gene recombination and natural mutation have resulted in a high degree of heterozygosity and polyembryonic [6]. Although the phenotype of the seedlings grown directly from sowing mainly depends on the genetic characteristics of the mother plant, the offspring cannot completely inherit the superior traits of the parent plants. However, the grafted plants maintain the superior characteristics of the scion.
Grafting is a widely used and highly efficient asexual propagation technique in citrus production and research [7]. Common grafting techniques employed in citrus cultivation include bud grafting (such as chip bud, T-bud, inverted T-bud), branch grafting (including splice grafting, cleft grafting, whip & tongue grafting), and inarching grafting. High-quality citrus grafted seedlings, which combine the advantageous traits of both rootstocks and scions, form the foundation for achieving consistent, high-yield, and high-quality citrus production [8,9]. Meanwhile, selecting an optimal citrus rootstock–scion combination can significantly enhance the plant’s resilience to both biotic and abiotic stresses, including drought [10], low-temperature stress [11], high-temperature stress [12], salinity, waterlogging [13], and Huanglongbing (HLB) disease [14]. Low fruit quality, weak stress resistance, and delayed fruiting caused by inappropriate combinations of rootstocks and scions seriously hinder the development of the citrus industry [15,16]. Investigating the interaction mechanisms between citrus rootstocks and scions, and selecting suitable rootstock–scion combinations for cultivation, is of significant importance for advancing the theoretical understanding of citrus, enabling science-based selection of grafting combinations, and addressing practical challenges in citrus production. This article systematically summarizes the relevant research on the interaction between citrus rootstocks and scions over the years, aiming to provide a reference for the selection and application of citrus rootstocks and scions in the future.

