Citrus Genotypes Research Articles

Resistance of citrus crops in Abkhazia to damage by the woolly whitefly Aleurothrixus floccosus (Maskell)

Citrus crops are the most important among subtropical crops in the Republic of Abkhazia. In 2019-2020 a new pest was discovered in the citrus agrocenosis of Abkhazia – the woolly whitefly Aleurothrixus floccosus (Maskell). The pest has been identified in all regions of the country. The degree of damage to mandarin on industrial plantations reaches 50% and more. An assessment of the resistance of 79 varieties of citrus crops from the collection of the Institute of Agriculture of the Academy of Sciences of Abkhazia to damage by a woolly whitefly (Gulrypsh district of the Republic of Abkhazia) was carried out. The degree of damage to citrus genotypes was different. It was found that the most affected varieties are Citrus limon (L.) Osbeck, as well as C. × meyeri and C. aurantifolia Sw. Tangerine, orange varieties (Hamlin, Maro and Grushevidny Koroliok) and pompelmus varieties (Mato Buntan, Natsu mican, Meteleva) are the least damaged.

Triploidy in Citrus Genotypes Improves Leaf Gas Exchange and Antioxidant Recovery From Water Deficit.

The triploidy has proved to be a powerful approach breeding programs, especially in Citrus since seedlessness is one of the main consumer expectations. Citrus plants face numerous abiotic stresses including water deficit, which negatively impact growth and crop yield. In this study, we evaluated the physiological and biochemical responses to water deficit and recovery capacity of new triploid hybrids, in comparison with diploid hybrids, their parents (“Fortune” mandarin and “Ellendale” tangor) and one clementine tree used as reference. The water deficit significantly decreased the relative water content (RWC) and leaf gas exchange (Pnet and gs) and it increased the levels of oxidative markers (H2O2 and MDA) and antioxidants. Compared to diploid varieties, triploid hybrids limited water loss by osmotic adjustment as reflected by higher RWC, intrinsic water use efficiency (iWUE Pnet/gs) iWUE and leaf proline levels. These had been associated with an effective thermal dissipation of excess energy (NPQ) and lower oxidative damage. Our results showed that triploidy in citrus enhances the recovery capacity after a water deficit in comparison with diploids due to better carboxylation efficiency, restored water-related parameters and efficient antioxidant system.

Patterns of genetic structure and evidence of Egyptian Citrus rootstock based on informative SSR, LTR-IRAP and LTR-REMAP molecular markers

BackgroundReleasing the draft genome of sweet orange provides useful information on genetic structure and molecular marker association with heritable breeding traits in citrus species and their structures. Last decades, microsatellite and retrotransposons are well known as a significant diverse component of the structural evolution. They represented the most potent elements for assessing sustainable utilization of the complicated classification in citrus breeding. Our study was performed to verify the structure analysis and the parentage genetic diversity among the Egyptian citrus rootstocks and the related species. ResultsHere, the performance of 26 SSR and 14 LTR-IRAP in addition to 20 LTR-REMAP markers have been used to conduct the discriminating power and the status of the genetic structure analysis among twenty specimens of citrus genotypes. As a result, the three markers approach exhibited a remarkable variation among the tested genotypes. Overall, the three markers have different discrimination power; the co-dominant SSR markers can differentiate within the group level only in addition to the species level of sour orange, while the dominant markers LTR-IRAP had the ability to discriminate among the group level in addition to species level and the origin of acids. Similarly, LTR-REMAP is suitable for classifying the group level and species level for mandarins as well the origin of Egyptian acids; probably due to it is integration of SSR and LTR-IRAP techniques. Structure and PCoA results of LTR-REMAP marker in strong support for the group structure of citrus species have been divided into four sets: acids, grapefruit/pummelo, mandarin/orange, and sour orange. ConclusionOur findings of the genetic structure analysis support the monophyletic nature of the citrus species; are able to provide unambiguous identification and disposition of true species and related hybrids like lemon, lime, citron, sour orange, grapefruit, mandarin, sweet orange, pummelo, and fortunella; and resulted in their placement in individual or overlap groups. The outcomes of these results will offer helpful and potential information for breeding programs and conservation approaches as a key stage toward identifying the interspecific admixture and the inferred structure origins of Egyptian citrus rootstock and acid cultivars.

