Genomic and co-expression network analyses reveal candidate genes for oil accumulation based on an introgression population in Upland cotton (Gossypium hirsutum)

Abstract

Cotton is an economical source of edible oil for the food industry. The genetic mechanism that regulates oil biosynthesis in cottonseeds is essential for the genetic enhancement of oil content (OC). To explore the functional genomics of OC, this study utilized an interspeci c backcross inbred line (BIL) population to dissect the quantitative trait locus (QTL) interlinked with OC.In total, nine OC QTLs were identi ed, four of which were novel, and each QTL explained 3.62-34.73% of the phenotypic variation of OC. The comprehensive transcript pro ling of developing cottonseeds revealed 3,646 core genes differentially expressed in both inbred parents. Functional enrichment analysis determined 43 genes were annotated with oil biosynthesis processes. Implementation of weighted gene co-expression network analysis showed that 803 differential genes had a signi cant correlation with the OC phenotype. Further integrated analysis identi ed seven important genes located in OC QTLs. Of which, the GhHSD1 gene located in stable QTL qOC-Dt3-1 exhibited the highest functional linkages with the other network genes. Phylogenetic analysis showed signi cant evolutionary differences in the HSD1 sequences between oilseed-and starchcrops. Furthermore, the overexpression of GhHSD1 in Arabidopsis yielded almost 6.78% higher seed oil. This study not only uncovers important genetic loci for oil accumulation in cottonseed, but also provides a set of new candidate genes that potentially in uence the oil biosynthesis pathway in cottonseed. Key messageIntegrated QTL mapping and WGCNA condense the potential gene regulatory network involved in oil accumulation. Finally, a novel glycosyl hydrolases gene (GhHSD1) for oil biosynthesis was con rmed in Arabidopsis, which will provide useful knowledge to understand the functional mechanism of oil biosynthesis in cotton.

Recent advances in exploring transcriptional regulatory landscape of crops

“…Several high-ranking causal genes identified from the GRN were validated for their functional impacts on cotton seed development (Zhao et al, 2023). (Fu et al, 2024) Cotton Biology question Oil accumulation (Ma et al, 2024) Cotton Biology question Low light intensity (Zhao et al, 2024) Cotton Biology question Seed yield (Zhao et al, 2023) Rapeseed Biology question Oleic acid content (Yao et al, 2020) Soybean Biology question Salt stress (Yang et al, 2019) Tomato Biology question Drought-responsive (Chowdhury et al, 2023) Sweet potato Biology question Chlorogenic acid biosynthesis (Xu et al, 2022a) Banana Biology question Fruit ripening (Kuang et al, 2021) Multiple species Methodology cisDynet software (Zhu et al, 2023a)…”