Identification and analysis of oil candidate genes revealed the molecular basis of oil accumulation in Gossypium hirsutum L. for cottonseed biofuels development

Abstract

Background Cottonseed oil is increasingly becoming a promising target for biodiesel production with its high content of unsaturated fatty acids as greenhouse gases emission and global warming become more severe. However, the molecular regulatory basis of cottonseed oil accumulation is still unclear so far, and it is necessary to identify vital genes and regulators involved in oil accumulation during developing cottonseed ovules. Results In this study, a recombinant inbred line (RIL) population, developed from a cross between upland cotton cultivars 0-153 and sGK9708, was used to detect quantitative trait loci (QTLs) associated with cottonseed oil content and further identify candidate factors regulating cottonseed lipid synthesis. A total of 39 QTLs located on eighteen different chromosomes were identified across eight different environments. Of these, five QTLs were stable in at least three environments. By integrating candidate gene approach and physical mapping data, we preliminary obtained 43 candidate genes potentially involved in carbon metabolism, fatty acid (FA) synthesis and transcription, and triacylglycerol (TAG) synthesis around the stable QTLs. KEGG pathway enrichment analysis and local BLAST with Arabidopsis oil-related genes, as well as transcriptome analysis further showed that 19 candidate genes, expressed during developing cottonseed ovules, could influence cottonseed oil accumulation. Transcription factors (TFs) and microRNAs (miRNAs) regulatory network analyses suggested six genes, two core miRNAs (ghr-miR2949b and ghr-miR2949c), and one TFs GhHSL1 were considered to be closely associated with cottonseed lipid content. Conclusions The study provides an unprecedented level of insight from QTL mapping and regulatory network analysis to reveal the oil accumulation mechanism in developing cottonseed ovules through the construction of a detailed oil accumulation model. Moreover, the present study of cottonseed oil also lays a foundation for further oil production improvement in oil crops, and contributes to renewable energy production for solving the energy shortage and stabilizing greenhouse gases at a certain extent.