Comparing bacterial properties in relation to the virulence factors of Xanthomonas citri subsp. citri strains and evaluating resistance of subtribe Citrinae cultivars to the most virulent strain

Citrus Bacterial Canker disease, caused by Xanthomonas citri subsp. citri (Xcc), is one of the most devastating diseases that attacks citrus, especially in the southern areas of Iran. The objective of this investigation was to analyze several characteristics involved in Xcc virulence in relation to strain aggressiveness. To achieve this, swarming motility, biofilm formation, resistance to H2O2, and production of xanthan were evaluated considering 44 local strains causing citrus bacterial canker disease in Iran. All strains showed differential swarming motilities, biofilm formation abilities, and xanthan production. The most virulent strain, Xcc-KVXCC1, exhibited the greatest capability to form biofilm on solid surfaces, xanthan production, and pathogenicity on detached leaves of Citrus aurantifolia as well as positive chemotaxis toward C. aurantifolia extract. In this study, a total of 14 common and commercial citrus genotypes were evaluated for resistance to Xcc-KVXCC1. Genotypes were categorized into susceptible and resistant groups based on lesion number per inoculation site. Based on our results, C. aurantifolia was the most susceptible citrus cultivar to Xcc-KVXCC1. In contrast, C. aurantium, C. jumbhori, and C. reticulata cv. ponkan demonstrated high and moderately high resistance against Xcc-KVXCC1.

Citrus Vascular Proteomics Highlights the Role of Peroxidases and Serine Proteases during Huanglongbing Disease Progression

Huanglongbing (HLB) is the most devastating and widespread citrus disease. All commercial citrus varieties are susceptible to the HLB-associated bacterium, Candidatus Liberibacter asiaticus (CLas), which resides in the phloem. The phloem is part of the plant vascular system and is involved in sugar transport. To investigate the plant response to CLas, we enriched for proteins surrounding the phloem in an HLB susceptible sweet orange variety, Washington navel (Citrus sinensis (L) Osbeck). Quantitative proteomics revealed global changes in the citrus proteome after CLas inoculation. Plant metabolism and translation were suppressed, whereas defense-related proteins such as peroxidases, proteases and protease inhibitors were induced in the vasculature. Transcript accumulation and enzymatic activity of plant peroxidases in CLas infected sweet orange varieties under greenhouse and field conditions were assessed. Although peroxidase transcript accumulation was induced in CLas infected sweet orange varieties, peroxidase enzymatic activity varied. Specific serine proteases were up-regulated in Washington navel in the presence of CLas based on quantitative proteomics. Subsequent activity-based protein profiling revealed increased activity of two serine proteases, and reduced activity of one protease in two C. sinensis sweet orange varieties under greenhouse and field conditions. The observations in the current study highlight global reprogramming of the citrus vascular proteome and differential regulation of enzyme classes in response to CLas infection. These results open an avenue for further investigation of diverse responses to HLB across different environmental conditions and citrus genotypes.

