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

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 3years 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. We applied meta-analysis to integrate QTLs of seed oil, fatty acid composition, and protein contents from multiple environment experiments and identified a group of trait-associated meta-QTLs. We constructed a chromosome segment substitution lines (CSSLs) library carrying 194 stable CSSLs by screening the homozygous recombinant BC3F2, BC3F3, BC3F4, BC3F5, and BC3F6 lines, purifying the self-crossing lines to at least F6 generation, and measuring the seed oil and protein contents in field across 3years. We selected 4 CSSLs with the most distinct protein and oil features as well as their back-crossing genotype SN14 to carry out a strand-specific RNA-sequencing experiment to profile the stage-specific genes and CSSL-specific genes and their time-course transcriptome patterns during seed development and nutrition accumulation. Using coexpression networks analysis and meta-analysis, we uncovered 7 hub genes involved in soybean oil and protein accumulation providing the candidate regulatory genes and resources for the further research.