Development and Characterization of a Soybean Experimental Line Lacking the α' Subunit of β-Conglycinin and G1, G2, and G4 Glycinin

Bowman-Birk Inhibitor Mutants of Soybean Generated by CRISPR-Cas9 Reveal Drastic Reductions in Trypsin and Chymotrypsin Inhibitor Activities

Despite the high quality of soybean protein, raw soybeans and soybean meal cannot be directly included in animal feed mixtures due to the presence of Kunitz (KTi) and Bowman-Birk protease inhibitors (BBis), which reduces animal productivity. Heat treatment can substantially inactivate trypsin and chymotrypsin inhibitors (BBis), but such treatment is energy-intensive, adds expense, and negatively impacts the quality of seed proteins. As an alternative approach, we have employed CRISPR/Cas9 gene editing to create mutations in BBi genes to drastically lower the protease inhibitor content in soybean seed. Agrobacterium-mediated transformation was used to generate several stable transgenic soybean events. These independent CRISPR/Cas9 events were examined in comparison to wild-type plants using Sanger sequencing, proteomic analysis, trypsin/chymotrypsin inhibitor activity assays, and qRT-PCR. Collectively, our results demonstrate the creation of an allelic series of loss-of-function mutations affecting the major BBi gene in soybean. Mutations in two of the highly expressed seed-specific BBi genes lead to substantial reductions in both trypsin and chymotrypsin inhibitor activities.

Breeding of Penta Null Soybean [Glycine max (L.) Merr.] for Five Antinutritional and Allergenic Components of Lipoxygenase, KTI, Lectin, 7S α' Subunit, and Stachyose

Soybean [Glycine max (L.) Merr.] is an excellent source of protein, oil, carbohydrates and many other bioactive ingredients for humans. However, several antinutritional and allergenic components such as lipoxygenase, KTI, lectin, 7S α' subunit, and stachyose exist in the raw mature seed. Genetic removal of these components would be the best method to improve soybean food quality. The objectives of this research were to breed a new soybean line with penta null recessive alleles (lox1/lox1/lox2/lox2/lox3/lox3-ti/ti-le/le-cgy1/cgy1-rs2/rs2) for these five components and to evaluate agronomic traits for a breeding line with penta null alleles. Seven germplasms were used to breed the penta null strain. Analysis of lipoxygenase, KTI, lectin, 7S α' subunit, and stachyose components in mature seeds was conducted by SDS-PAGE, western blot, and HPLC. One breeding line with penta null recessive alleles was developed. The breeding line has purple flowers, tawny pubescence, a determinate growth habit, and light yellow pods at maturity. The seed of the breeding line has a yellow hilum and yellow seed coat color. The stem height of the breeding line was 53.0 cm. The stachyose content of the breeding line was 2.9 g/kg. The 100-seed weight of the breeding line was 31.1 g and yield (t/ha) was 2.80. This is the first soybean strain with the penta null (lox1lox2lox3/lox1lox2lox3-ti/ti-le/le-cgy1/cgy1-rs2/rs2) genotype (free of lipoxygenase, KTI, lectin, and 7S α' subunit proteins, and with low stachyose content).

Linkage and association study discovered loci and candidate genes for glycinin and β-conglycinin in soybean (Glycine max L. Merr.)

KEY MESSAGE

Linkage mapping and GWAS identified 67 QTLs related to soybean glycinin, β-conglycinin and relevant traits. Polymorphisms of the candidate gene Gy1 promoter were associated with the glycinin content in soybean. The major components of storage proteins in soybean seeds are glycinin and β-conglycinin, which play important roles in determining protein nutrition and soy food processing properties. Increasing the protein content while improving the ratio of glycinin to β-conglycinin is substantially important for soybean protein improvement. To investigate the genetic mechanism of storage protein subunits, 184 recombinant inbred lines (RILs) derived from a cross of Kefeng No. 1 and Nannong 1138-2 and 211 diverse soybean cultivars were used to detect loci related to glycinin (11S), β-conglycinin (7S), the sum of glycinin and β-conglycinin (SGC), and the ratio of glycinin to β-conglycinin (RGC). Sixty-seven QTLs and 11 hot genomic regions were identified as affecting the four traits. One genetic region (q10-1) on chromosome 10 was associated with multiple traits by both linkage and association analysis. Eight genes in 11 hot genomic regions might be related to soybean protein subunit. The candidate gene analysis showed that polymorphisms in Gy1 promoters were significantly correlated with the 11S content. The QTLs and candidate genes identified in the present study allow for further understanding the genetic basis of 11S and 7S regulation and provide useful information for marker-assisted selection (MAS) in soybean quality improvement.

Soybean Mutants Lacking Abundant Seed Storage Proteins Are Impaired in Mobilization of Storage Reserves and Germination

Spontaneous and radiation-induced mutants of soybean, despite loss of abundant seed proteins, have been reported to grow and reproduce normally without any apparent physiological abnormalities. Here, we report the development and characterization of a soybean line (BSH-2) that lacks several abundant seed storage proteins. One-dimensional and high-resolution two-dimensional gel electrophoresis revealed the absence of the α' and α subunits of β-conglycinin and G1, G2, G4, and G5 glycinin in the newly developed mutant line (BSH-2). Like our earlier developed soybean mutant line (BSH-3), the seeds of BSH-2 also accumulated high levels of free amino acids as compared with wild-type DN47 seeds. An examination of the germination rates revealed that both BSH-2 and BSH-3 had significantly lower germination rates compared with the parent line DN47. Two-dimensional gel electrophoresis analysis demonstrated that these mutants had slower rates of mobilization of seed storage proteins. The delayed mobilization of storage proteins in BSH-2 and BSH-3 seeds was also correlated with a delayed induction of proteolytic activity in the mutants when compared to DN47. Similarly, qRT-PCR analysis revealed distinct expression pattern of genes involved in proteolytic pathway in the mutants when compared to DN47. Transmission electron microscopy observation of soybean seeds at two germination stages revealed striking differences in the breakdown of protein storage vacuoles and lipid bodies in the mutants. Our study demonstrates that BSH-2 and BSH-3 are compromised in mobilization of storage reserves and the absence of abundant storage proteins may affect the seed germination efficiency and post-germinative seedling establishment.

Identification of Soybean Genes Related to Soybean Seed Protein Content Based on Quantitative Trait Loci Collinearity Analysis

Increasing the protein content of soybean seeds through a higher ratio of glycinin is important for soybean breeding and food processing; therefore, the integration of different quantitative trait loci (QTLs) is of great significance. In this study, we investigated the collinearity of seed protein QTLs. We identified 192 collinear protein QTLs that formed six hotspot regions. The two most important regions had seed protein 36-10 and seed protein 36-20 as hub nodes. We used a chromosome segment substitution line (CSSL) population for QTL validation and identified six CSSL materials with collinear QTLs. Five materials with higher protein and glycinin contents in comparison to the recurrent parent were analyzed. A total of 13 candidate genes related to seed protein from the QTL hotspot intervals were detected, 8 of which had high expression in mature soybean seeds. These results offer a new analysis method for molecular-assisted selection (MAS) and improvement of soybean product quality.