Disease Resistant Citrus Breeding Using Newly Developed High Resolution Melting and CAPS Protocols for Alternaria Brown Spot Marker Assisted Selection

Alternaria alternata is a fungus that causes a serious disease in susceptible genotypes of citrus, particularly in mandarins. The Alternaria citri toxin (ACT) produced by the pathogen induces necrotic lesions on young leaves and fruits, defoliation and fruit drop. Here, we describe two methods of marker-assisted selection (MAS) that could be used for the early identification of Alternaria brown spot (ABS)-resistant mandarin hybrids. The first method is based on a nested PCR coupled to high resolution melting (HRM) analysis at the SNP08 locus, which is located at 0.4 cM from the ABS resistance locus, and was previously indicated as the most suitable for the selection of ABS-resistant hybrids. The method was validated on 41 mandarin hybrids of the CREA germplasm collection, and on 862 progenies generated from five crosses involving different susceptible parents. Four out of five populations showed Mendelian segregation at the analyzed locus, while a population involving Murcott tangor as male parent showed distorted segregation toward the susceptible hybrids. The second method is based on a cleaved amplified polymorphic sequences (CAPS) marker that was developed using the same primers as the nested PCR at the SNP08 locus, coupled with BccI restriction enzyme digestion. To verify the reliability of the two genotyping methods, in vitro leaf phenotyping was carried out by inoculating A. alternata spores onto young leaves of 101 hybrids, randomly chosen among the susceptible and resistant progenies. The phenotyping confirmed the SNP08 genotyping results, so the proposed method of selection based on HRM or CAPS genotyping could be routinely used as an alternative to KBioscience competitive allele specific polymerase chain reaction (KASPar) single nucleotide polymorphism (SNP) genotyping system to improve citrus breeding programs. While the study confirmed that the SNP08 marker is a reliable tool for MAS of new citrus hybrids with different genetic backgrounds, it also identified a small group of genotypes where the resistance mechanism requires further investigation.

Target-Genes Reveal Species and Genotypic Specificity of Anthocyanin Pigmentation in Citrus and Related Genera

Background: Anthocyanin pigmentation characterizes a number of tissues of Citrus and its relatives. The gain and loss of pigmentation is intriguing and is inherited variously among species. Methods: Citrus germplasm was used to investigate the anthocyanin pigmentation of tissues never before considered, including stamen, style and stigma, and of young leaves, petals, rind and flesh of 28 genotypes belonging to 14 species. Citrus genotypes encompassed citron, lemon, sweet orange, lime, and Citrus relatives included Microcitrus, Murraya, and Severinia. A relative qRT-PCR analysis was carried out on the structural and regulatory genes: phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3′-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), uridine diphosphate glucose flavonoid glucosyl-transferase (UFGT), glutathione S-transferase (GST), Ruby and Noemi. Image analysis and a genomic approach were employed to evaluate how the red pigmentation is inherited among tissues and species. Results: Pigmentation of young leaves and petals is specific to citron and its hybrids. Ruby controls the pigmentation of petals, but not of leaves. The red color of the rind and flesh is a trait that particularly characterizes a diversity of sweet oranges, citron hybrids and Citrus relatives. Color expression depends on external factors and also on developmental stage. The coloration of stamen and style is citron-specific, while a red stigma is exclusive to Moro orange and its hybrids. Conclusion: It is hypothesized that there is a relationship among Citrus species and genes controlling anthocyanin pigmentation.

Influence of Citrus Scion/Rootstock Genotypes on Arbuscular Mycorrhizal Community Composition under Controlled Environment Condition.

Citrus is vegetatively propagated by grafting for commercial production, and most rootstock cultivars of citrus have scarce root hairs, thus heavily relying on mutualistic symbiosis with arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community composition, and its differences under different citrus scion/rootstock genotypes, were largely unknown. In this study, we investigated the citrus root-associated AMF diversity and richness, and assessed the influence of citrus scion/rootstock genotypes on the AMF community composition in a controlled condition, in order to exclude interferences from environmental factors and agricultural practices. As a result, a total of 613,408 Glomeromycota tags were detected in the citrus roots, and 46 AMF species were annotated against the MAARJAM database. Of these, 39 species belonged to Glomus, indicating a dominant role of the Glomus AMF in the symbiosis with citrus. PCoA analysis indicated that the AMF community’s composition was significantly impacted by both citrus scion and rootstock genotypes, but total samples were clustered according to rootstock genotype rather than scion genotype. In addition, AMF α diversity was significantly affected merely by rootstock genotype. Thus, rootstock genotype might exert a greater impact on the AMF community than scion genotype. Taken together, this study provides a comprehensive insight into the AMF community in juvenile citrus plants, and reveals the important effects of citrus genotype on AMF community composition.