2. The Commonly Used Rootstocks in Citrus Production

In long-term citrus cultivation, various regions have developed and identified locally adapted rootstocks that are specifically optimized for their unique environments. China primarily utilizes cold-tolerant trifoliate orange (Citrus trifoliata) as a rootstock, along with locally selected mandarin hybrids such as Hongju (C. reticulata) and Xiangcheng (C. junos). North American orchards feature Phytophthora-resistant hybrids including ‘Troyer/Carrizo’ citranges (C. trifoliata × C. sinensis), and ‘Swingle’ citrumelo (C. trifoliata × C. paradisi) [17]. Tropical regions utilize drought-tolerant genotypes, including Brazil’s ‘Rangpur’ lime (C. limonia) and India’s rough lemon (C. jambhiri), whereas Mediterranean climates are more suited to disease-resistant sour orange (C. aurantium). Arid regions, such as Israel, employ salt-tolerant ‘Palestine’ sweet lemon (C. × limon) for rootstock under saline conditions [18]. However, each rootstock still possesses certain limitations that hinder its ability to meet the diverse demands of production in complex cultivation environments. The information on the main citrus rootstocks, including their scientific names, main features, and suitable scions, is summarized in Table 1.
Trifoliate orange is the most commonly utilized rootstock in citrus cultivation, as it is compatible with the majority of citrus varieties [18,19]. Citrus grafted onto trifoliate orange displayed excellent tolerance to low-temperature stress, drought, and soil impoverishment [20,21]. In addition, citrus/trifoliate orange plants exhibited characteristics such as a dwarfed tree structure, early fruiting, and superior fruit quality [22,23]. In addition, trifoliate orange rootstock is resistant to foot rot/gummosis and nematode diseases. However, trifoliate orange rootstock exhibits susceptibility to cracking bark disease and broken leaf disease. Furthermore, when cultivated in saline-alkali soils (e.g., coastal tidal flats), trifoliate orange rootstocks frequently developed iron deficiency chlorosis due to reduced iron availability in high-pH conditions [24].
Citrange is a genetic hybrid between C. trifoliata and C. sinensis ‘Washington’ [25]. Citrus grafted onto citrange exhibits resistance or tolerance to citrus tristeza virus (CTV) and root rot disease [25]. Citrange is an appropriate rootstock for sweet lime, satsuma mandarin, Bendizao, Pokan, sweet orange, and grapefruit [19]. The widely used citrange in production is ‘Carrizo’, a variety developed in the USA [19].
Citrumelo is a genetic hybrid of trifoliate orange and grapefruit [26]. As a rootstock, the grafting plant exhibits vigorous growth, a well-developed root system, strong cold tolerance, and effective resistance to citrus tristeza virus (CTV) and foot rot disease. However, citrumelo is highly sensitive to cracking bark disease. Sweet orange grafted onto citrumelo showed a strong compatibility [16]. Lime grafted onto tetraploid ‘Swingle’ citrumelo showed better tolerance to Huanglongbing [14].
Hongju is a traditional citrus cultivar with a long history of cultivation in China, with color, delightful flavor, and aroma [19]. With an average of 8–20 seeds per fruit, Hongju exhibits desirable rootstock traits, making it a preferred rootstock for oranges, mandarins, and lemons. Citrus grafted onto Hongju rootstock exhibited an upright tree architecture, a well-developed root system with abundant fibrous roots, as well as enhanced tolerance to drought, waterlogging, and poor soil conditions [27]. Additionally, Hongju rootstock was demonstrated to exhibit strong resistance to root rot disease and Citrus excocortis virus disease (CEVd) [27]. Ponkan grafted onto Hongju exhibits high yield, large fruit size, thin and smooth skin, and excellent quality [27]. However, when employed as rootstocks for sweet oranges, Hongju resulted in excessive vegetative growth, delayed fruit maturation, and reduced yields and fruit quality compared to trifoliate orange.
Xiangcheng is a genetic hybrid of orange and tangerine. As a citrus rootstock, Xiangcheng exhibits vigorous tree growth, a robust root system characterized by deep main roots and abundant fibrous roots, early fruiting, high yield, superior fruit quality, heat tolerance, adaptability to poor soils and iron-deficient conditions, although it shows relatively low tolerance to excessive moisture [27]. Moreover, Ziyang Xiangcheng serves as an effective rootstock for cultivation in alkaline soil conditions [28,29]. Shuzhen No. 1 is a newly selected rootstock, which exhibits good compatibility with hybrid citrus and excellent fruit quality [30].
Sour orange (Citrus aurantium) serves as a rootstock that supports vigorous growth of the scion, develops a strong root system, enhances drought and salt tolerance, adapts to varying moisture conditions, and contributes to superior fruit quality [31]. Sour orange is an appropriate rootstock for oranges, tangerines, satsuma mandarin, lemons, and grapefruits. However, citrus scion grafted onto sour orange is sensitive to Citrus tristeza virus (CTV) and exhibits a late fruiting period. Commonly used sour orange varieties include ‘Goutoucheng’, ‘Daidai’, and ‘Zhuluan’ [19].
Sour pomelo (Citrus grandis) serves as an excellent rootstock for pomelo cultivars with superior compatibility and vigor in grafted plants. Sour pomelo fruits exhibit remarkably high seed counts, typically ranging from 80 to 130 seeds per fruit [19]. Grafted onto sour pomelo rootstock, the scion plants grow rapidly during the seedling stage, and the plants exhibit strong tree vigor and are relatively drought-tolerant. However, citrus varieties grafted onto sour pomelo rootstock exhibit limited waterlogging tolerance and produce fruits with significantly thicker pericarp compared to other rootstocks.
Rough lemon is an Indian native citrus with small, polyembryonic seeds and flowering and fruiting year-round. As a rootstock, it develops a well-established taproot system, which promotes vigorous growth in scions. Citrus grafted onto rough lemon showed broad soil adaptability, including tolerance to waterlogged conditions, moderate saline-alkaline soils, and resistance to CTV and CEVd [32]. However, the rough lemon used as a rootstock is sensitive to low temperatures and highly susceptible to foot rot disease [33].
Forner-Alcaide 5 (F-A 5) and Forner-Alcaide 13 (F-A 13) are two interspecific hybrids of ‘Cleopatra’ mandarin and trifoliate orange. As a rootstock, F-A 5 and F-A 13 are resistant to CTV. F-A 5 is resistant to the citrus nematode Tylenchulus semipenetrans Cobb, while F-A 13 is susceptible [34].
Table 1. The information on the main citrus rootstocks.
Table 1. The information on the main citrus rootstocks.
NameScientific NameFeaturesInsufficiencySuitable ScionsReference
Trifoliate orangeCitrus trifoliata(1) tolerance to low-temperature stress, drought, and soil impoverishment, (2) dwarfed tree structure, early fruiting, and superior fruit quality, (3) resistant to foot rot disease, gummosis, and nematode diseases(1) Susceptible to cracking bark disease and broken leaf disease, (2) Sensitive to iron deficiency and boron deficiencyThe vast majority of citrus varieties[18,19,20,21,22,23,24]
CitrangeC. trifoliata × C. sinensis ‘Washington’(1) robust root system, vigorous growth, (2) resistance to CTV, foot rot sensitive to iron deficiency and salinitysweet lime, satsuma mandarin, Bendizao, Pokan, sweet orange, and grapefruit[19,25,35]
CitrumeloC. grandi × C. trifoliata(1) vigorous growth, a robust root system, strong cold resistance, (2) resistance to CTV, foot rot, and HLBsensitive to cracking bark diseaseloose-skin mandarin and Hamlin sweet orange[27]
HongjuC. reticulata(1) upright tree structure, a robust root system with prolific fibrous roots, (2) tolerance to drought, waterlogging, and poor soil conditions, (3) resistance to root rot and CEVddelaying maturation timeoranges, mandarins, and lemons[27]
XiangchengC. junos(1) vigorous tree growth, lush root systems, deep main roots, numerous fibrous roots, early fruiting and high yield, good fruit quality, (2) tolerance to heat, poor soil, and iron deficiencysensitive to moistureLemon, sweet orange, hybrid citrus, Pokan, satsuma mandarin[28,29,30,36]
Sour orangeC. aurantium(1) scion plants grow vigorously, robust root system, good fruit quality, (2) tolerance to drought, salt, moisture, and aluminum stress(1) delaying maturation time, (2) sensitive to CTVorange, tangerine, satsuma mandarin, lemons, and grapefruit[31,37,38]
Sour pomeloC. grandi(1) strong tree vigor (2) tolerance to droughtsensitive to waterlogging‘Shatian’ pomelo, ‘Guanxi’ pomelo[39,40]
Rough lemonC. jambhiri(1) vigorous growth, robust taproot system, (2) tolerance to waterlogging and aluminum stress, (3) resistance to CTV and CEVd(1) sensitive to low temperatures, (2) highly susceptible to foot rot diseaselemon, lime, Ponkan, clemenules, grapefruit[37]
Forner Alcaide C. reshni × C. trifoliata(1) substandard to semidwarfing, (2) resistance to nematode Tylenchulus semipenetrans and Phytophthora sp.F-A13 is susceptible to the citrus nematodesweet orange, lemon[35,41,42]
US-812C. reticulata × C. trifoliata(1) highly productive, good fruit quality, moderate-sized tree, (2) tolerance or resistance to citrus tristeza virus (CTV) and citrus blightsusceptible to Phytophthora palmivorasweet orange, grapefruit, tangelo, citrus hybrids[43]
US-942C. trifoliata ‘Flying Dragon’ × C. reticulate ‘Sunki’(1) medium-sized tree, highly productive, good, (2) tolerance to mild salt stress, (3) tolerance to CTV, Phytophthora root rot/gummosis,susceptible to CEVd‘hamlin’ and ‘Valencia’ orange, mandarin[39,44]
X639C. reticulata ‘Cleopatra’ × C. trifoliata ‘Rubidoux’ (1) medium-sized tree, good internal fruit quality, (2) performs well on higher pH soil, (3) tolerance to Phytophthora root rot/gummosis, nematode, and CTV(1) sensitive to Phytophthora root rot, (2) Susceptible to creasinggrapefruit, Eureka lemons[45]

