Updated December 7, 2019:
Demand for soybean is mainly driven by its highly valued seed oil for dietary and industrial use and seed protein that makes soybean meal a valuable commodity for animal feed and producing plant-based protein. Approximately 60% of the soybean value comes from soybean meal and 40% from oil. Unfortunately, although it is not always, it is observed that seed protein content is often negatively associated with seed oil content and yield. A century of soybean breeding in the US has focused primarily on improving yield and oil content, which is believed to cause seed protein content decline. In recent years, protein content decease in some commercial soybean cultivars has become more difficult for meal processors to meet the minimum protein content required for high-protein meal designation. Lower protein levels also put US growers at a disadvantage in the international marketplace.

To reverse this trend and develop new germplasm/cultivars containing protein content meeting the requirement of the market through molecular breeding and biotechnology, it is critical and urgent to discover genes contributing to seed protein content decrease in soybean, understand their underlying molecular and genetic basis, and to further develop new breeding and biotech strategies including gene editing for reversing the trends with no or minimal impact on yield and oil content. For the past several decades, soybean researchers showed that more than 100 QTL (quantitative trait loci) contribute to protein content change in soybean natural population. However, only two oil and protein QTL have been consistently mapped in various populations, one on chromosomes 20 and one on chromosome 15. Significant efforts have also been made to identify their QTL genes/alleles since they were identified 27 years ago, however, progress is limited.

In the project, we have applied a big-data driven technology platform, which integrates computer technology with soybean genetics, molecular biology and genomic approaches, to analyze 15 terabyte DNA sequencing data of 1,500 soybean accessions generated by next-generation sequencing technologies. The interdisciplinary big-data driven technology platform enables us to effectively discover both QTL genes (candidates) on chromosome 20 and on Chromosome 15 and a set of candidate genes involved in their pathways regulating oil and protein content. We demonstrated that two QTL genes (candidates) are likely the major genetic components contributing to soybean protein content decrease in US soybean cultivars through soybean domestication and breeding processes.

We designed and conducted a set of experiments to confirm the functions of the gene on Chromosome 20 in controlling seed oil, protein and eventually seed yield to further understand their relationship, and test biotech strategies to produce high-protein soybean cultivars using traditional and new genetic engineering technologies such as gene-editing technology. In the effort, we screened and analyzed over one hundred of soybean plants containing modified genes, and provided evidence supporting its functions regulating soybean seed oil and protein content. In addition, we developed an in-silico genotyping approach and a wet-lab perfect DNA assay for its high protein allele/version of the gene. Having screened 1261 wild and cultivated soybean lines, we identified 217 soybean accessions containing the high-protein allele at most maturity groups in US. Knowledge of the protein QTL gene (candidate) at a molecular level, the high-protein allele assay and the collection of high-protein soybean accessions enables breeders to effectively introgress the high-protein trait into elite soybean cultivars.