NRGene constructs comprehensive soy genome diversity-haplotype database

Aug 28 2018

All-by-all full genome comparison of 30+ varieties to rapidly improve nutrition and hardiness and reduce resource requirements

NRGene, the leading genomic big data company, has constructed a comprehensive soy genome diversity-haplotype database based on results from GenoMAGIC™, allowing commercial and academic researchers never-before-available insights into the genomic diversity within the soybean crop. The database contains de novo assemblies and all-to-all comparison of 34 varieties of soybean, a set of breeding germplasm covering the full range of maturity groups.

This database is a fundamental resource for basic research, genetic resource management, and breeding of elite soy varieties. Scientists studying gene function can now analyze every experiment in the broader view of dozens of genomes rather than a single reference genome, as it is often done today.

Breeders can now more accurately relate genetic diversity with field performance, thereby accelerating the breeding of more nutritious and hardier varieties that need fewer resources and less land to deliver higher yields.

Previously, NRGene, in cooperation with a global consortium of researchers, assembled two out of three available reference-level soy genomes using its DeNovoMAGIC™ technology.

NRGene then compared the three genomes on an all-to-all basis using PanMAGIC™, creating a new pangenome. Recently, a diverse soy sequence dataset of 481 lines produced by the Nguyen Lab and Associates in cooperation with the United Soybean Board, Monsanto, Dow AgroSciences, and Bayer CropScience was made publicly available.

“Our mission has always been to provide the soy research community with the tools to efficiently improve the crop in a sustainable manner,” said Jacqueline Weiss, Director of Molecular Biology and Digital Agriculture at the United Soybean Board. “By supporting genetic data production, researchers can create better seeds for farmers who face myriad challenges, such as soil condition, water availability, and climate extremes.”

NRGene, together with commercial partners, has chosen 31 lines relevant to global soy breeding. Using DeNovoMAGIC™, NRGene assembled those 31 soy lines, which were then processed by GenoMAGIC™ to construct the first-ever comprehensive diversity and haplotype database of commercial soybeans.

Using this integrated database of sequence information, NRGene has identified an unprecedented number of sequence variants across multiple genomes including structural variants, such as insertions and deletions as well as single and multiple nucleotide polymorphisms. All variants are dynamically positioned across all reference genomes. This is made possible through the GenoMAGIC™ system, which also allows for accurate and high-density sequence imputation from low density genotyping.

The Soy framework is now being offered to select collaborators as part of an initial release for testing and feedback.

Soybean is a crop of great economic importance. It’s used globally as livestock feed as well as for human consumption. It is highly valued for its high protein and high oil content. Approximately 85% of the world's soybean crop is processed into soybean meal and soybean oil; the remainder is processed or consumed otherwise. Soybeans are the second-most valuable agricultural export in the United States, after corn.

World soybean production in 2017-2018 is projected to reach 348 million tons, with the soybean market in the United States alone to be $40 billion.

“Leveraging biodiversity strengthens the ability to breed better varieties of any crop,” says Dr. Gil Ronen, CEO of NRGene. “With the new database, researchers can get there faster, and we continue to transform the world’s food supply.”

See NRGene at the upcoming 17th Biennial  Conference on the Molecular and Cellular Biology of the Soybean, August 26-29, 2018 at the University of Georgia in Athens, Ga.