Efficient creation and phenotypic differentiation mechanism of autotetraploid soybean

Soybean is an important food and oil crop worldwide, but its narrow genetic background constrains the breeding of high-quality varieties. To expand soybean germplasm resources and investigate the effects of polyploidization on soybean agronomic and quality traits, three autotetraploid materials from two cultivated (W82 and JD17) and one wild soybean (W006) were successfully created through colchicine induction. The 12-h treatment of seeds with 0.2 % colchicine solution achieved optimal induction efficiency, with a chromosome doubling success rate of 11.76 %. Compared to diploids, autotetraploid soybeans exhibited significant phenotypic and physiological changes: increase tissue and cell size, thicker leaf with three to five leaflets, 16.71 % increase of chlorophyll content, and 14.52 % increase of photosynthetic rate. The fertility of autotetraploid soybean decreased, the average of single-seed pod ratio increased to 50.64 %, but the hundred-grain weight increased by 43.11 %. Notably, autotetraploid soybeans maintain oil content while achieving 8.89 % average protein content increase, with significant elevations in oleic acid, water-soluble proteins and essential amino acids (e.g., lysine and leucine). For genomic changes, 7457, 41,497, and 110,970 genetic variations were detected in tetraploid W82, JD17, and W006, respectively, these variations including SNP, InDel, and structural variation. The genes containing these variations were rich in defense response, lipid metabolic, DNA repair, transcription regulation, and amino acid synthesis, indicating that the genetic variations may be responsible for the phenotypic variation of tetraploid soybeans, and also indicating that tetraploid soybeans may has great potential in stress resistance. Besides, the chromosome number variation of three tetraploid plants indicating the genome of tetraploid soybeans were unstable. This study first reveals the differentiation in lipid metabolism pathways between diploid and tetraploid soybeans, providing critical germplasm resources and theoretical foundations for deciphering polyploid soybean nutrient synthesis mechanisms and breeding high-protein, high-oleic-acid varieties.