Primer sequences of ReG-SSR markers in flax

A genome-wide set of 580 simple sequence repeat markers were derived from transcription factor coding genes and long non-coding RNA sequences of flax genome. These markers were named ReG-SSRs as they were derived from the regulatory genes. In silico anchoring of 559 ReG-SSR markers was successful on the draft assembly of 15 chromosomes. A set of ReG-SSR primers was employed to characterize fibre flax accessions

Summary results of AMOVA analyses within and among populations of 95 accessions of the domesticated and wild groups.

<p>d.f.: Degrees of freedom; SS, sum of squared observations; MS, mean of squared observations; Est. var., estimated variance % Var., percentage of total variance; Fct, proportion of the total genetic variance between groups; FSc, proportion of the total genetic variance among populations within a group; Fst, proportion of the total genetic variance within populations.</p

Phylogeny of <i>Cajanus</i> species depicted as a 50% majority rule consensus tree.

<p>Tree topology was inferred with maximum parsimony via heuristic searches among 1000 trees. Numbers above branches indicate bootstrap support (>50%). The vertical bar indicates the putative projentitor species (two <i>C. Cajanifolius</i> accessions). Tree length  = 2145, consistency index (CI)  = 0.638, and retention index (RI)  = 0.837. The Bootstrap support for the sister relationship between wild-Australia and Wild-India clades (in the absence of the two <i>C. cajan</i> accessions) is 100% (data not shown).</p

Inferred relationships among admixed <i>Cajanus cajan</i> accessions.

<p>An un-rooted Neighbor Joining tree depicting pairwise similarity between genotypes with simple admixture between domesticated-India and domesticated-tropical accessions. Admixed genotypes were identified based on mixed-group membership defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039563#pone-0039563-g005" target="_blank">Figure 5B</a>. Accession ICP 8817 has an identical haplogype to accession ICP 9236, and thus only ICP 8817 is shown.</p

Population structure of cultivated <i>Cajanus cajan</i>.

<p>Panel <b>A</b>, Weighted Neighbor-Joining tree depicting pairwise relationships between accessions. Colors denote the nature of individual accessions: Blue diamonds, cultivars and elite varieties; Pink diamonds, landraces; purple diamonds, ICRISAT reference material; Green diamonds, Core collection; Red diamonds, R-line; Orange diamonds, Minicore; Light green diamonds, Tropical; light blue, Indian; Light brown diamonds, Philipines. Genotypes with admixture between Indian and Tropical subgroups are designated by both light green and light blue diamonds. Panel <b>B</b>, population subdivisions with cultivated genotypes revealed by STRUCTURE. Green diamonds, genotypes with tropical distribution; blue diamonds, genotypes with an Indian sub-tropical distribution. Admixed genotypes are those with fractional membership in multiple groups. Likelihood values for each value of K are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039563#pone.0039563.s004" target="_blank">Table S4</a>.</p

Pairwise estimates of FST among wild and domesticated groups.

<p>Pairwise estimates of FST among wild and domesticated groups.</p

Population structure among the wild and domesticated genotypes of <i>Cajanus</i>.

<p>Output of the population genetic program STRUCTURE at increasing K values of 2 to 5. The primary divisions at increasing K values mirror phylogenetic groupings shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039563#pone-0039563-g001" target="_blank">Figures 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039563#pone-0039563-g002" target="_blank">2</a>. Memberships of individual genotypes to specific subgroupings are indicated by colored bars. Genetic admixture is evidenced by fractional membership in multiple subgroups. The correspondence between numbers below each genotype and specific accessions is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039563#pone.0039563.s001" target="_blank">Table S1</a>. Likelihood values for each value of K are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039563#pone.0039563.s003" target="_blank">Table S3</a>.</p

Percentage of Polymorphic loci in wild and domesticated groups.

<p>Percentage of Polymorphic loci in wild and domesticated groups.</p

Principal coordinates analysis of domesticated pigeonpea and wild relatives.

<p>Red diamonds, wild <i>C. scarabaeoides</i>; green squares, wild-Australia <i>Cajanus</i> spp; dark blue triangles, wild-India <i>Cajanus</i> spp; light blue squares and pink diamonds represent domesticated <i>C. cajan</i> of tropical and Indian origin, respectively. Admixed genotypes between domesticated and wild species are labeled with yellow circles, or in the case of admixed Philippines accessions with dark red triangles. Accession numbers were added for accessions mentioned in the text.</p

Correspondence among consensus and component maps of LG1.

<p>Depiction of common markers between the consensus and individual genetic maps for the LG01 pigeonpea linkage group aligned together using the Genetic Map Comparator software.</p