Comparative transcriptome profiling provides insights into endocarp lignification of walnut (Juglans Regia L.)

Abstract

Background Lignin is the main component of walnut endocarp, although we know little about the molecular mechanism of lignin formation in walnut endocarp. To understand the molecular mechanisms behind the two kinds of walnut phenotype and explore the genes involved into lignin formation, transcriptome sequencing was conducted in the walnut endocarp of the ‘Zanmei’ (ZM) and ‘Liaoning 7’ (L7) cultivars, which have different endocarp thicknesses. Compared with L7 walnut endocarp, the endocarp of ZM walnut is thicker, which decreases dehiscent nuts and compromised kernels.Results There are more differentially expressed genes (DEGs) in the ZM walnut cultivar. The DEGs involved in the phenylpropanoid biosynthesis were significantly upregulated in both cultivars 45 days after full bloom (DAFB), but more genes were upregulated in ZM than in L7. Moreover, the same DEGs showed different expression levels in the two cultivars. Most of the key genes in ZM had more different multiples than those in L7. Interestingly, when qRT-PCR was used to determine the expression of the key genes in different development stages of the two varieties, the expression patterns were different from those known in other species. Furthermore, transcription factors regulating secondary cell wall and lignin biosynthesis were identified. Quantitative real-time PCR results were consistent with transcriptome data.Conclusion In this study, transcriptome analysis was used to understand the molecular mechanisms of lignin formation in two walnut cultivars with different shell thickness. Several important key genes in the phenylpropanoid biosynthesis pathway were significantly different in the two cultivars, which may be the reason for the phenotypic differences. The analysis of transcription factors revealed that the regulation network in endocarp of walnut may be different from that of drupe such as apricot or peach. This study provides important candidate genes for exploring the complicated metabolic processes involved in the formation of walnut lignin.