Diagrammatic representation of the distribution of mutations identified by classical TILLING and by SCAMPRing.

<p>The BnSAD gene was used as a test to compare the effectiveness of NGS sequencing (SCAMPRing) vs. classical TILLING. Purple arrows indicate silent changes in the gene that are predicted to have no effect on the protein gene product. Black arrows indicate predicted missense mutations that alter the amino acid sequence of the protein product. Red arrows indicate predicted nonsense mutations that result in premature truncation of the protein. Circles indicate mutations that were detected using SCAMPRing but not originally found with classical TILLING.</p

Sequencing read depth and mutation frequencies identified in 384 lines of the <i>B. napus</i> population.

<p>The top panel represents the coverage of Illumina read depth (vertical axis) across the four amplicons developed for the target gene (bn1); a total of 1,530 bp (horizontal axis). The second, third and bottom panels represent the frequency (vertical axis) of candidate mutations (C to T, G to A, and A to G, respectively) identified in three pools (circled in red) of the 12 pools used in the analysis across the length of the target region in base pairs (horizontal axis). No A to G mutations were identified in the target locus and this is consistent with the mechanism of mutation induction by EMS.</p

Database accession numbers for orthologues to the major trichome regulatory genes (<i>GL1</i>, <i>Gl2</i>, <i>EGL3</i>, <i>TTG1</i> and <i>TRY</i>) in <i>B. villosa.</i>

<p>Genes in the same row are closest orthologues to each other. NA = Sequence not available.</p

Specific amino acids in five trichome regulatory genes within the <i>Brassicaceae</i>.

<p>*Selected positions in the aligned consensus amino acid sequence (CAA) were selected from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095877#pone.0095877.s001" target="_blank">Figure S1</a> if they distinguished hairy from glabrous germplasm (dark arrows in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095877#pone.0095877.s001" target="_blank">Fig. S1</a>) or were unique to <i>B. villosa</i> (*red arrows in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095877#pone.0095877.s001" target="_blank">Fig. S1</a>). ND, not determined (sequence not available). NIL, missing amino acid. NA, not applicable. Note: Multiple gene copies are only indicated if an amino acid differed between the copies.</p

<i>Ka</i>/<i>Ks</i>^* ratios for trichome regulatory gene comparisons between <i>B. villosa</i> and three other <i>Brassica</i> species and Arabidopsis.

<p>*<i>Ka</i>/<i>K_S</i> (Yang Z, 1997): <i>Ka</i>, non-synonymous nucleotide substitution. <i>Ks</i>, synonymous nucleotide substitution value.</p>+<p><i>B. rapa</i>-2 (BRTRY-2) and <i>B. rapa</i>-3 (BRTRY-3) amino acid sequences were too short to be included. NA, <i>B. napus</i> sequence not available.</p

Theoretical protein size (Mr/Number of amino acid) and isoelectric point (<i>pI</i>) of trichome regulatory coding sequences in the <i>Brassicaceae</i>.

<p>ND, not determined (sequence not available). Closest orthologues between the species are positioned within the same row. Data represents all known orthologues and homologues for each species.</p

Mapping of chickpea TACs onto <i>Medicago</i> genome.

<p>Mapping of chickpea TACs onto <i>Medicago</i> genome.</p

A sample view of chickpea TACs, markers and candidate ISR markers onto <i>Medicago</i> Genome sequence.

<p>This image is from Legume Information System (LIS) GBrowse viewer at <a href="http://medtr.comparative-legumes.org/gb2/gbrowse/3.5.1/" target="_blank">http://medtr.comparative-legumes.org/gb2/gbrowse/3.5.1/</a>, shows 1 Mb (17,648,842.18,648,841 of <i>Medicago</i>, chromosome Mt1). Red: There was at least one additional reported CaTA v2 alignment Green: There were no other reported alignments.</p

Correspondences of chickpea genic molecular markers to <i>Medicago</i>.

<p>Correspondences of chickpea genic molecular markers to <i>Medicago</i>.</p

Details on NGS (FLX/454 and Illumina) and Sanger sequencing datasets used for developing comprehensive chickpea transcriptome assembly (CaTA v2).

1<p>Tissues collected: a) 2-week old leaf, b) stem before flowering, c) 1-week-old etiolated seedling, d) mixed flower stages and e) developing seed at mixed stages.</p>*<p>NIPGR- National Institute of Plant Genome Research, India; ICRISAT- International Crops Research Institute for the Semi-Arid Tropics, India; JCVI- J. Craig Venter Institute, USA; NRC- National Research Council Canada.</p