3. The Healing of the Grafting Union and the Compatibility Between the Stock and Scion

Complete healing of the cambium between rootstocks and scions is the prerequisite for successful grafting. The cambium connection process is involved in five biological stages: (1) the formation of the isolation layer and the initial adhesion between the rootstock and the scion; (2) the proliferation of callus cells; (3) the formation of the callus bridge at the grafting surface; (4) the repair of the xylem by differentiating the vascular cambium; (5) the reconstruction of vascular tissues between the rootstock and the scion [46]. Early studies demonstrated that vascular reconnection was established via the differentiation of newly formed vascular cambium from the callus, resulting in the formation of secondary xylem and phloem [47]. Recent research demonstrated that vascular bundle reconstruction occurred through the segmentation and interlocking of mature vascular tissue between rootstocks and scions. When the overlapping vascular tissues aligned, the continuous vascular bundles were reconstructed [48]. Treatment of citrus buds with 5 mM 6-benzylaminopurine (6-BA) significantly improves grafting survival rates by promoting cambium connection [49].
The survival rate of grafting mainly depends on the compatibility between the scion and the rootstock. The connection of vascular bundles after grafting is highly associated with the compatibility [50]. The incompatibility between rootstock and scion is common in citrus production [15]. In addition, grafting incompatibility often manifests several years after the procedure, causing yellowing of citrus leaves, premature tree decline, as well as reduced fruit yield and quality. This phenomenon represents one of the key factors constraining the sustainable development of the citrus industry [51]. Research on pomelo indicated that a significant increase in the abscisic acid (ABA) content in leaves was observed, along with upregulated expression of ABA biosynthesis genes (NCED2 and NCED3) in the incompatibility grafted combinations [51]. This grafting incompatibility was accompanied by starch accumulation and excessive glucose buildup in the phloem. Furthermore, chlorophyll content in the leaves significantly decreased, ultimately resulting in yellowing [51,52].

4. The Macromolecules and Information Exchange Between the Rootstock and the Scion

When a graft union forms, the cell walls of the rootstock and scion integrate tightly, establishing direct intercellular connections via plasmodesmata. These specialized channels facilitate the exchange of small molecules and signaling compounds between the rootstock and the scion [3]. Recent studies have revealed that plasmodesmata facilitate long-distance transport of macromolecules (DNA, RNA, miRNA, and proteins) between rootstocks and scions [53,54]. Integrated transcriptomic and single-nucleotide polymorphism (SNP) analyses demonstrated that mRNA is transmitted bidirectionally between citrus rootstocks and scions [55,56]. When trifoliate orange is employed as a rootstock, the root-to-shoot translocation of 24-nucleotide small RNAs is impaired, leading to a reduction in 24-nt small RNAs (sRNAs) in orange scions compared to autografting [18]. The citrus FLOWERING LOCUS T protein was observed to be bidirectionally transported between the rootstock and the scion through the graft interface, which regulated citrus plant flowering [57,58]. DNA methylation is also involved in the signal communication between the scion and the rootstock. Trifoliate orange as the rootstock obviously induces DNA demethylation in sweet orange scions [18]. These demethylated genes were mainly enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, pentose phosphate pathway, and plant—pathogen interaction, which might be one of the important reasons for the improvement of fruit quality and better resistance to both biotic and abiotic stresses of trifoliate orange rootstocks [18].

