Citation: Belamkar, V., Farmer, A.D., Weeks, N.T., Kalberer, S.R., Blackmon, W.J., Cannon, S.B. 2016. Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume. Nature Scientific Reports. 6:34908. doi: 10.1038/srep34908.
Interpretive Summary: A native North American bean relative, Apios americana (sometimes called "potato bean" or "ground nut"), was once a staple crop of Native American Indians. This plant produces high-protein, potato-like tubers, which grow along underground stolons. This paper describes a large set of gene sequences for this plant, as well as a set of several thousand genetic markers that can be used for crop improvement in Apios. This research also describes associations between particular genetic markers and some valuable plant traits in Apios, including the size of the edible tubers. These genetic markers can be used to speed varietal improvement in this promising but under-utilized native North American species.
Technical Abstract: For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates a wide range of soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, and a set of 58,154 SNP and 39,609 gene expression markers (GEMs) for characterization of a breeding collection. Both SNPs and GEMs identify six genotypic clusters in the collection. Transcripts mapped to the Phaseolus vulgaris genome – another phaseoloid legume with the same chromosome number - provide provisional genetic locations for 46,852 SNPs. Linkage disequilibrium decays within 10 kb (based on the provisional genetic locations), consistent with outcrossing reproduction. SNPs and GEMs identify more than 21 marker-trait associations for at least 11 traits. These results provide an example of a holistic approach for mining plant collections.