CE and HRM profiles of the genotypes analyzed with the marker 115.

<p>While normalized HRM plot shows ambiguous genotype separation, further analysis with difference curve resolves the genotypes clearly. <b>A</b>. CE profile of 5 different genotypes. Four different alleles (155 bp, 157 bp, 159 bp and 169 bp) form 2 homozygous and 3 heterozygous genotypes. Fragment size includes the M13 primer tail (19 bp). <b>B</b>. Normalized HRM melting curves showing 4 genotypes - two ambiguous genotypes not resolved. <b>C</b>. Difference plot showing 5 distinct genotypes which resolved two ambiguous genotypes shown in B, which was consistent with CE results. The exact genotypes are indicated in the rectangular boxes.</p

CE and HRM profiles of the genotypes analyzed with the marker 482 showing 10 genotypes shown by both CE and HRM analysis. A

<p>. CE profiles of 10 different genotypes. Seven different alleles (220 bp, 222 bp, 228 bp 232 bp, 238 bp, 240 bp and 246 bp) form 2 homozygous and 8 heterozygous genotypes. Fragment size includes the M13 primer tail (19 bp). <b>B</b>. Normalized HRM plot showing two similar melting curves produced from different genotypes (arrows). <b>C</b> difference plot - two ambiguous genotypes were resolved (arrows) thus 10 genotypes were distinguished which was in agreement with the CE results. The exact genotypes are indicated in the rectangular boxes.</p

Citrus genotypes used for EST- SSRs analysis by capillary electrophoresis and high resolution melting.

<p>Citrus genotypes used for EST- SSRs analysis by capillary electrophoresis and high resolution melting.</p

CE and HRM profiles, and sequence alignment of genotypes/alleles analyzed with the marker 93.

<p>A monomorphic marker in the population under study is shown polymorphic by HRM analysis. <b>A</b>. Monomorphic CE profile obtained from the analysis of 15 citrus genotypes. <b>B</b>. Polymorphic HRM melting curves showing 4 genotypes in normalized melting plot (upper) and difference melting curve (lower). The curves with different color represent different genotypes which are also shown in <b>A</b>. The exact genotypes are indicated in the rectangular boxes. <b>C</b>. Sequence alignment of the amplicons from 4 distinct genotypes. Two SNPs are shown and highlighted in the yellow boxes.</p

A panel of markers selected for CE and HRM analyses of 15 citrus genotypes.

<p>A panel of markers selected for CE and HRM analyses of 15 citrus genotypes.</p

CE and HRM profiles of the genotypes analyzed with the marker 1527.

<p>The HRM analysis produced consistent result with CE when only length polymorphisms were present in the amplicon. <b>A</b>. CE profiles of 4 different genotypes, two homozygous (128/128 bp, and 138/138 bp) and two heterozygous (128/129 bp, and 129/138 bp). Fragment size includes the M13 primer tail (19 bp). <b>B</b>. HRM melting profiles showing 4 distinct genotypes in normalized melting plot which are consistent with the CE results. The exact genotypes are indicated in the rectangular boxes.</p

Dendrogram representing the structure of genetic diversity and relationships among 15 citrus genotypes by CE (A) and HRM (B).

<p>Genetic distance analysis allowed discrimination of most of the 15 citrus genotypes except those belonging to the same species (3 sweet orange and 3 clementine varieties). Citrus genotypes sharing same parental origin clustered in the same group. This fact is especially evident in HRM dendrogram in which all mandarin and clementine genotypes (except Satsuma) are grouped together. The genetic distance was calculated by Powermarker (shared alleles), and clustering was produced using Neighbor-joining method.</p

Elucidating the contribution of wild related species on autochthonous pear germplasm: A case study from Mount Etna

<div><p>The pear (genus <i>Pyrus</i>) is one of the most ancient and widely cultivated tree fruit crops in temperate climates. The Mount Etna area claims a large number of pear varieties differentiated due to a long history of cultivation and environmental variability, making this area particularly suitable for genetic studies. Ninety-five pear individuals were genotyped using the simple sequence repeat (SSR) methodology interrogating both the nuclear (nDNA) and chloroplast DNA (cpDNA) to combine an investigation of maternal inheritance of chloroplast SSRs (cpSSRs) with the high informativity of nuclear SSRs (nSSRs). The germplasm was selected ad hoc to include wild genotypes, local varieties, and national and international cultivated varieties. The objectives of this study were as follows: (i) estimate the level of differentiation within local varieties; (ii) elucidate the phylogenetic relationships between the cultivated genotypes and wild accessions; and (iii) estimate the potential genetic flow and the relationship among the germplasms in our analysis. Eight nSSRs detected a total of 136 alleles with an average minor allelic frequency and observed heterozygosity of 0.29 and 0.65, respectively, whereas cpSSRs allowed identification of eight haplotypes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198512#pone.0198512.s006" target="_blank">S4 Table</a>). These results shed light on the genetic relatedness between Italian varieties and wild genotypes. Among the wild species, compared with <i>P</i>. <i>amygdaliformis</i>, few <i>P</i>. <i>pyraster</i> genotypes exhibited higher genetic similarity to local pear varieties. Our analysis revealed the presence of genetic stratification with a ‘wild’ subpopulation characterizing the genetic makeup of wild species and the international cultivated varieties exhibiting the predominance of the ‘cultivated’ subpopulation.</p></div

Polymorphism information for the nuclear and chloroplast markers.

<p>Polymorphism information for the nuclear and chloroplast markers.</p

STRUCTURE results.

<p>Inferred population structure: Bar plot generated by STRUCTURE according to the K = 2 model based on eight nSSRs.</p