5. Effect of Rootstock–Scion Interactions on Plant Growth, Development, and Precocity

The interaction between rootstocks and scions has significant effects on the growth and development of citrus plants, including the tree architecture, tree vigor, and juvenile stage. Trifoliate orange, ‘Flying Dragon’ trifoliate orange, and Xiangcheng rootstocks exhibit a dwarfing effect on citrus plant growth, whereas sour orange, Hongju, and rough lemon promote more vigorous growth [59]. Liu studied the effects of five rootstocks on the growth of citrus trees and found that mandarin trees grafted onto ‘Canton’ lemon and rough lemon rootstocks showed significantly larger canopies than autografting and those grafted onto Hongju and sweet orange rootstocks [60]. Zhu et al. evaluated the growth performance of three late-ripening navel oranges grafted onto different rootstocks and found that the scions grafted onto ‘Carrizo’ citrange exhibited the most vigorous growth, while those grafted onto trifoliate orange showed the weakest growth [61]. rootstock–scion interactions affecting citrus growth may be strongly linked to variations in photosynthetic efficiency [11]. Sweet orange grafted onto two different rootstocks (‘Swingle’ citrumelo and ‘Sunki’ mandarin) showed significant differences in gas exchange capacity of the scion leaves [62]. Comparative anatomical studies revealed that variations in vascular bundle differentiation and connectivity across different grafting combinations may constitute a key physiological mechanism underlying rootstock-mediated regulation of scion growth. Rough lemon (vigorous rootstock) possessed lower proportions of phloem in the stems and roots as well as larger vessel elements in the xylem, when compared with ‘flying dragon’ trifoliate orange (dwarfing rootstock) [63]. Subsequent studies demonstrated that impaired hydraulic conductivity resulting from anatomical disparities in vascular tissues between rootstock and scion served as a primary physiological mechanism underlying the dwarfing effect induced by ‘flying dragon’ trifoliate orange [64]. Transcriptomic analyses revealed that the dwarfing effect in trifoliate orange and its ‘flying dragon’ variant was associated with significant down-regulation of auxin synthesis genes (YUC and AUX) and auxin response genes (Aux/IAA and SAUR) [59].
Citrus precocity is largely influenced by the rootstock and is closely dependent on the dynamic interactions between the rootstock and the scion. ‘Mandared’ mandarin grafted C35 citrange, Carpenter (C54) citrandarin, and Bitters (C22) citrandarin started to set fruits one year earlier than the trifoliate orange, Troyer citrange and Swingle citrumelo [65]. A similar trial was observed in Scirè Tarocco blood orange [66]. The maturation of citrus fruits is mainly regulated by abscisic acid and ethylene [67]. The differences in fruit maturity periods among different rootstocks might be caused by the rootstock–scion interaction affecting hormone homeostasis.

6. Effect of Rootstock–Scion Interactions on Nutrient Absorption

The nutrient utilization of citrus involves absorption, transportation, conversion, and utilization. The nutrient uptake and utilization in grafted citrus plants are collectively influenced by the rootstock’s capacity to absorb and translocate minerals, as well as the scion’s efficiency in transporting, assimilating, and utilizing these nutrients [68]. Ahmed et al. compared the mineral nutrient contents of leaves of ‘Kinnow’ mandarin grafted onto nine different rootstocks and found that the nitrogen and phosphorus contents grafted onto rough lemon were significantly higher than those of tangerine [69]. The absorption, transportation, and utilization efficiency of boron by different citrus rootstocks were significantly different [70]. The boron absorption, transportation, and utilization efficiency of navel oranges grafted onto citrange rootstock was higher than trifoliate orange [71,72,73], and the combination of ‘Fengjie’ navel orange scions had a higher boron utilization efficiency than ‘Newhall’ navel orange [74]. Cleft grafting ‘Carrizo’ citrange onto ‘Newhall’ navel orange (grafted onto trifoliate orange) effectively enhanced boron uptake and alleviated boron deficiency symptoms [75]. The absorption efficiency of iron varies significantly among different citrus rootstocks [76]. In alkaline soil, satsuma mandarin grafted onto trifoliate orange rootstock exhibited severe iron deficiency chlorosis, whereas those grafted onto ‘Zhique’ (Citrus wilsonii) rootstock grew normally [24]. Transcriptomic analysis revealed that, in a high pH environment, the expression of iron absorption-related genes (FRO and IRT) in ‘Zhique’ was significantly higher than that in trifoliate orange [76]. The transcriptional activation of plasma membrane H+-ATPase mediated by MYB308 might be the main reason for the iron absorption capacity of the ‘Zhique’ (C. wilsonii) rootstock [77]. Simultaneously, different scion cultivars significantly influence rootstock nutrient uptake through regulating the diversity of rhizosphere microbial communities. For example, Song et al. employed 18S rRNA sequencing analysis to demonstrate that scion genotypes significantly alter arbuscular mycorrhizal fungal community diversity in the rootstock rhizosphere, consequently affecting citrus nutrient acquisition [78].

