Pan-genome analysis of the LATERAL ORGAN BOUNDARIES domain family in camelina and function investigation of LATERAL ORGAN BOUNDARIES domain 40 in fatty acid synthesis.

Abstract

Camelina (Camelina sativa (L.) Crantz) is an allohexaploid oilseed crop with a cultivation history of about six thousand years, yet its pan-genome was poorly studied. Moreover, Lateral Organ Boundary Domain (LBD) transcription factor family remains uninvestigated. Here, we performed a pan-genome analysis of LBD genes across 13 camelina accessions, identifying 1487 members classified into 44 Core, 2 SoftCore, 15 Dispensable, and 21 Private orthologous groups. Camelina LBDs were classified into Class I (six subclasses) and Class II (two subclasses). Selection pressure analysis showed that compared with Core LBD genes and SoftCore genes, Dispensable genes have undergone obvious relaxed selection. Promoter analysis identified subclass-specific regulatory elements, with Class IIB significantly enriched in endosperm-specific expression motifs and Class IA1 associated with stress responses. Transcriptome profiling revealed some tissue-specific expression patterns, including potential roles of LBD40/41 in seed development. Functional validation demonstrated that AtLBD40 overexpression in Arabidopsis and camelina remodeled fatty acid composition by suppressing FAD3 and KCS18, thereby reducing the relative contents of 18:3 and 22:1. Arabidopsis lbd40-1 and lbd40-2 mutant analyses suggested a possible functional redundancy between LBD40 and LBD41. This study elucidates the dynamic evolution of the camelina LBD family and its pivotal role in regulating the fatty acid profile in seeds, establishing a foundation for targeted oil quality improvement in this versatile crop.