Transcriptomic analyses reveal physiological changes in sweet orange roots affected by citrus blight

Background Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is made by demonstrating physical blockage of xylem cells that prevents the movement of water. This test was used to identify symptomatic trees from four commercial groves in Florida. Total RNA extracts of phloem-enriched scaffold root tissues were prepared from seven trees that failed to take up water and from one healthy tree. These RNA extracts were used for transcriptomic analyses using paired end RNA-Seq from an Illumina 2500 system. The expression of transcripts annotated as polyprotein of citrus endogenous pararetrovirus were estimated by both RT-qPCR and RNA-Seq. Results Transcripts from seven RNA-Seq libraries from trees affected by citrus blight were compared to a control tree. 129–148 million RNA fragments (two paired-end reads/fragment) were generated per library and were mapped to the sweet orange reference genome. In response to citrus blight stress, genes encoding aquaporins, proteins with water channel activity and several cellulose synthase genes were down-regulated, whereas genes involved in lignin and glucosinolate biosynthesis were up-regulated. Transcripts encoding proteins in pathways of carbohydrate metabolism, nucleotide synthesis, signaling, hormone metabolism, secondary metabolism, transport, and biotic stress pathways were overwhelmingly down regulated in all libraries. Conclusion Reduced water intake and xylem plugging were observed in the trees tested and the changes in their transcriptome were analyzed. Plants adapted to reduced water flow by regulating primary and secondary metabolism, nuclear transport and hormone associated pathways. The patterns of energy generation, transcription, translation and protein degradation were consistent with irreversible decline. The down regulation of cellulose synthase transcripts and up regulation of transcripts related to lignin production likely lead to an imbalance in the pathways leading to wood formation, and may lead to the blockage of the xylem vessels seen as the cardinal symptom of citrus blight. Transcripts of a pararetrovirus were elevated in the transcriptome of roots used in this study.

IDENTIFICATION AND QUANTIFICATION OF DIFFERENTIALLY EXPRESSED GENES ASSOCIATED WITH CITRUS BLIGHT (Citrus spp.)

Brazil is the largest citrus producer in the world, being responsible for more than 20% of its production, which is, however still low due to phytosanitary issues such as citrus blight. Citrus blight is an anomaly whose causes still have not yet been determined, therefore there are no efficient control measures to minimize the production losses with the use of resistant varieties being considered the most appropriate method. However, little is known about the genes involved in the defense response of the plants to this anomaly. Considering that many physiological alterations associated with plant stress responses are controlled at a transcriptional level, in this study we sought the identification and characterization of the gene expression products differentially expressed in the response to the citrus blight. Through the suppressive subtractive hybridization technique, expressed cDNA libraries were built using mRNAs isolated from "Cravo" lemon tree roots (Citrus limonia L. Osbeck) under "Pera" orange (Citrus sinensis L. Osbeck) of healthy and sick plants. 129 clones were obtained by subtraction and their sequences were compared in databases. 34 of them linked to proteins associated to stress processes, while the others were similar to sequences of unknown functions or did not present similarity with sequences deposited in the databases. 3 genes were selected and their expressions were studied by RT - qPCR in real-time. Plants with citrus blight presented an increase of the expression level in two of those genes, suggesting that these can be directly involved with this anomaly.

First Report of Citrus Blight in Costa Rica

Citrus blight (CB), causing a chronic decline of citrus, has been an important disease in Florida for over 100 years. CB was first reported in Brazil in the 1980s and is now responsible for the removal of nearly 10% of the trees from production annually. No causal agent has been identified, but CB has been root-graft transmitted to healthy trees, suggesting that the causal agent is infectious (3). Since 1997, CB symptoms were observed in several groves in northern Costa Rica, the most important citrus area of approximately 25,000 ha. Symptoms observed include a general decline and wilt of the tree canopy, off-color leaves, leaf drop, twig dieback, small fruit, delayed blossom, poor growth, and death. A survey near Guanacaste revealed CB symptoms in 7-yr-old Valencia and Pineapple orange trees (Citrus sinensis (L.) Osbeck) grafted on Carrizo citrange (C. sinensis (L.) Osbeck × Poncirus trifoliata (L.) Raf.) rootstock. Since 1997, 6% of the trees in this area have been replanted annually because of CB symptoms. Similar situations were observed in other groves in the northern citrus area. Dot immunobinding assays (DIBA) (1) were used to detect the P12 protein associated with CB with 20 of 22 trees showing CB-like symptoms giving a positive test. Zinc (Zn) accumulation in trunk wood and water uptake tests were done according to Roistacher (2) in 8 healthy and 20 symptomatic trees which were positive for CB using DIBA. The average Zn concentration of 16 declining trees was 4.6 ± 1.9, whereas the average concentration for 8 healthy trees was 2.0 ± 0.9. The average water uptake in 1 min was 14 ml for healthy trees, and virtually zero for the 20 symptomatic trees. These diagnostic tests confirm the presence of CB in the northern citrus area of Costa Rica, and the surveys indicate the disease is beginning to spread and become economically important. To our knowledge, this is the first report of CB in commercial citrus in Costa Rica. References: (1) K. S. Derrick et al. Plant Dis. 74:168, 1990. (2) C. N. Roistacher. Pages 57–66 in: Graft-Transmissible Diseases of Citrus. Handbook for Detection and Diagnosis. C.N. Roistacher, ed. Food and Agriculture Organization, Rome, 1991. (3) D. P. H. Tucker et al. Plant Dis. 68:979, 1984.