Open Access Research article

Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

Xuehui Li1, Ananta Acharya2, Andrew D Farmer3, John A Crow3, Arvind K Bharti3, Robin S Kramer3, Yanling Wei1, Yuanhong Han1, Jiqing Gou1, Gregory D May3, Maria J Monteros1 and E Charles Brummer1*

Author Affiliations

1 The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

2 Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, 30602, USA

3 National Center for Genome Resources, Santa Fe, NM, 87505, USA

For all author emails, please log on.

BMC Genomics 2012, 13:568  doi:10.1186/1471-2164-13-568

Published: 29 October 2012

Additional files

Additional file 1:

Gene ontology assignments for M. sativa, compared to A. thaliana. Gene ontology assignment was found for the 11,222 Arabidopsis best-hit gene models (1× 10-10). Numbers of best hits in each GO category were plotted and compared to that of all of the gene models in the Arabidopsis genome annotation.

Format: DOC Size: 234KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

SNP distribution along the M. truncatula chromosomes. The X-axis represents the genome location (Mbp) for each chromosome. The number of SNP per 1000 bp was calculated for each 0.5 million base pairs interval and plotted on the Y-axis.

Format: DOC Size: 47KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 3:

The numbers of SNP homozygous and heterozygous for each genotype based on 173,947 SNPs for which sequence information was available for all genotypes.

Format: DOC Size: 48KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

Potential candidate genes involved with domestication and/or selection.

Format: XLS Size: 31KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Potential candidate genes differentiating subsp. falcata from subsp. sativa.

Format: XLS Size: 57KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

SNP primer sequences used for validation using high resolution melting (HRM).

Format: DOC Size: 304KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data