title: Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume.
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. This study demonstrates a holistic approach for mining plant collections to accelerate crop improvement.
authors.affiliation: Interdepartmental Genetics, Iowa State University, Ames, IA 50011, USA.|Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
authors.forename: Vikas
authors.initials: V
authors.lastname: Belamkar
authors.affiliation: National Center for Genome Resources, Santa Fe, NM 87505, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.
authors.forename: Nathan T
authors.initials: NT
authors.lastname: Weeks
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.
authors.forename: Scott R
authors.initials: SR
authors.lastname: Kalberer
authors.affiliation: Department of Horticulture, Louisiana Agricultural Experiment Station, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Blackmon
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA.|United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
mesh_terms: D001947:Breeding; D016000:Cluster Analysis; D007887:Fabaceae / Q000235:genetics* / Q000254:growth & development*; D020869:Gene Expression Profiling; D023281:Genomics; D005838:Genotype; D015810:Linkage Disequilibrium; D027805:Phaseolus / Q000235:genetics; D010945:Plants, Edible / Q000235:genetics* / Q000254:growth & development*; D020641:Polymorphism, Single Nucleotide