Identification of Differentially Expressed Genes for Mummy Berry (Monilinia vaccinii-corymbosi) Resistance in Blueberry

With an increasing consumer focus on healthy eating habits and antioxidant intake, blueberries are steadily rising in sales, and by consequence, are also increasing in the amount of agricultural land they cover. More cultivars continue to be developed, with particular interest in traits for fruit firmness, allowing for mechanical harvest, early or late fruit ripening for longer spans of local availability, and the classical trait of interest, yield. However, with an increased amount of acreage comes an increase in the prevalence of certain diseases. One of the most devastating diseases of blueberry (Vaccinium corymbosum and V. virgatum) in the U.S. is mummy berry. The causal fungus of the disease is Monilinia vaccinii-corymbosi. The disease was first reported in Europe in 2002 and has become important in Europe since then. Crop loss due to mummy berry has been reported repeatedly from 1960s until now. In 1969, growers in British Colombia, Canada lost 8.1% of their crop due to mummy berry estimating $750,000. Back in 1974, New Hampshire’s blueberry producers lost 70-80% of their crop. In 2002 in no-spray rabbiteye blueberry fields in North Carolina, 70-80% of crop loss was reported. Current methods of controlling the disease are including cultural practices and chemical controls. Developing resistant cultivars not only reduces the cost of fungicide application(s), but also is an environmentally friendly measure to control the disease. Complexity of the disease and long juvenility life of blueberry hampers the breeding efforts. Our knowledge about the mode of action of the pathogen and its interaction with the plant is very limited. In order to identify genes that are differentially expressed in response to the disease, we used an untreated and a treated susceptible blueberry cultivar, Arlen, for gene expression analysis of mummy berry pathogen infection. A total of 16 barcoded RNA-Seq libraries of leaf, flower and fruit tissues were constructed and 24 million raw reads (150 bases long, single-end) equivalent to 3.6 Gb of nucleotides were generated. The reads were mapped to the blueberry reference genome to identify differentially expressed genes and a genome guided transcriptome assembly of blueberry was made. The implication of leveraging RNA-Seq technology in identification of differentially expressed genes will be discussed. This work could lead to development of molecular marker that can be used in marker assisted selections for genomic selection and new cultivar development.