Ovipositional antixenosis to Phyllocnistis citrella Stainton in Citrus genotypes and related genera

This study evaluated oviposition of citrus leaf miner (CLM), Phyllocnistis citrella Stainton (Lepidoptera: Gracillariidae), in different Citrus genotypes and related genera to search for resistance sources of type antixenosis or no preference for oviposition. Initially, we screened 23 genotypes and we used lime ‘Rugoso’ (Citrus jambhiri Lush.) as the susceptibility standard. Based on the number of eggs and pupae found on the plants, five genotypes were most promising to significantly reduce pest population: trifoliata ‘Limeira’ (Poncirus trifoliata), hybrids M x P222 [Citrus sinensis × Tangor Murcott (Citrus sinensis × C. reticulata)], C x R4 (Citrus sunki × P. trifoliata) and C x R315 (C. sunki × P. trifoliata) and tangerine ‘Sunki’ (C. sunki). In the preference test for oviposition with choice, trifoliata ‘Limeira’ and hybrid C x R315 were the least preferred genotypes by CLM, while in the no choice test, the effect of the genotypes was less evident, with a difference only between trifoliata ‘Limeira’ (less oviposited) and lime ‘Rugoso’ (more oviposited). Thus, trifoliata ‘Limeira’ and hybrid C x R315 are potential sources of antixenosis resistance and could be used in breeding programs to incorporate CLM resistance factors in improved genotypes.

Identification of Citruses from Montenegro Based on Microsatellite Clustering Analyses

A set of 32 citrus genotypes were selected from Montenegro collection and analyzed by the use of 11 microsatellite markers. Analyses harvested 72 different alleles having 6.5 alleles per locus and discovered presence of 23 unique genotypes. Distance analysis and model-based clustering revealed both the presence of 4 groups: satsuma (Citrus unshiu Marc.) mandarins, clementine (Citrus reticulata) mandarins, sweet oranges (Citrus × sinensis) and lemons (Citrus limon). Distance based clustering enabled the differentiation between red and yellow flashed fruits due to the presence of allele 158 on the locus AC01 in blood oranges. Specific goal of the study was to clarify the identity of 3 local citrus genotypes through observing their relationships within well-established clustering with the rest of genotypes being known citruses. Local orange ‘Domaca Pomorandza’ grouped with other sweet oranges but could not be differentiated from ‘Navelina’ and ‘Skagss Bonanza Navel’. ‘Gorka Pomorandza’ had unique fingerprint and showed to be sour orange. Local lemon ‘Mjesecar’ showed to may be belonging to the Femminello group of lemons. Genetic characterization of local genotypes will serve for cultivar recognition and their future improvement.

Callogenesis and plant regeneration of sweet orange cv. Washington Navel from floral organ cultures

Washington Navel orange (Citrus sinensis L.) can be infected with virus and virus like diseases that affect not only the production but also fruit quality and the plant’s longevity. For viral sanitation, Washington Navel regeneration was investigated in vitro via floral organ culture. Flowers were collected before opening from healthy Washington Navel trees kept under greenhouse. Floral organs (style/stigma and ovary) were cultured on Murashige and Skoog (MS) medium containing various plant growth regulators combinations of naphthalene acetic acid (NAA), 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-benzylaminopurine (BAP). The highest rate of callogenesis (95%) was obtained from style/stigma explant cultures on MS medium enriched with 3 mgL-1 BAP, which also resulted in 100% rooted plantlets. Ovary cultures did not show any success on the culture medium with various plant growth regulators combinations. The acclimatization success of rooted plantlets by grafting on Citrus volkameriana rootstocks was about 83%. Thus, these results can be used for mass production of disease-free citrus plants and improve sanitation program of the local citrus genotypes in Tunisia.

