LAUSR

Abstract Lignin is the main component of walnut endocarp, however, we know little about the transcriptional responses and its potential regulatory mechanisms of lignin formation in walnut endocarp. Here we selected two walnut genotypes with different endocarp thickness, ‘Liaoning 7’ (L7) and ‘Zanmei’ (ZM; thicker than L7), to study the transcriptional response mechanism that caused the difference in this character between them. The time and regularity of lignin deposition were studied by microsection and it was found that the key period of lignification was 30–45 days after full bloom (DAFB); Then, transcriptome sequencing was performed to identify the key genes and the pathways during this period. The differentially expressed genes (DEGs) were significantly enriched in several pathways such as plant hormone signal transduction, phenylpropanoid biosynthesis and starch and sucrose metabolism in both cultivars. DEGs involved in the phenylpropanoid biosynthesis were significantly upregulated 45 DAFB, but more genes were upregulated in ZM than in L7. Several important key genes in the phenylpropanoid biosynthesis pathway expressed significantly different in the two cultivars. Quantitative real-time PCR (RT-qPCR) results were consistent with transcriptome data. This study provides candidate genes and pathways for exploring metabolic processes involved in walnut lignin.