Meta-Analysis and Gene Co-Expression Network Analysis of Citrus-HLB Transcriptome Datasets Identify Candidate Citrus Genes for Engineering HLB Resistance

The bacterial disease Huanglongbing (HLB) poses the most serious threat to the U.S. citrus industry and the citrus industries in many other countries in the world. Development and deployment of citrus scion and rootstock cultivars with HLB resistance/tolerance will be essential and vital to the long-term survival and sustainability of the citrus industries. Recently, we used the Limma and RankProd methods and completed a meta-analysis of 22 publicly available citrus transcriptome datasets from HLB-resistant or susceptible citrus genotypes inoculated or not inoculated with Candidatus Liberibacter, the causal agent of HLB. These analyses led to the identification of 7,412 differentially expressed probesets (DEPs). The DEPs were further classified according to tissue specificity and disease response, leading to the identification of 65 most significant common differentially expressed genes (DEGs) and 30 resistance-specific DEGs. Gene ontology analysis suggested that carbohydrate metabolism and transport and stress response would be the core pathways in citrus modulated by HLB. Resistance-specific DEGs mainly code for chitinases, miraculins, terpene synthases, and aquaporins. Co-expression gene network analyses revealed hub genes that controlled the expression of common and resistance-specific DEGs. These hub genes and the common and resistance-specific DEGs may serve as candidate genes for genetic engineering towards increased HLB resistance in citrus.