Morphology and heterochromatin distribution on pachytene chromosomes 3 and 4 of cucumber.

<p><b>A</b> Pachytene chromosome of cucumber. Chromosome 3 is traced by green line, and chromosome 4 is traced by red line. Identification of individual chromosome was confirmed by FISH mapping of satellites DNA and chromosome-specific fomsids. <b>B</b> Computationally straightened chromosomes 3 and 4 from the image shown in (A). Large arrows point to the positions of centromeres, and small arrows point to the knobs in the short and long arm of chromosome 4 and in the region of proximal centromere of chromosome 3. <b>C</b> Ideograms of chromosomes 3 and 4. Heterochromatic regions are represented by solid/shaded thickenings. Shaded thickenings indicate the chromosome primary constrictions detected by the probe of centromere specific satellite DNA Type III. These regions were less stained by DAPI compared to the regions of solid thickenings. Bars = 5 µm.</p

Genetic and physical position of SSR marker-anchored cucumber chromosome 3-specific fosmid clones and satellite DNAs.

a<p>Fraction length (FL) = (S/T)×112.7, where S is the distance (micrometers) from the FISH site to the end of the short arm, T is the total length of the chromosome (micrometers), and 112.7 is the length (in centimorgans) of the linkage map of chromosome 3.</p

Distribution of gene density along the chromosome 3 of cucumber.

<p>The predicted gene location and number were from the cucumber genome draft published by Huang et al. <i>(2</i>009). They were accessed through Cucumber Genome Database (<a href="http://cucumber.genomics.org.cn/page/cucumber/index.jsp" target="_blank">http://cucumber.genomics.org.cn/page/cucumber/index.jsp</a>). The number of genes per 100 kb was plotted against the physical distance along the chromosome (in base pair). The red line showed the overall trend of gene density. The positions of knobs in the both arms were pointed by red arrows. Three regions, the short arm (green), the long arm (green), and the pericentromeric heterochromatin region (gray) were divided along the chromosome according to the structure of pachytene chromosome and FISH results.</p

FISH mapping of cucumber chromosome 3-specific fosmid clones and satellite DNAs on the pachytene chromosome 3.

<p><b>A</b> Fish mapping of 10 fosmid clones on the pachytene chromosome 3 of cucumber. <b>B</b> Fish mapping of 45S rDNA (red), Type I/II (red), Type III (green), and Type IV (green) clones on the same slide as A using reprobing method. <b>C</b> The DAPI-stained chromosomal image was converted as a black–white image to enhance the visualization of chromosome structure. <b>D</b> Fish mapping of 3 fosmid clones on the pachytene chromosome 3 of cucumber. <b>E</b> Fish mapping of Type III (red) and two fosmid clones on the same slide as D using reprobing method. <b>F</b> The DAPI-stained chromosomal image was converted as a black–white image to enhance the visualization of chromosome structure. The pachytene chromosome 3 was orientated with red line. Bars = 5 µm.</p

Fish mapping of cucumber chromosome 4-specific fosmid clones and satellite DNAs on the pachytene chromosome 4.

<p><b>A</b> Fish mapping of 10 fosmid clones on the pachytene chromosome 4 of cucumber. <b>B</b> Fish mapping of 45S rDNA (green) and Type III (red) clones on the same slide using reprobing method. <b>C</b> The DAPI-stained chromosomal image was converted as a black–white image to enhance the visualization of chromosome structure, and the pachytene chromosome 4 was orientated with red line. Bars = 5 µm.</p

Genetic and physical position of SSR marker-anchored cucumber chromosome-4 specific fosmid clones and satellite DNAs.

a<p>Fraction length (FL) = (S/T)×37.3, where S is the distance (micrometers) from the FISH site to the end of the short arm, T is the total length of the chromosome (micrometers), and 37.3 is the length (in centimorgans) of the linkage map of chromosome 4.</p

Length, arm ratio and percentage of heterochromatin, and centromere position of chromosomes 3 and 4.

a<p>[Total heterochromatin/total chromosome length]×100.</p>b<p>Centromere position (%) is (S/T)×100, where S = distance of centromere from the end of the short arm, and T = total length of chromosome.</p

Integration of genetic linkage map of cucumber chromosome 4 with cucumber pachytene chromosome 4.

<p>The genetic linkage map of cucumber chromosome 4 on the left lane is according to Ren et al. (2009). The sequence map of cucumber chromosome 4 on the right lane is according to Huang et al. (2009).</p

Integration of genetic linkage map of cucumber chromosome 3 with cucumber pachytene chromosome 3.

<p>The genetic linkage map of cucumber chromosome 3 on the left lane is according to Ren et al. (2009). The sequence map of cucumber chromosome 3 on the right lane is according to Huang et al. (2009).</p

Model-based populations in the cucumber mega-population.

<p>(A) Delta K values for different numbers of populations assumed (K) in the STRUCURE analysis. (B) Classification of 3,342 accessions into three populations using STRUCTURE 2.3.1. The distribution of the accessions to different populations is indicated by the color code (P1: red, P2: yellow, P3: blue). Numbers on the y-axis show the subgroup membership, and the x-axis shows the different accession. (C) Unrooted Neighbor-Joining (NJ) tree of the 3,342 accessions. Bootstrap values are indicated at the major branches. (D) Principal Component Analysis (PCA) of the 1,026 accessions without missing SSR fingerprinting data. Color codes for each population and admixture are consistent in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046919#pone-0046919-g002" target="_blank">Figure 2C, 2D</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046919#pone-0046919-g003" target="_blank">Figure 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046919#pone-0046919-g004" target="_blank">Figure 4C</a>.</p