Meta-analysis and transcriptome profiling reveal hub genes for soybean seed storage composition during seed development

Abstract

Soybean is an important crop providing edible oil and protein source. Soybean oil and protein contents are quantitatively inherited and significantly affected by environmental factors. In this study, meta-analysis was conducted based on soybean physical maps to integrate quantitative trait loci (QTLs) from multiple experiments in different environments. Meta-QTLs for seed oil, fatty acid composition, and protein were identified. Of them, 11 meta-QTLs were located on hot regions for both seed oil and protein. Next, we selected 4 chromosome segment substitution lines with different seed oil and protein contents to characterize their 3 years of phenotype selection in the field. Using strand-specific RNA-sequencing analysis, we profile the time-course transcriptome patterns of soybean seeds at early maturity, middle maturity, and dry seed stages. Pairwise comparison and K-means clustering analysis revealed 7,482 differentially expressed genes and 45 expression patterns clusters. Weighted gene coexpression network analysis uncovered 46 modules of gene expression patterns. The 2 most significant coexpression networks were visualized, and 7 hub genes were identified that were involved in soybean oil and seed storage protein accumulation processes. Our results provided a transcriptome dataset for soybean seed development, and the candidate hub genes represent a foundation for further research.

Identification of soybean genes related to fatty acid content based on a soybean genome collinearity analysis

“…The CSSLs were grown at the Xiangyang Crop Breeding Base of Northeast Agricultural University (45.75°N, 126.53°E) in 2014, 2015, and 2016. On the basis of a previous study (Qi et al, ), two materials were selected for a qRT‐PCR analysis. Their basic phenotypes were consistent, but the fatty acid contents differed significantly over three years.…”

Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains

“…cDNA samples were analyzed using quantitative PCR with SYBR Premix Ex Taq (Takara, Shiga, Japan) and a Biorad CFX96 real-time PCR system. The P. lactiflora Actin transcript sequence (JN105299) was used as endogenous reference genes to design primers to normalize the expression levels among samples (Qi et al, 2018;Yuan et al, 2013). The qRT-PCR reactions were carried out with two-step cycles (5 s 95 C denaturation, 30 s 60 C annealing and extension) and 45 cycles of amplification (Fig.…”

Peer Review #2 of "Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains (v0.1)"

“…cDNA samples were analyzed using quantitative PCR with SYBR Premix Ex Taq (Takara) and a Biorad CFX96 real-time PCR system. The P. lactiflora Actin transcript sequence (Available at https://www.ncbi.nlm.nih.gov/nuccore/JN105299) was used as endogenous reference genes to design primers to normalize the expression levels among samples (Qi et al 2018;Yuan et al 2013). The qRT-PCR reactions were carried out with two-step cycles (5 second 95℃ denaturation, 30 second 60℃ annealing and extension) and 45 cycles of amplification (Supplemental Fig.…”