Comparative transcriptome analysis during seeds development between two soybean cultivars

Abstract

Soybean is one of the important economic crops, which supplies a great deal of vegetable oil and proteins for human. The content of nutrients in different soybean seeds is different, which is related to the expression of multiple genes, but the mechanisms are complicated and still largely uncertain. In this study, to reveal the possible causes of the nutrients difference in soybeans A7 (containing low oil and high protein) and A35 (containing high oil and low protein), RNA-seq technology was performed to compare and identify the potential differential expressed genes (DEGs) at different seed developmental stages. The results showed that DEGs mainly presented at the early stages of seeds development and more DEGs were up-regulated at the early stage than the late stages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs have diverged in A7 and A35. In A7, the DEGs were mainly involved in cell cycle and stresses, while in A35 were the fatty acids and sugar metabolism. Specifically, when the DEGs contributing to oil and protein metabolic pathways were analyzed, the differences between A7 and A35 mainly presented in fatty acids metabolism and seeds storage proteins (SSPs) synthesis. Furthermore, the enzymes, fatty acid dehydrogenase 2, 3-ketoacyl-CoA synthase and 9S-lipoxygenase, in the synthesis and elongation pathways of fatty acids, were revealed probably to be involved in the oil content difference between A7 and A35, the SSPs content might be due to the transcription factors: Leafy Cotyledon 2 and Abscisic acid-intensitive 3, while the sugar transporter, SWEET10a, might contribute to both oil and protein content differences. Finally, six DEGs were selected to analyze their expression using qRT-PCR, and the results were consistent with the RNA-seq results. Generally, the study provided a comprehensive and dynamic expression trends for the seed development processes, and uncovered the potential DEGs for the differences of oil in A7 and A35.

Using transcriptomic and metabolomic data to investigate the molecular mechanisms that determine protein and oil contents during seed development in soybean

“…Metabolites and gene regulatory networks for soybean seed development have been studied in previous reports ( Collakova et al, 2013 ; Peng et al, 2021 ). More recently, comparative metabolome and transcriptome analyses were performed in the developing seeds of grain and vegetable soybeans at R6 stage, 299 DAMs and and 20,546 DEGs were identified between the two varieties ( Chen et al., 2022 ).…”

Differential gene expression provides leads to environmentally regulated soybean seed protein content

“…Expression of genes involved in seed protein and oil is most highly expressed during the middle and late stages of development ( Severin et al., 2010 ). Genes involved in fatty acid synthesis and elongation ( fad2 , lox , and kcs ) contribute to the differences seen between high-protein-low-oil and low-protein-high-oil cultivars, while seed protein content differences are influenced by transcription factors (including abi3 and lec2 ), and sugar transporter SWEET10a plays a role in both protein and oil accumulation ( Wang et al., 2020 ; Peng et al., 2021 ). In a recent study, lipid and carbohydrate metabolism were found to be differentially expressed high-protein and high 11S soybeans in comparison to their low-protein and low-11S counterparts grown in the same conditions ( Hooker et al, 2023 ).…”

Transcriptome Analysis Reveals Key Pathways and Candidate Genes Controlling Seed Development and Size in Ricebean (Vigna umbellata)

“…Therefore, it is of great importance to decipher the molecular mechanism underlying seed development and size determination process in this minor but potential pulse crop. In recent years, with the advent of nextgeneration sequencing technology, key gene regulatory networks governing pod and seed development have been well characterized in both model plants like rice (Herridge et al, 2011), Arabidopsis (Herridge et al, 2011;Mahto et al, 2017), and also in non-model legume species like black gram (Souframanien and Reddy, 2015), cowpea (Lonardi et al, 2019), chickpea (Pradhan et al, 2014), mungbean (Tian et al, 2016a), and soybean (Jones and Vodkin, 2013;Qi et al, 2018;Peng et al, 2021). These studies revealed that seed development in higher plants is a highly complex process and governed by phytohormone signaling including cytokinins (CKs), gibberellins (GAs), brassinolides (BRs), ethylene (ET), and their associated genes and transcription factors.…”