OrphanCap: Massive-scale Evolutionary Study of Germplasm Databases Using the Orphan Crop Amaranthus as a Case Study

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2017. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The host institution for the fellowship is Columbia University and the sponsoring scientist is Dr. Deren Eaton.

Despite advances in agricultural technology, sustainable access to food remains a major problem throughout many parts of the world. Orphan crops are regionally important food sources that are often genetically diverse and adapted to harsh environments, yet remain understudied because they are not exported widely. They are important targets for new plant breeding programs aimed at developing crops for sustainable agricultural practices. Vast resources exist for studying orphan crops in the form of large-scale and exhaustive seed collections (germplasm databases). This research will investigate the genus Amaranthus, which includes grain amaranths and herbicide-resistant weedy relatives, as a case-study and resource for demonstrating how new massive-scale genomic sequencing methods can be used to exploit and understand the diversity of orphan crops in germplasm databases. Broader impacts include developing a workshop (OrphanCap) and website detailing the protocol, and teaching wet-lab and phylogenomic data analysis to high school students.

Using the novel library preparation method, RADcap, which can efficiently and economically allow for unprecedented sampling of thousands of genomic markers from thousands of individuals, genomic data from a comprehensive sampling of Amaranthus species will be sequenced. Combining this dataset with new phylogenomic methods, the Fellow will (1) Reconstruct species relationships, the history of domestication, and introgression within and between different species and landraces of Amaranthus; (2) Compare genetic diversity in historical accessions versus contemporary field-collected samples at neutral loci, and at loci sampled from known herbicide resistance genes; and (3) Develop a workshop and online resource (www.OrphanCap.org) to demonstrate and teach the laboratory and bioinformatic workflow for developing massive-scale RADcap libraries and their analysis. Raw data will be deposited in the NCBI sequence read archive (http://www.ncbi.nlm.nih.gov/sra), phylogenetic trees will be uploaded to TreeBASE (http://treebase.org), and code will be available at www.OrphanCap.org.