7. Effect of Rootstock–Scion Interactions on Fruit Quality

As economic conditions improve, consumers’ demand for both the external appearance and internal quality of fresh citrus fruits has increased significantly. The citrus appearance quality includes the individual fruit weight, the color of the fruit skin, the thickness of the fruit skin, the fruit shape index, and the smoothness of the fruit surface. Internal qualities include the content of soluble solids, sugar, organic acids, vitamin C, phenolic substances, volatile substances, etc. Citrus fruit size can be significantly influenced by different rootstock cultivars. For example, the fruit weight of ‘Nehall’ navel oranges grafted onto the dwarf hybrid rootstock ‘Forner-Alcaide 418’ was significantly higher than that onto ‘Carrizo’ citrange [79]. Interestingly, similar results were also observed in ‘Shatangju’ Mandarin. ‘Shatangju’ trees grafted onto ‘Canton’ lemon produced larger fruits in terms of fruit weight and fruit transverse diameter than those grafted onto trifoliate orange [80]. The difference in fruit size might be caused by an increase in auxin levels and upregulation of AUX1 in fruits from trees grafted onto ‘Canton’ lemon [80].
The color of citrus peels is mainly dependent on the accumulation and composition of pigments such as chlorophyll, carotenoids, and anthocyanins [81]. Color in Citrus fruits is mainly provided by carotenoids and anthocyanins, specifically in blood oranges [81]. Numerous studies have revealed that the rootstock–scion interaction affects the color of citrus peels. For example, ‘Star Ruby’ grapefruit scions grafted onto ‘Cleopatra’ mandarin rootstock showed yellow peel, whereas those grafted onto ‘Swingle’ citrumelo rootstock exhibited pink [82]. The fruit color index of ‘Nehall’ navel oranges grafted onto the dwarf hybrid rootstock ‘Forner-Alcaide 418’ was significantly lower than that of the ‘Carrizo’ citrange [79]. Anthocyanin content is a paramount importance quality trait to “blood oranges”. Rootstock affects anthocyanin biosynthesis and accumulation in citrus. The ‘Tarocco Scirè’ grafted onto ‘Bitters’ ‘Troyer’ and ‘Carrizo’ exhibits a significantly higher level of anthocyanins in fruit pulp, compared with ‘Swingle’ citrumelo [66]. The accumulation of carotenoids and anthocyanins in citrus fruits is predominantly influenced by genetics, hormone metabolism, environmental factors, and cultivation management techniques. The choice of different rootstocks impacts the growth of scions and nutrient absorption, thus regulating the pigment content of citrus fruits. However, the physiological and molecular mechanisms of pigment accumulation in citrus fruits through rootstock–scion interactions remain to be further investigated and explored.
Soluble solids content (SSC) is a key biochemical parameter used to assess the internal quality of citrus fruits. Research on navel oranges showed that the SSC of fruits grafted onto trifoliate oranges is significantly higher than those onto ‘Ziyang’ Xiangcheng and Hongju rootstocks [61]. The sugar content of Kiyomi tangerines grafted onto ‘Ziyang’ Xiangcheng is lower compared to that of trifoliate oranges [83]. The SSC of grapefruit grafted onto lime rootstocks was 9.93, significantly higher than that grafted onto ‘Volkamer’ lemon rootstocks (7.81) [84]. The rootstock–scion interaction significantly altered phytohormone homeostasis in shoot tissues. Abscisic acid (ABA) is a key phytohormone that modulates ripening progression and sugar metabolism in citrus fruits [85]. Lemon scions grafted onto ‘Swingle’ citrumelo exhibited a 40% increase in IAA/ABA ratio, whereas scions grafted onto ‘Flying Dragon’ trifoliate oranges showed a 30% reduction compared to that of trifoliate orange [86]. ‘Shatangju’ mandarin grafted onto tangerine rootstock also exhibited significantly higher ABA levels compared to those grafted onto ‘Canton’ lemon rootstock [80]. This elevated ABA content likely contributed to the increased SSC accumulation observed in the tangerine-grafted fruits. The sucrose accumulation in citrus fruits is principally regulated by sucrose-phosphate synthase (SPS) and neutral invertase (NI) [87,88]. Rootstock selection significantly influences these enzymatic activities in scion fruits. Trifoliate orange rootstock increased SPS and NI activity and gene expression level in scions [83]. MicroRNAs (miRNAs) play a crucial regulatory role in rootstock–scion interactions in citrus plants. The rootstock might downregulate Cre-miR399-3p expression in scion, leading to the upregulation of its target gene CreINVE, thereby enhancing sugar metabolism and improving fruit quality [89].
Citrus fruits are abundant in functional components beneficial to human health, including flavonoids, phenolic acids, terpenes, and other functional substances [90]. Extensive research demonstrated that the functional compounds and antioxidant capacity in citrus fruits were significantly modulated by rootstock selection [91,92,93]. For example, metabolomic analysis revealed that trifoliate orange significantly enhanced the deacetylnomylinic acid and sudachinoid A contents of citrus fruits, while ‘Carrizo’ citrange dramatically increased evodol and rutaevin contents [92]. Citrus peel flavonoids serve as both major secondary metabolites and the principal bioactive constituents of Chénpi, a valued traditional Chinese medicinal material [90,94]. Multi-omics analysis demonstrated that ‘Chachi’ (Citrus reticulata) grafted onto the trifoliate orange rootstock exhibited significantly higher flavonoid content in peel compared to both autografting plants and those grafted onto lemon rootstocks. Gene expression analysis revealed that the trifoliate orange rootstock up-regulated the expression of genes related to flavonoid synthesis in the ‘Chachi’ scion, consequently enhancing flavonoid accumulation [95]. Moreover, he interactions between rootstock and scion can also influence the accumulation of ascorbic acid in citrus fruits. Compared with Volkamer lemon, SB812, and C. macrophylla rootstocks, the pomelo grafted onto sour orange showed the highest ascorbic acid concentration [38]. The interstock is a crucial horticultural technique employed to address the incompatibility issues in grafting between the scion and the rootstock of certain citrus varieties. The research on grapefruit revealed that the grafting combination of grapefruit with Changshanhuyou as the interstock presented better fruit appearance, higher sugar content, and greater aromatic substance content [96].

