Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans

Area of Science:

• Plant genetics
• Molecular biology
• Agricultural science

Background:

• Soybean (Glycine max) was domesticated from wild soybean (Glycine soja).
• Genetic variations driving soybean domestication remain largely unknown.
• Understanding these variations is crucial for crop improvement.

Purpose of the Study:

• To investigate genetic variations and gene expression alterations during soybean domestication.
• To identify key molecular mechanisms underlying soybean seed development and domestication.

Main Methods:

• Comparative transcriptomics of wild and cultivated soybeans.
• Identification of divergent gene expression clusters and co-expression modules.
• Analysis of differentially expressed genes (DEGs), quantitative trait loci (QTLs), and selection sweeps.

Main Results:

• A small fraction of orthologous genes showed rapid evolution.
• Three gene expression clusters, comprising 37.44% of genes, were identified as divergent.
• The most significant gene expression divergence occurred at 15 days after fertilization (G15) during seed development.
• Candidate DEGs related to cell division, storage accumulation, hormone response, and maturation were identified.
• Chromosomal-linked DEGs and QTLs for seed weight and oil content were associated with divergence.

Conclusions:

• Gene expression alteration plays a critical role in soybean domestication.
• A transcriptomic selection mechanism underlies soybean domestication.
• Findings provide insights into molecular networks for soybean seed development and breeding strategies.