Transcriptome Analysis of Black and White Sesame Seed Reveals Candidate Genes Associated with Black Seed Development in Sesame (Sesamum Indicum)

Abstract

Background: Seed coat color is a key agronomic characteristic in sesame (Sesamum indicum) since it is strongly linked to seed oil, proteins, and lignans content and it influences consumer preferences. Even though some QTL and candidate genes have been detected for sesame seed coat color, the mechanism and regulation of black pigmentation are not entirely understood. This study provides an overview of developing seeds transcriptome of two varieties of sesame “Zhongfengzhi No.1” (white seed) and “Zhongzhi No.33” (black seed) and shed light on genes involving in black seed formation.Results: Both black and white sesame showed similar trend expressed genes with the numbers increased at the early stages of seed development. The differentially expressed genes (DEGs) number increased with seed development in the two sesame varieties. We examined the DEGs and uncovered that the early stage, which is from 8 to 17 days post-anthesis (DPA) plays an important role in black pigment biosynthesis and accumulation. The gene expression patterns were consistent with the seed color change. Besides, we studied the shared DEGs between the black and white sesame. We figured out 17 candidate genes associated with pigments biosynthesis in black sesame seed including 2 chalcone synthase genes SIN_1018961 and SIN_1018959 which may function in the phenylpropanoid pathway. 5 of these candidate genes, SIN_1006242 and SIN_1016759/PPO, SIN_1026689 and SIN_1006025, SIN_1025056 are located on chromosomes 4, 8 and 11 respectively, in conformity with previous QTL mapping. These genes were believed to play a major role in black seed development in sesame. Conclusion: This work illuminated the different expression profiles in black and white sesames and unfolded pivotal stages and a catalog of candidate genes associated with black seed formation in sesame. These findings provide a vast transcriptome dataset and list of genes that will be targeted for functional studies related to the molecular mechanism involved in biosynthesis and regulation of seed coat color in sesame and for molecular breeding of high-quality sesame varieties.