8. Effect of Rootstock–Scion Interactions on Responses to Biotic and Abiotic Stresses

Numerous studies have demonstrated that rootstock–scion interaction significantly regulates the response of grafting plants to abiotic stresses. Under drought, extreme temperatures (low and high), and salinity stress, citrus plants enhance their stress resilience primarily through three key mechanisms: (1) accumulation of osmoregulatory compounds (e.g., proline, soluble sugars), (2) upregulation of antioxidant enzyme activities (e.g., SOD, CAT, POD), and (3) efficient scavenging of reactive oxygen species (ROS) and malondialdehyde (MDA) [97].

8.1. Drought

With global warming, extreme weather events are occurring more frequently in citrus-growing areas. Seasonal drought is a significant limiting factor that hinders the growth of citrus fruits, resulting in a decline in fruit yield and quality [98]. Under water deficiency, the stomata conductivity, transpiration, and net carbon dioxide assimilation of citrus trees all declined [99]. Beyond irrigation optimization, proper rootstock–scion pairing serves as a key approach to mitigate water stress in citrus production. The tolerance of different citrus rootstocks to drought stress varies significantly. For example, Shafqat evaluated and analyzed the drought tolerance of 10 citrus rootstocks in Pakistan and found that Brazilian sour orange was tolerant to drought, while ‘Sovage’ citrange and ‘Yuma’ citrange were sensitive to drought [100,101]. The rootstock’s inherent drought tolerance capacity significantly influences the scion performance through rootstock–scion interactions. Under drought stress, ‘Carrizo’ citrange positively influenced scion by reducing H2O2 accumulation, increasing superoxide dismutase (SOD) and ascorbate peroxidase (APX) enzymatic activities, and inducing SOD1, APX, and catalase (CAT) protein accumulations [102]. Ploidy plays a crucial role in determining the drought tolerance of citrus [103]. RNA-Seq revealed that rootstock-conferred drought tolerance in sweet orange involves transcriptional regulation, including upregulation of cell wall, antioxidant, and ABA pathway genes, alongside downregulation of starch metabolism and ethylene signaling [104]. Tetraploid rootstocks confer superior long-term drought tolerance to sweet oranges via ABA-mediated stomatal control and enhanced cuticular wax deposition [10,105].

