Lily RNA-Seq Analysis Reveals Candidate Genes Resistant to Botrytis Disease

Due to large genome size and long juvenile stage, advance in a new cultivar development using a molecular tool has been limited so that lily breeding is mainly depending on conventional pollination method. In the present study we have developed 24 different lily hybrids showing various in Botrytis disease responses and obtained leaf transcriptome data from 16 different hybrid libraries. A total of 446,616,718 pair-end reads were generated on an Illumina Hi-Seq 2000 platform and were assembled into 752,502 unique transcripts. Digital gene expression profiling showed that some of the common and unique genes were differentially expressed in the susceptible and resistant hybrids as a result of Botrytis pathogen infection. A total of 108 candidate genes were selected from the five different groups consisted of resistant and susceptable lines, and some of them were found to be WRKY transcription factor, 22-like tir-nbs-lrr type disease resistance protein, f-box proteins, leucine rich repeat and Chitinase genes, indicating a response towards defense. All the DEGs were assigned to known Gene Ontology categories and grouped into cellular and metabolic processes, response to stimuli, biological regulation, biogenesis and localization. Ten candidate genes were randomly selected and their expression levels were validated to DEG data by quantitative real-time PCR (qRT-PCR). Taken together, our results revealed that the transcriptional changes between resistance and susceptible lily lines during their interaction with Botrytis, could provide useful information for defence related gene mining and may further helps to develop molecular markers for breeding Botrytis resistant lily cultivars.