Update:
refer to final report

This is the final technical report for the 3rd year of a three-year project originally initiated in 2014. The 3rd year project started on May 1, 2016 and ended on October 31 2017 after a 6-months' no-cost extension. The central goal of the whole project was to use the cutting-edge genetics and genomics technologies, as well as field data, to create and identify high-yielding, SCN-resistant experimental lines of soybean by backcrossing of wild soybean-derived lines with elite soybean cultivars assisted by marker and genomic selections. In FY2016, we proposed to achieve the following specific research objectives towards completion of the whole project: 1) Identify genomic regions and genes associated with some desirable and undesirable traits associated with soybean yeild potential; 2) compare the genomic regions harboring loci associated with the desirable and undesirable traits and develop effective markers for trait enhancement and selection; 3) continue advanced backcrosses with elite soybean cultivars and Williams 82 as recurrent lines for effective pyramiding of multiple traits in single individual lines for improved yield potential and SCN resistance through marker-assisted and genomic selection.

Upon the completion of the project, we we have identified and cloned a gene, named B1, which not only controls seed coat bloom but also modulate seed oil content. Intriguingly, the B1 gene doesn’t control oil biosynthesis in seeds, but the mutation that causes loss of bloom heightens the activity of other genes that result in an increase of oil accumulation. The findings show that there may be genetic targets outside those responsible for seed traits that could affect soybean oil content. Soybean breeders working to increase seed oil content tend to focus their efforts on genes known to impact the plant’s seeds, but our study shows that genes affecting other plant parts deserve more attention in the future.

We have identified QTLs controlling stem vininess, stem architecture (e.g., branch angles), leave shape, pod node density, seed number per pod, and seed sizes, some of which are important yield component traits. Molecular markers from these QTL regions have been designed and used for tracking these QTLs for selection in breeding.

We have introgressed two SCN QTLs derived from the wild soybean accession P I468916 into eight elite soybean lines that show high-yielding potential, and selected experimental lines carrying the two SCN QTLs. These lines have been genotyped and the introgressed QTLs have been confirmed. These novel resources can be used as valuable pre-breeding lines for soybean breeding.

We have phenotyped a set of progeny lines for agronomic traits including seed sizes, branching angles, stem diameter, stem vininess, plant height, leave shapes, and developed molecular markers targeting these traits. Some experimental lines showing desirable yield component traits have been selected.

We think the proposed objectives, including development of a set of valuable experimental soybean lines and generation of a set of useful genotypic and phenotypic data, for soybean breeders to exploit in breeding program have been fully achieved, though the targeted traits were shifted around according to the complexity of the genetic bases underlying those traits. We will proliferate seeds from promising experimental lines for further evaluation of SCN resistance and yield as the next step.

This project has yielded one publication in a peer reviewed journal Nature Plants (https://www.nature.com/articles/s41477-017-0084-7), describing the identification and functional analysis of the genes/genomic regions associate with seed coat bloom and elevated seed oil content. In collaboration with co-PI Randy Nelson, we have presented some data from this project in the SOY2016 Molecular and Cellular Biology of the Soybean 16th Biennial Conference held on August 7-10 in Columbus, OH, the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America meeting 2016 held in Phoenix. In these meetings, Dr. Ma was invited to give an oral presentation entitled “Genetic Basis and Process of Soybean Domestication”, and the Ph.D. student Stephen Swarm who has been working on this project presented two posters in Soy2016, one is entitled “Using Wild Soybean as a Resource to Increase Soybean Seed Yield" and the other is entitled ”Mapping Traits Related to the Domestication of Soybean from Glycine soja”. The graduate student Stephen Swarm was partially supported by this project and has finalized up his Ph.D. dissertation in May 2017. In addition, we are drafting a manuscript describing the identification of QTLs controlling leave shape. Partially supported by this project, we have trained four undergraduate students (Chancelor Clark, Gabriel Fear, HyeSu Lee, and Landyn McCormick), a graduate student, in addition to a postdoctoral associate, and additional technical supports.