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Background Brassica napus  is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses.  B. napus  is susceptible to a variety of fungal diseases, so identify the  BnLTPs  and their expression in disease responses is very important. The common reference genome of  B. napus  does not contain all  B. napus  genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate  BnLTP  genes in the  B. napus  pangenome. Results In the present study, the  BnLTP  genes were identified throughout the pangenome, and different  BnLTP  genes were presented among varieties. Totally, 246  BnLTP  genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all  BnLTP  genes. RNA sequencing analysis showed that the  BnLTP  genes were involved in the response to  Sclerotinia sclerotiorum  infection. We identified 32  BnLTPs  linked to blackleg resistance quantitative trait locus (QTL). Conclusion The identification and analysis of  LTP  genes in the  B. napus  pangenome could help to elucidate the function of  BnLTP  family members and provide new information for future molecular breeding in  B. napus .

Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation