Identification of gene co-expression networks involved in cold resistance of Lilium lancifolium

Low temperature can affect the growth and development of lily, limiting the application of commercial cultivars in outdoor. Lilium lancifolium is an important cold-resistant wild lily, but little is known about how L. lancifolium tolerates cold stress at the molecular level. In this study, we identified and characterized genes and transcription factors associated with cold stress in control plants and plants treated by 4° C for 1 - 24 h. The construction of a highest reciprocal rank-based gene co-expression network along with its partition into defined functional modules using Markov cluster algorithm resulted in identification of 30 gene modules and some of them were significantly enriched with various kinds of stress response under 4° C. These gene modules were associated with metabolic processes, cellular processes, regulation of biological processes, establishment of localization, and responses to stimuli. Moreover, three transcription factors that may regulate the downstream genes involved in response to stimuli were also found. We further studied the expression pattern and tissue specificity of these transcription factors. The functional evaluation of the various interesting genes in this study will probably provide novel discovery of pathway members and regulators associated with cold resistance in lily.