8.2. Cold

Citrus fruits evolved in southern China and are naturally suited to warm, humid climates [106]. During the process of gradually decreasing temperature, citrus can better adapt to cold stress that is not too low through cold acclimation [107,108]. However, the rapid temperature decline associated with cold waves often results in devastating losses for the citrus industry. The optimal annual average temperature for citrus growth is 16.5–23 °C. Low-temperature stress induces structural alterations in citrus cell membranes, leading to impaired functionality of membrane-associated proteins and ion channels, ultimately compromising membrane integrity and promoting intracellular solute leakage [97]. The cold tolerance of Valencia delta seedless oranges grafted onto ‘Carrizo’ citrange (cold-tolerant) is significantly greater than that of those grafted onto C. macrophylla (cold-sensitive) [109]. Comprehensive analysis of the transcriptome and metabolome revealed that sweet oranges grafted onto cold-resistant rootstocks accumulated more abscisic acid, upregulated the expression of cold-adaptation-related genes, and thereby enhanced the cold tolerance of the citrus plant [109]. The sensitivity of different citrus rootstocks to low temperatures varies significantly. Trifoliate orange is currently recognized as the most cold-tolerant rootstock among citrus. The effects of low-temperature stress on citrus grafted onto different rootstocks also differ markedly. Under low-temperature stress, the decline in net photosynthetic rate, stomatal conductance, chlorophyll fluorescence, and starch content of clementine oranges grafted onto tetraploid orange rootstocks was significantly lower than that of grafted onto diploid rootstocks. Furthermore, the activities of CAT, APX, and dehydroascorbate reductase in clementine oranges grafted onto tetraploid rootstocks were considerably higher than those in diploid rootstocks [11]. In addition to air temperature, soil temperature significantly influences citrus growth and root physiology. Citrus root systems exhibit distinct thermal responses: initial growth commences at 12 °C, with optimal growth and nutrient uptake occurring between 23 and 31 °C. Root activity declines when soil temperatures fall below 19 °C and ceases entirely above 39 °C. Notably, cold tolerance thresholds vary among species: sweet orange, mandarin, grapefruit, and lemon roots lose nutrient absorption capacity below 7.2 °C, while trifoliate orange and sour orange maintain uptake functionality even at temperatures below 5 °C [27]. The observed variation in cold resistance among different rootstock–scion combinations may be attributed to differences in rootstock performance regarding mineral nutrient and water uptake under low-temperature stress.

8.3. Salinity

Salinity stress represents a major abiotic constraint that significantly impairs citrus growth and development [110]. Major citrus-producing regions, including Israel, Australia, the United States, Pakistan, and Spain, frequently experience severe salt-induced damage in commercial orchards [111,112]. In addition to soil salinity, high salt concentrations in irrigation water significantly contribute to citrus salt stress [113]. Furthermore, with the expansion of protected cultivation, secondary soil salinization resulting from prolonged rain exclusion and elevated evaporation rates in greenhouses has emerged as a critical constraint on citrus yield and fruit quality [31]. The tolerance of different citrus rootstocks to salt damage also varies significantly. The most commonly used rootstock of citrus, trifoliate orange, is relatively sensitive to salt stress [114]. In coastal citrus production areas, citrus grafted onto trifoliate orange rootstocks frequently exhibit salt stress symptoms, including leaf chlorosis, defoliation, and premature decline. In contrast, sour orange rootstocks demonstrate significantly greater salt tolerance. Studies indicate that sour orange rootstocks (locally termed ‘Goutoucheng’) mitigate salt damage by restricting sodium ion translocation to both roots and aerial parts, thereby protecting scion physiology [115]. Physiological and anatomical studies have found that US-942 hinders the absorption of NaCl through the formation of an apoplastic barrier in the root, thus demonstrating a tolerance to mild salt stress (30 mM NaCl) [39]. Therefore, strategic rootstock selection represents an effective approach to enhance citrus salt tolerance, serving as a crucial cultivation practice in saline-affected regions.

8.4. High Soil pH

The optimal soil pH range for citrus cultivation is 5.5–6.5 [27]. Cultivated in alkaline soil, citrus exhibits symptoms of iron deficiency chlorosis [24]. This phenomenon is especially prominent in the middle and upper reaches of the Yangtze River in China, including Yichang in Hubei Province, Chongqing, Sichuan, southern Shanxi, and the Danjiang Reservoir region [116]. The resulting leaf yellowing significantly compromises both fruit yield and quality. Notably, different citrus rootstocks exhibit substantial variation in their tolerance to elevated soil pH. For instance, satsuma mandarin grafted onto trifoliate orange rootstocks demonstrate pronounced iron deficiency symptoms with severe leaf chlorosis, whereas those grafted onto ‘Zhique’ rootstocks showed normal growth under identical soil conditions [24,77].

8.5. Huanglongbing

Huanglongbing (HLB), also known as citrus greening disease, represents the most devastating phytopathological threat to global citrus production, resulting in substantial economic losses worldwide [117,118]. Citrus HLB can be mainly classified into Asian HLB and African HLB based on the types of pathogen vectors, characteristics, and geographical distribution. The primary pathogen vectors responsible for the transmission of citrus HLB include the African citrus psyllid (Trioza erytreae) and the Asian citrus psyllid (Diaphorina citri), and Cacopsylla citrisuga Yang & Li. Emerging evidence suggests that rootstock–scion interactions enhanced citrus tolerance to HLB. For example, Australian lime-derived hybrids as rootstocks to increase HLB tolerance in citrus through alternating chlorophyll biosynthesis, starch accumulation, and levels of phenolic and flavonoid compounds [119]. The ‘Mexican’ and ‘Persian’ limes grafted onto the tetraploid ‘Swingle’ citrumelo rootstock exhibited significantly higher tolerance to HLB than those grafted onto the diploid rootstock [14]. Histopathological analysis revealed that more pronounced degeneration of secondary root structures was observed in diploid rootstocks relative to tetraploid rootstocks [14]. Meanwhile, differential susceptibility of citrus rootstock–scion combinations to HLB infection may be partially mediated by rootstock-induced modifications in host plant volatiles. As a result, this could influence Trioza erytreae feeding preferences and transmission efficiency. Trioza erytreae clearly preferred to host and feed on C. macrophylla and ‘Carrizo’ citrange [120].