Triploid Citrus Genotypes Have a Better Tolerance to Natural Chilling Conditions of Photosynthetic Capacities and Specific Leaf Volatile Organic Compounds.

Low temperatures during winter are one of the main constraints for citrus crop. Polyploid rootstocks can be used for improving tolerance to abiotic stresses, such as cold stress. Because the produced fruit are seedless, using triploid scions is one of the most promising approaches to satisfy consumer expectations. In this study, we evaluated how the triploidy of new citrus varieties influences their sensitivity to natural chilling temperatures. We compared their behavior to that of diploid citrus, their parents (Fortune mandarin and Ellendale tangor), and one diploid clementine tree, as reference, focusing on photosynthesis parameters, oxidative metabolism, and volatile organic compounds (VOC) in leaves. Triploid varieties appeared to be more tolerant than diploid ones to natural low temperatures, as evidenced by better photosynthetic properties (Pnet, gs, Fv/Fm, ETR/Pnet ratio), without relying on a better antioxidant system. The VOC levels were not influenced by chilling temperatures; however, they were affected by the ploidy level and atypical chemotypes were found in triploid varieties, with the highest proportions of E-β-ocimene and linalool. Such compounds may contribute to better stress adaptation.

New insights into the resistance of four citrus genotypes to Xanthomonas citri subsp. citri

The resistance of different citrus genotypes to citrus canker, caused by Xanthomonas citri subsp. citri (Xcc), is quite different. In this study, four citrus genotypes with different resistance, including resistant kumquat ‘Luofu’ (Fortunella margarita), moderately resistant Ponkan ‘18–1-10’ (Citrus reticulata), moderately susceptible sweet orange ‘Newhall’ (C. sinensis) and susceptible grapefruit ‘Duncan’ (C. paradisi) were used to elucidate the resistance mechanism. The antibacterial analysis in vitro showed low concentration of H2O2 promoted growth of Xcc, whereas high concentration inhibited growth. In addition, NADPH oxidases, also known as respiratory burst oxidase homologues (rbohs), are required for H2O2 burst during infection. Subsequently, Xcc accumulation, H2O2 production and expression of CsrbohD was measured to elucidate their roles in citrus-Xcc interaction. Through the Spearman correlation and multiple linear regression analysis, we found all three factors were significantly correlated with variety resistance, which was significantly affected by H2O2 content and expression of CsrbohD. Taken together, these data indicate a feedback regulation of CsrbohD and H2O2 in citrus. When the H2O2 content was lower than the threshold, it was not sufficient to suppress Xcc growth, and more Xcc populations suppressed H2O2 production, thus forming a vicious circle. By contrast, it can suppress Xcc growth, then CsrbohD was suppressed to reduce the oxidative damage.

Comparative Genomics Screen Identifies Microbe-Associated Molecular Patterns from 'Candidatus Liberibacter' spp. That Elicit Immune Responses in Plants.

Citrus huanglongbing (HLB), caused by phloem-limited 'Candidatus Liberibacter' bacteria, is a destructive disease threatening the worldwide citrus industry. The mechanisms of pathogenesis are poorly understood and no efficient strategy is available to control HLB. Here, we used a comparative genomics screen to identify candidate microbe-associated molecular patterns (MAMPs) from 'Ca. Liberibacter' spp. We identified the core genome from multiple 'Ca. Liberibacter' pathogens, and searched for core genes with signatures of positive selection. We hypothesized that genes encoding putative MAMPs would evolve to reduce recognition by the plant immune system, while retaining their essential functions. To efficiently screen candidate MAMP peptides, we established a high-throughput microtiter plate-based screening assay, particularly for citrus, that measured reactive oxygen species (ROS) production, which is a common immune response in plants. We found that two peptides could elicit ROS production in Arabidopsis and Nicotiana benthamiana. One of these peptides elicited ROS production and defense gene expression in HLB-tolerant citrus genotypes, and induced MAMP-triggered immunity against the bacterial pathogen Pseudomonas syringae. Our findings identify MAMPs that boost immunity in citrus and could help prevent or reduce HLB infection.

