Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume
| Autor: | Steven B. Cannon, Scott R. Kalberer, Nathan T. Weeks, Vikas Belamkar, William J. Blackmon, Andrew Farmer |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Linkage disequilibrium Genotype De novo transcriptome assembly Outcrossing Genomics Breeding Polymorphism Single Nucleotide Article Linkage Disequilibrium Crop 03 medical and health sciences Botany Cluster Analysis Legume Phaseolus Multidisciplinary biology Gene Expression Profiling Fabaceae Apios biology.organism_classification 030104 developmental biology Plants Edible |
| Zdroj: | Scientific Reports |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/srep34908 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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