9. Conclusions and Prospects

Grafting, an ancient horticultural technique, has been practiced and applied in citrus cultivation for over three millennia. In recent years, high-throughput genomic sequencing and advanced molecular biology techniques have been increasingly employed in citrus graft biology research. The physiological and molecular mechanisms underlying citrus rootstock–scion interactions have been progressively elucidated. Compatible rootstock–scion combinations effectively regulate plant growth and development, enhance water and nutrient uptake efficiency, improve fruit yield and quality, and increase tolerance to various abiotic stresses, including drought, low temperature, and soil salinity, as well as improve resistance to biotic threats such as HLB. However, the rootstock–scion interaction mechanisms remain poorly understood, particularly at the molecular level. In addition, numerous studies focus on investigating rootstock-mediated effects on scion performance, while the reciprocal influence of scions on rootstock growth, development, and stress responses remains poorly understood. Recent research on the bidirectional transport of genetic material in grafting systems revealed that the quantity of genetic material moving downward from scion to rootstock was significantly greater compared to upward transport [18]. This transport bias highlights the essentials to elucidate the underlying molecular mechanisms of the scion on the rootstock. The application of high-throughput sequencing technologies coupled with advanced molecular biology approaches will substantially advance our understanding of rootstock–scion interactions in citrus. Current understanding of long-distance transport mechanisms for nucleic acids and proteins in citrus graft unions remains limited. While preliminary evidence confirms bidirectional macromolecule trafficking between rootstocks and scions, the precise molecular mechanisms governing this transport, including regulatory pathways and signaling networks, remain largely uncharacterized and warrant systematic investigation.
Extensive research has demonstrated that hybrid rootstocks (such as X639 [121], US-812 [43], US-942 [39]) exhibit remarkable environmental adaptability. The high interspecific compatibility within the Citrus genus makes hybridization a crucial approach for developing superior novel rootstocks. Recent studies reveal that polyploid citrus varieties display exceptional environmental resilience and agronomically desirable traits (e.g., dwarfing, drought tolerance [10,103], salt tolerance [122,123], cold tolerance [11] and better tolerance to HLB [14]). The application of somatic hybridization techniques to produce tetraploid and allotetraploid rootstock materials represents a promising direction in citrus rootstock breeding [124]. With advancements in modern molecular biology, targeted trait improvement in citrus can now be achieved through precision molecular breeding techniques, including transgenic and gene editing technologies [125,126]. The integration of multi-omics association analyses enables the identification of key genes governing critical agronomic traits in rootstocks and elucidation of their molecular regulatory mechanisms, thereby providing valuable genetic resources for molecular breeding programs. As technological iterations progress, molecular breeding is poised to play an increasingly pivotal role in the development of novel citrus rootstock cultivars.

Author Contributions

Conceptualization, P.W. and L.J.; investigation, L.J., F.L., Y.S. and X.L.; writing—original draft preparation, L.J.; writing—review and editing, P.W. and L.J.; supervision, P.W.; funding acquisition, P.W. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Key Research and Development Program, grant number 2024YFD2300804.

Conflicts of Interest

The authors declare no conflicts of interest.

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Wang, P.; Liu, F.; Sun, Y.; Liu, X.; Jin, L. Physiological and Molecular Insights into Citrus Rootstock–Scion Interactions: Compatibility, Signaling, and Impact on Growth, Fruit Quality and Stress Responses. Horticulturae 2025, 11, 1110. https://doi.org/10.3390/horticulturae11091110

AMA Style

Wang P, Liu F, Sun Y, Liu X, Jin L. Physiological and Molecular Insights into Citrus Rootstock–Scion Interactions: Compatibility, Signaling, and Impact on Growth, Fruit Quality and Stress Responses. Horticulturae. 2025; 11(9):1110. https://doi.org/10.3390/horticulturae11091110

Chicago/Turabian Style

Wang, Peng, Feng Liu, Yueting Sun, Xiao Liu, and Longfei Jin. 2025. "Physiological and Molecular Insights into Citrus Rootstock–Scion Interactions: Compatibility, Signaling, and Impact on Growth, Fruit Quality and Stress Responses" Horticulturae 11, no. 9: 1110. https://doi.org/10.3390/horticulturae11091110

APA Style

Wang, P., Liu, F., Sun, Y., Liu, X., & Jin, L. (2025). Physiological and Molecular Insights into Citrus Rootstock–Scion Interactions: Compatibility, Signaling, and Impact on Growth, Fruit Quality and Stress Responses. Horticulturae, 11(9), 1110. https://doi.org/10.3390/horticulturae11091110

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