Co-expression network analysis of the genes associated with pistillody-stamen development in wheat

Abstract Background: Crop male sterility has great values in both theoretical research and breeding application. Wheat pistillody-stamen is an important male sterility phenomenon, and HTS-1 is an important pistillody-stamen material. However the molecular mechanism of HTS-1 stamens transformed into pistils or pistil-like structures remains a mystery. Weighted gene co-expression network analysis (WGCNA) are widely used to explore hub genes and gene interaction networks from high throughput data in various plants. Results: In the present study, for exploring gene networks associated with wheat pistillody-stamen development, WGCNA was employed to analyze 11 RNA-sequencing (RNA-seq) data of wheat tissues, including stamens of CSTP, pistils and pistillody-stamen of HTS-1. 19 out of 25 merged modules were highly associated with specific wheat tissues, and the MEdarkseagreen1 module was highly related to wheat pistillody-stamen (correlation with weight r =0.7, correlation p-value p =0.02). Then 180 genes about wheat flower development were identified from the MEdarkseagreen1 module by GO term analysis. Among 180 genes, the hub gene number associated with anther, filament, style, and ovary development were 12, 3, 3, and 10, respectively. We compared the published pistillody related proteins with proteins of HTS-1 by BLAST. A total of 58 pistillody-stamen development associated proteins were validated by BLAST. MADS-box and YABBY transcription factor about pistillody-stamen development were also analyzed in wheat flower. There were 47 of MADS-box and 17 of YABBY transcription factors were identified. BLAST program was used to align the published pistillody associated MADS-box and YABBY transcription factors with transcription factors identified in wheat flower. Totally, 36 of 47 MADS-box and 14 of 17 YABBY transcription factors were considered to regulate the development of pistillody-stamen, which had never been reported yet. Conclusion: These results have systematically identified the key candidate genes about the development of HTS-1 substructures flower. The tissue-specific correlation network analyses provide important insights into the molecular interactions underlying psitillody-stamen development.