Breeding’s main purpose is to increase genetic gain for agronomic traits such as yield but this selection over many breeding cycles will decrease and potentially eliminate genetic diversity. If new diversity is not introduced on a continual basis then a breeding program will no longer have any diversity available to continue breeding. Currently, this diversity is introduced into the Nebraska soybean breeding program by Dr. Graef selecting soybean lines to likely not be related to his current breeding material through coefficient of parentage analysis or 50k marker analysis. Ultimately, this may or may
not introduce diverse variation into his program. Without the underlying sequence information, the gene alleles from these lines may or may not be different from his current breeding lines. This project will remove this unknown and allow us to directly evaluate and catalog the genetic diversity within the breeding program and how diverse lines are really impacting the future health of the breeding program. This project will allow us to leverage valuable resources being created such as the project currently underway to resequence the USDA germplasm collection. Through a better understanding of the diversity within the breeding program, how to maintain and even increase the diversity within the
breeding program, we will help to ensure that the University of Nebraska breeding program can continue to make genetic gain over the long-term for important agronomic traits for Nebraskan soybean producers.
(Year 2)

Objective 1: Identify regions of low sequence or haplotype diversity in the breeding program and identify potential germplasm from the USDA germplasm collection that could be used to decrease this vulnerability of low diversity.

Objective 2: Identify genomic regions of positive selection in the UNL breeding program that need to be maintained while incorporating diverse germplasm.

Until now there has been limited resequencing of germplasm. One group in Canada resequenced 296 historical lines from two breeding programs. This gave them an initial look at diversity of their two breeding programs. This project, if funded, will be a more comprehensive evaluation of lines throughout the UNL breeding program. It will provide us a complete library of diversity currently present in the breeding program. In addition, with the USB project currently sequencing the USDA germplasm collection, no other program has had the opportunity yet to mine it to this level of precision for novel genetic diversity. This will create a type of roadmap for incorporating novel diversity that has never been created before and will help ensure genetic health of the breeding program for decades.
Research findings and potential intellectual property developed from the proposed research will be disseminated to the Nebraska Soybean Board through electronic reports or through presentations. Pending patent filings, if necessary, results generated from these studies will be made available to the public through presentations at national and international meetings and by publication in refereed scientific journals.

Genetic diversity is key to continued genetic gains from breeding for agronomic traits such as yield. The selection done during breeding will eventually eliminate genetic diversity over time. If diverse breeding lines are not continually introduced into a breeding program then genetic gains from breeding will eventually plateau. To help ensure the long-term success of Nebraskan soybean genetics, this project will make a detailed evaluation of genetic diversity in the breeding program.
- This project will catalog all genetic diversity currently contained within the breeding program and identify regions of the genome that have low diversity.
- It will identify germplasm from the USDA germplasm collection that can be prioritized to be used to introduced new diversity into the program
- It will identify regions important for local adaptation so that they can be maintained while introducing diverse germplasm increases the chance of successfully increasing the diversity within the program