Description of the WRRC Brachypodium distachyon T-DNA collection and the generation of homozygous lines

During the initial phase of our T-DNA tagging project we generated 8,491 fertile T-DNA lines in the model grass Brachypodium distachyon (Brachypodium). Data from 17,637 sequencing reactions for 7,145 of the lines were compared to the Brachypodium genome assembly, and 7,389 sequences (average 195 bases) matched to the Brachypodium genome. The top scoring match from each sequence was assigned as a flanking sequence tag (FST). FSTs were assigned to insertions sites (ISs) in 4,402 of the lines. These represent 5,285 unique loci. The distribution of ISs across the chromosomes was analyzed by plotting the number of insertions within 500 kb windows. Insertions span the length of all five chromosomes and are generally proportional to chromosome length (average 19-21 IS/Mb), except for Bd4 (16 IS/Mb). The number of ISs is positively correlated with regions of higher gene density and 28% of the ISs reside in genic regions (exons, introns, UTRs) and 21% are within 1 kb of genes. The WRRC T-DNA population contains >2,400 tagged genes and can be viewed at http://brachypodium.pw.usda.gov/ and http://www.brachypodium.org/browse. Lines can be ordered through the USDA site. We currently are using a PCR screen with primers flanking the predicted ISs to identify individuals homozygous for insertions within genes for high-throughput phenotyping analyses.