This project will address the identification of genes and pathways controlling seed protein synthesis and storage and the development of markers to create soybeans with sustainable protein levels in the problem production areas; these results will aid in the development of commercial soybean varieties with an improved nutritional bundle and thus provide profitability for US soybean producers. Our approach is to develop a foundation of knowledge of protein genes through a deep analysis of the soybean genome sequences available including the ancestral and elite varieties that have been characterized for variation in protein and oil content as well as yield. The impact of this project is an enhanced ability to breed for higher protein soybeans while maintaining yield.

1) Develop a comprehensive understanding of soybean allele diversity and gene networks in the US soybean ancestors and released US soybean varieties.

2) Provide context of genetic source, allele impact, and potential positive alternate alleles once the genes are cloned underlying key protein QTL on chromosomes 20 and 15.

3) Incorporate protein, oil, and yield component gene and network knowledge into genomic selection strategies for maximum effectiveness.

Quarterly technical reports will be provided to USB according to their schedule. Research results will be disseminated through publication and presentation and tool and dataset release on appropriate platforms (SoyBase and SoyKB).

Updated January 12, 2021:
We are working on a computational approach to utilize the genomic differences in the various soybean ancestors, elite, landraces, cultivars and wild soybeans to create a master list of significant differences for every gene. We have defined a panel of 775 soybean lines for creating list of positions for this master catalog and are also building a website where any user can query this list and get information about such genomic positions and their distribution in the various categories described above along with the impact these differences have on the traits potentially.

Updated December 2, 2021:
In this project we worked on developing strategies and building a computational approach to utilize the genomic differences in the various soybean ancestors, elite, landraces, cultivars and wild soybeans to create a master list of significant differences for every gene. We used bioinformatics and computational methods to identify genomic differences from four large collections of sequenced soybean lines and have successfully developed the Soy775 panel, consisting of 775 soybean lines that includes a comprehensive list of SNPs and Indel positions as our master catalog. We have also built a new “Allele Catalog” web based tool in SoyKB, where any user can query this Soy775 panel with a gene name or soybean line accession number and get information about such genomic positions, the effect the change has on the gene, and their distribution in the various categories described above. We have applied this to several traits that impact soybean yield and value. We have analyzed the recently cloned major protein gene on chromosome 15 (Glyma.15g049200) and have determined that one soybean accession (PI374207) from the Soy775 putatively contains a novel defunct allele of the gene that could be used in breeding programs to modulate seed protein content. Our developments and discoveries we have made in this project have allowed us to leverage and expand existing whole genome sequencing resources, tools, and technologies to put soybean at the forefront of crop improvement with applied genomics. We have achieved all of our proposed objectives which included generating new knowledge, research publications, automated pipelines, online tools, and a team of multi-disciplinary researchers dedicated to advancing soybean applied genomics.

The tools developed in this program will help public breeders use modern breeding strategies to accelerate the incorporation of new traits for growers.