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

Authors: FU, SHIMIN - Southwest University; Shao, Jonathan; Roy, Avijit; BRLANSKY, RONALD - University Of Florida; ZHOU, CHANGYONG - Southwest University; Hartung, John

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/26/2019
Publication Date: 12/11/2019
Citation: Fu, S., Shao, J.Y., Roy, A., Brlansky, R., Zhou, C., Hartung, J.S. 2019. Transcriptomic analyses reveal physiological changes in sweet orange roots affected by citrus blight. BMC Genomics. 20:969. https://doi.org/10.1186/s12864-019-6339-0.
DOI: https://doi.org/10.1186/s12864-019-6339-0

Interpretive Summary: Citrus blight is a very important progressive decline disease of commercial sweet orange and grapefruit, and has been a major production problem in Florida for 140 years. The cause of the disease is not known, although the disease can be transmitted by root grafts, suggesting that a virus is responsible. Trees affected by citrus blight have physical blockages in the vessels inside the trunk in which water moves from the roots to the leaves. Trees with blight can be identified by drilling a hole in the trunk with an electric drill and attempting to force water into the trunk with a syringe. Water cannot be forced into trees with blight but moves freely into healthy trees. The clogging of the water vessels in trees with blights is a very unusual symptom for a disease caused by a virus, so we were interested to understand the physiological changes that lead to this condition. We used laboratory methods to detect and analyze the biochemical pathways that were different in blighted vs healthy trees. We found that holes in the membranes that surround cells in the roots were normally allow the uptake of water were closed, and that the cell wall chemistry itself was changed. It appears that biochemical pathways that normally lead to new growth and wood production are diverted to the overproduction of water soluble 'gunk' that accumulates in the water vessels and that in turn leads to blockage. Once the blockage occurs other biochemical pathways are mostly shut down and relatively little physiological activity occurs. The trees linger in the field in an unproductive state, as if they had become 'zombies'. Our results provide new insight into biological processes that underlie the diseased state in these trees. Our results will be useful to specialists that work with growers to control this disease and with future research may lead to the identification of the cause of this disease.

Technical Abstract: 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. In addition, the expression of transcripts annotated as polyprotein of citrus endogenous pararetrovirus were estimated by both RT-qPCR and RNA-Seq. The seven RNA-Seq libraries fell into two groups based on the correlation between RIN and successful mapping of transcripts to the sweet orange genome. 129-148 million RNA fragments (two paired-end reads/fragment) were generated per library and more were mapped to sweet orange genome in group I as compared to group II. 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. Reduced water intake and xylem plugging was 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.