Comparative analysis of transcriptome and metabolome explores the underlying mechanism of pod color variation in pea (Pisum sativum L.)

Abstract

The pea (Pisum sativum L.) is one of widely cultivated crops over the world, but the mechanism of pod coloration is still unclear. Understanding the underlying mechanism regulating pea pod coloration can broaden pea breeding. In this study, the comparative analysis of transcriptome and metabolome was performed to examine the changes in metabolites accumulation and gene expression at two pod developmental stages in two pea accessions with green pods (GP) and yellow pods (YP). At the two omics levels, a total of 4504 differential metabolites (DEMs) were detected in four samples, and 2709 and 3725 differential expression genes (DEGs) were detected at two pod developmental stages between GP and YP, respectively. The verification results of RT-qPCR showed that the relative expression of ten genes randomly detected showed statistically high correlations between RT-qPCR and RNA-seq. The functional analysis of DEMs and DEGs found that the flavonoid metabolism pathway was the most direct metabolic pathway for the variation of pod coloration between two pea accessions. The 34 DEMs and 21 DEGs related to flavonoid metabolism pathway exhibited different expression pattern between GP and YP samples. Additionally, the combined analysis of transcriptome and metabolome in flavonoid biosynthesis pathway revealed that a direct correlation between the decreased expression level of genes and reduction accumulation of metabolites in the delphinidin biosynthesis pathway. The obtained results of this study provided a foundation to reveal the candidate genes controlling the pod color variation, and provide new germplasm resources for genetic improvement in pea.