pseudo‐GhFAD2‐1 Is a lncRNA Involved in Regulating Cottonseed Oleic and Linoleic Acid Ratios and Seed Size in Gossypium hirsutum

ABSTRACT Long non‐coding RNAs (lncRNAs), defined as transcripts > 200 nt without protein‐coding capacity, play crucial regulatory roles in plant growth and development. While numerous lncRNAs exist in plants including cotton ( Gossypium spp.), few are functionally characterised. G. hirsutum serves as both a premier fibre crop and significant oil source, where fatty acid desaturase 2 ( GhFAD2‐1 ) is a key gene for the synthesis of polyunsaturated fatty acids in cottonseed. In this study, we confirmed that the GhFAD2‐1 located on the D subgenome generated a tightly linked homologous copy through a tandem duplication event. Due to sequence divergence in the promoter and gene body following the duplication event, this homologous sequence was identified as a long non‐coding RNA (lncRNA) and designated as pseudo ‐ GhFAD2‐1 ( pGhFAD2‐1 ). Knocking out pGhFAD2‐1 increased linoleic acid content and reduced seed size, whereas over‐expressing pGhFAD2‐1 had opposite effects. pGhFAD2‐1 interacts with histone deacetylase GhHDT1 and 40S ribosomal protein GhRPS12, transcriptionally recruiting GhHDT1 to suppress GhFAD2‐1 expression and translationally inhibiting GhFAD2 protein synthesis by competitively binding RPS12 with GhFAD2‐1 mRNA, ultimately disrupting cottonseed fatty acid biosynthesis. The impact of pGhFAD2‐1 on seed size seems to be achieved through the ABA biosynthesis and signalling pathways via GhHDT1, with an increasing level of ABA leading to smaller seeds. The results expand our knowledge on the origin, function and regulatory mechanism of plant lncRNAs and provide new targets and pathways for genetic manipulation of cottonseed oil and seed size.