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ARS Home Midwest Area Columbia, Missouri Plant Genetics Research Research





- Gillman, Jason
- Bilyeu, Kristin
- Krishnan, Hari
- 2023
- Publications
- Plant Genetic Resources, Genomics and Genetic Improvement (301)

Research Project: **Location:
                            Plant Genetics Research** Project Number: 5070-21000-044-000-D
                        
                        Project Type: In-House Appropriated Start Date: Jan 24, 2023
                        
                        End Date: Jan 23, 2028 **Objective:**
                        
                        Objective 1: Conduct research to characterize the biochemical processes that control amino acid biosynthesis in soybean, use the information to develop soybean containing reduced levels of trypsin and chymotrypsin inhibitors, and work with breeders to incorporate these desirable traits into modern soybean backgrounds.
Sub-objective 1.A: Molecular and biochemical characterization of soybean plants with enhanced protein and sulfur amino acid content.
Sub-objective 1.B: Down regulation of soybean Bowman-Birk protease inhibitor by CRISPR-Cas9 genome editing.
Sub-objective 1.C: Incorporation of anti-nutritional traits into at least one modern soybean background.

Objective 2: Conduct research to identify new genomic regions associated with improved stress tolerance and/or desirable seed quality traits in multi-parent soybean populations, use high throughput seed analysis techniques combined with modern genomic tools to discover desirable genes or genomic regions, and investigate with breeders to develop improved germplasm.
Sub-objective 2.A: Application of high-throughput near-infrared robotic seed analysis on multiple soybean populations for identification and mapping of seed compositional causative alleles.
Sub-objective 2.B: Conduct high-throughput near-infrared robotic seed analysis on multiple populations and select value-added soybean germplasm to share with public and private breeders.
Sub-objective 2.C: Genotyping and genetic analysis in replicated, multi-location studies using a unique Multi-Parent Advanced Generation InterCross soybean (MAGIC) population created to combine beneficial alleles for seed value, abiotic stress tolerance and agronomic potential.

Objective 3: Conduct research to determine the interactions and thresholds among soybean quality trait components, develop an effective genomics framework connecting phenotypes to genotypes, and use the information to improve soybean seed composition while maintaining seed yields and general agronomic performance. 
Sub-objective 3.A: SWEET protein trait plus CARB or HOLL.
Sub-objective 3.B: HOLL/CARB SWEET and HOLL/CARB/LIPOX SWEET soybeans.
Sub-objective 3.C: Alternate sources of elevated seed protein. **Approach:**
                        
                        Objective 1: Subobjective 1.A comprises in-depth molecular and biochemical characterization of select soybean experimental lines that accumulate enhanced protein and sulfur amino acids. Subobjective 1.B experiments will be performed to down-regulate antinutritional Bowman Birk inhibitor (BBi) genes towards development of soybean lines that accumulate no or very low BBi in the seeds. Subobjective 1.C uses experiment lines with CRISPR-Cas9 induced BBi mutations with demonstrated reductions in BBi backcrossed to define genetic loci and advanced to segregate transgene(s) away from BBi mutations and permit field testing to evaluate field performance and test for pleiotropic impacts of induced BBi mutations.

Objective 2: The potential of recently developed calibrations for a high throughput seed sorting optimal and NIRS robotic instrument will be thoroughly tested. The goal of these experiments is to enable genetic mapping (Subobjective 2.A) studies for seed size and composition and to develop and release value added germplasm (Subobjective 2.B). Subobjective 2.C utilizes a previously developed Multi-Parent Advanced Generation InterCross soybean (MAGIC) population which maximizes genetic and phenotypic diversity. The MAGIC population will be tested in a multi-location field study to collect seed data, measure agronomic performance, and apply several different high-throughput methods to infer water use efficiency, overall plant health status, and collect hyperspectral canopy data. We will test several different genetic mapping methodologies and attempt to fine map QTLs identified by these approaches. 

Objective 3: Recently alterations affecting one specific gene involved in sucrose transport have been identified as causative for high soybean seed protein. Prior ARS research has led to the discovery, characterization, and deployment of alleles of genes underlying various soybean seed oil composition and meal composition traits. Subobjective 3.A uses forward crossing population development, evaluation of seed phenotypes, and agronomic performance to test independent combinations of the high protein trait plus other value-added traits. Subobjective 3.B is development of novel value-added soybean germplasm through backcrossing and evaluation of seed phenotypes and agronomic performance for independent combinations of traits. Backcrossed soybean germplasm lines will be grown in a field environment along with parental lines as controls and evaluated for seed composition phenotypes. Subobjective 3.C is development of new soybean germplasm and evaluation of seed phenotypes for alternate sources of elevated seed protein content. Seed composition phenotypes will be analyzed for nitrogen as well as protein and oil. Additionally, seed composition phenotypes will be determined for developed germplasm that combines another high protein gene by creating new soybean germplasm with contrasting allele combinations and subsequent seed composition analyses.


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