Identification and analysis of BnKNOX gene family in Brassica napus

The plant specific KNOTTED-LIKE HOMEOBOX (KNOX) protein is a transcription factor family that plays an important role in plant growth and development, as well as responses to various stresses. KNOX proteins contain four conserved domains [a three amino acid loop extension (TALE) type homeodomain (HD), ELK domain, and two subdomains (KNOX1 and KNOX2)]. At present, the comprehensive study of BnKNOX genes in Brassica napus has not been reported yet. In this study, 36 BnKNOX family members were identified in B. napus genome via bioinformatic analyses, which were classified into three sub-families (I, II, and M-type) based on sequence alignment and phylogenetic analyses. Evolutionary analysis showed that the whole genome duplication (WGD) and segmental duplication were the main driving forces for the expansion of BnKNOX gene family. Based on the RNA-seq data of developing tissues and organs of B. napus, BnKNAT25/26/29/30 were specifically expressed in endosperm and developing seeds, while BnKNAT31/32/34 were highly expressed in mature seeds. We analyzed the cis-acting elements and expression pattern of BnKNOXs under various abiotic stresses, and identified 17 BnKNOX members that might be involved in drought and osmotic stress responses.