Detection of Phenylpropanoids in Citrus Leaves Produced in Response to Xanthomonas citri subsp. citri.

Citrus canker (CC), caused by the bacterial pathogen Xanthomonas citri subsp. citri, impacts citrus production in many areas of the world by reducing yields, degrading tree health, and severely blemishing the outer peels of fresh fruit. The relative susceptibility to CC among different species of Citrus varies from the highly susceptible lime (Citrus × aurantifolia), sweet orange (C. × sinensis), and grapefruit (C. × paradisi) to the much less susceptible calamondin (C. × microcarpa) and kumquat (C. japonica). This investigation compares the responses to infection with X. citri subsp. citri of these five genotypes with respect to phenylpropanoid compound profiles and relative increases or decreases of specific compounds postinoculation. In response to X. citri subsp. citri infection, all hosts possessed increased concentrations of phenylpropanoids in leaf tissue, whereas the similarly treated nonhost orange jessamine (Murraya paniculata) did not. Several of the tested genotypes exhibited notably increased production of fluorescent phenylpropanoids, including umbelliferone, herniarin, auraptene, scoparone, and others. The profiles of these compounds and their levels of production varied among the tested species yet all investigated Citrus genotypes exhibited increased concentrations of phenylpropanoids regardless of their degree of susceptibility to X. citri subsp. citri. Kumquat and calamondin, the tested genotypes least susceptible to X. citri subsp. citri, also exhibited the highest levels of the dihydrochalcone 3',5'-di-C-glucosyl phloretin, the aglycone portion of which, phloretin, is a known antibiotic, although levels of this compound were not affected by inoculation with X. citri subsp. citri.

Citrus rootstock genotypes response to drought: Alternation in morphology, physiology and leaf mineral content

The potted seedlings (18 months old) of seven citrus genotypes were imposed to drought-rewater cycles for every 24 days to study the alterations in morpho-physiological traits and leaf mineral nutrients. The continued growth under drought was observed in Soh sarkar (11.88% more), RLC-7 (10.25% more) and Karna Khatta (10.74% more) as of normal conditions. Moreover, after re-watering, RLC-7 enhanced the plant height to the great extent (17%) as compared to drought. RLC-7, RLC-5 and Soh sarkar maintained a leaf area ratio even under drought condition, while it was inhibited in Jatti khatti and Karna khatta significantly under drought as compared to well-watered conditions. Moreover, reduction in the root volume in most of the rootstocks except RLC-5 and Soh sarkar was noticed. Most of the rootstocks were able to maintain intrinsic water use efficiency after rewatering except RLC-6. Chlorophyll ‘b’ enhanced under drought in RLC-5, RLC-6 and RLC-7, while it was inhibited in Soh sarkar at the end of the drought. Concomitantly, Soh sarkar and RLC-5 exhibited a noticeable alternation of mineral nutrients, having sharp increase of K (RLC-5), but P, Fe and Zn were relatively stable throughout the experiment as compared to start of drought and after rewater stage. From the study, it could conclude that Soh sarkar and RLC-5 (Citris jambhiri) can escape moderate drought. Further, it can also be argued that differential mechanism works for drought tolerance in RLC-5 and Soh sarkar genotypes.

