Genomics-Assisted Characterization of a Breeding Collection of Apios americana, an Edible Tuberous Legume

Authors

Vikas Belamkar, University of Nebraska-LincolnFollow
Andrew Farmer, NCGRFollow
Nathan T. Weeks, United States Department of Agriculture, Agricultural Research ServiceFollow
Scott R. Kalberer, United States Department of Agriculture, Agricultural Research ServiceFollow
William J. Blackmon, Louisiana State University
Steven B. Cannon, United States Department of Agriculture, Agricultural Research ServiceFollow

Document Type

Article

Date of this Version

10-10-2016

Citation

Scientific Reports (October 10, 2016) 6: 34908. DOI: 10.1038/srep34908.

Comments

Copyright 2016, the authors. Open access, Creative Commons Attribution 4.0 International license.

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 10kb (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. This study demonstrates a holistic approach for mining plant collections to accelerate crop improvement.