Physiology of flowering in Citrus species

An experiment was conducted on the trees of acid limes (Pusa Udit, Pusa Abhinav and ALC-29), lemons (Konkan Seedless, Kagzi Kalan and Hill lemon) and sweet oranges (Pusa Sharad, Pusa Round and Mosambi) during 2017–18 with the objectives to understand the relationship of seasonal changes in physio-biochemical traits with the flowering behaviour of citrus species. Sweet oranges and Hill lemon expressed flowering once in a year (February to March), while lemons and acid limes bloomed almost round the year. The flowering genotypes showed lower value of photosynthetic rate (A) than non-flowering genotypes. C:N ratio ≥ 5.57 could initiate the flowering in lemon (except Hill lemon) and limes, while in other genotypes, it was ≥ 13.39 for flowering. In sweet orange and Hill lemon, GA3 followed an upward trend till January, and declined thereafter, however, the trend was reverse in other genotypes till December. During spring season, the trees having GA3 ranging between 0.12–0.93 mg g−1 FW showed the flowering. The content of free amino acids (FAA) increased till February and declined thereafter. Overall the level of FAA ≥ 10 mg g−1 FW proved to be the critical level to induce flowering in all the genotypes tested. The level of total antioxidant capacity (TAC) ≥ 18.12 μmol g−1 FW favoured the flowering in all citrus genotypes tested. Overall low level (96.45–108.27 mmol H2O2 mg−1 FW) of hydrogen peroxide (H2O2) favoured the flowering.

CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages.

Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

Variation in fruit quality traits and health promoting compounds of citrus fruits grown in semi-arid region

The present study was conducted to assess the variation in quality characteristics of nine commonly cultivated citrus genotypes grown in semi-arid region. Fruit weight varied from 130g (‘Minneola’) to 622g (‘Pummelo Red Flesh’) within different groups of citrus fruits. Juice content ranged from 31% (‘Pummelo Red Flesh’) to 54% (‘Mosambi’). Pummelo fruits were larger in size than fruits of other citrus groups. TSS varied from 8°B (‘Dancy’) to 11°B (‘Pummelo Red Flesh’), while ascorbic acid varied from 32 to 54 mg/100g. The maximum phenolic content was recorded in ‘Pummelo White Flesh’ fruits (44.66 mg GAE/100g) and the minimum was found in ‘Minneola’ (23.33 mg GAE/100g). The fruits of ‘Pummelo Red Flesh’ and ‘Pummelo White Flesh’ had highest flavonoids of 50.85 mg QE/100g and 48.10 mg QE/100g, respectively. The antioxidant activity was also high in the fruits of pummelo and grapefruit as compared to others. Principal Component Analysis revealed that TSS and acid content were the major quality attributes governing the citrus acceptability. Total flavonoid content and the in vitro FRAP antioxidant assay were the best to determine the functional quality of the fruits. Biplot analysis grouped the genotypes into two groups and the result was further verified by Agglomerative Hierarchical Clustering technique which too yielded similar results.

Unraveling the cryptic genetic variation and population structure of the citrus genotypes with unknown origin

The high diversity of Citrus genotypes can increase the probability of identifying new genetic makeups and even desirable traits. Hence, 76 genotypes with unknown origin and 34 known cultivars from several Citrus species were analyzed by SSR and AFLP markers. Overall, 326 alleles and 545 polymorphic bands were respectively scored for 28 SSR loci and 25 AFLP primer-enzyme combinations. The results of various analyses accomplished with SSR markers were in agreement with AFLP. Accordingly, the true species of citron, mandarin, and pummelo were nested into separate groups. In the studied germplasm, we succeeded in tracking three cryptic origin genomes (2 in SSR and 1 in AFLP analysis) which were distinct from 3 true species, and, interestingly, they contributed to the genetic composition of some control cultivars. The results suggested that the interspecific hybridization and genetic introgression were the main determinants of the Citrus genotypes genetic composition. Hereupon, the share of citron in 36%, mandarin in 34%, and pummelo in 22% of selected accessions estimated more than 50%. Despite the controversy about the origin of lemon and sour orange, the results of different grouping methods suggested that lemon had more affinity with lime, and the genetic contribution of mandarin in sour orange was stronger than that of pummelo.