Cell Wall Polysaccharide Chemistry of Peach Genotypes with Contrasted Textures and Other Fruit Traits

Cell wall composition, pectin, and hemicellulose fine structure variation were assessed in peach and related genotypes with contrasted texture and fruit shape. Cell walls were prepared from four commercial peaches, eight genotypes from the Jalousia × Fantasia peach cross, and six genotypes from the Earlygold peach × Texas almond cross. Sugar composition was determined chemically while fine structure of homogalacturonan pectin and xyloglucan hemicellulose were assessed by coupling pectin lyase and glucanase degradation, respectively, with MALDI-TOF MS analysis of the degradation products. The results indicate clear compositional and structural differences between the parents and their related genotypes on the basis of pectin versus cellulose/hemicellulose content and on the fine structure of homogalacturonan and xyloglucan. A relation between methyl- and acetyl-esterification of pectin with fruit shape is revealed in the Fantasia × Jalousia peach genotypes

Co-localization between candidate genes and QTL for the flowering date on ‘Lapins’ linkage group 1 and comparison with the peach physical map of the homologous/syntenic region.

<p>The region covered by the QTL for the flowering date is indicated in green. The candidate genes are indicated in bold. For peach, the physical position of the candidate genes and of the SNP markers refers to the Peach genome sequence v2.0.a1.</p

Co-localization between candidate genes and QTLs.

<p>QTLs detected in ‘Regina’ × ‘Lapins’ (R×L) (right) in ‘Regina’ × ‘Garnet’ (R×G) (left) progenies are indicated by grey bars for chilling requirements (CR), white bars for heat requirements (HR), and black bars for flowering date (FD). Candidate genes mapped on R×L are indicated on the left, and those mapped on R×G are indicated on the right. Those genetically mapped are in bold and are prefixed with ‘<i>Pav</i>’ for <i>Prunus avium</i>, and those mapped <i>in silico</i> using the Peach genome v2.0.a1 are preceded by the prefix “<i>is”</i>.</p

Candidate genes localization in linkage maps constructed from two progenies ‘Regina’ × ‘Garnet’ (R×G) and ‘Regina’ × ‘Lapins’ (R×L).

<p>The SNP maps were already reported for R×L [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143250#pone.0143250.ref029" target="_blank">29</a>] and for R×G [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143250#pone.0143250.ref025" target="_blank">25</a>]. The SNP markers are named according to the original full names used in the RosBREED cherry 6K SNP array, including the physical and genetic positions and the targeted genome [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143250#pone.0143250.ref055" target="_blank">55</a>] but with contraction: for example ‘RosBREED_snp_sweet_cherry_Pp1_00493090’ is written ‘Rsweet_1_00493090’. The candidate genes are indicated in red and were genetically mapped using SNP markers described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143250#pone.0143250.s007" target="_blank">S3 Table</a> and available in the GDR database.</p

Additional file 2: of Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars

Figure S1. Workflow of STRUCTURE 2.3.4 software implementation at MCIA cluster nodes. Figure S2. Genome coverage of 1,215 and 326 SNP sets across the eight linkage groups of sweet cherry. Figure S3. Graphical method (as in Evanno et al. 2005) allowing the detection of the number of groups K using ΔK. Figure S4. Graphical method (as in Evanno et al., 2005) allowing the detection of the number of groups K using the rate of change of the likelihood distribution (Mean log-likelihood values). Figure S5. Cumulative variance explained by the principal component analysis (PCA) relative to the number of principal components (PCs) retained in the analysis. Figure S6. Selection of the optimal number of clusters in the DAPC using the lowest Bayesian Information Criterion (BIC). Figure S7. Cross-validation procedure to choose the optimal number of Principal Components for the DAPC analysis. Figure S8. Eigenvalues of retained discriminant functions in the DAPC analysis. Figure S9. Assignment plots from DAPC for a K of nine populations. Figure S10. Comparison of clustering performed by DAPC (K=9) and origin of cultivars and landraces. Figure S11. Comparison of clustering performed by STRUCTURE and DAPC analysis. Figure S12. Discriminant Analysis of Principal Components Loading Plot. Figure S13. Comparison of clustering performed by DAPC using the whole (1,215 SNPs) and the linkagedisequilibrium-pruned (326 SNPs) SNPs datasets. Figure S14. Sphericity index and the length of pruned values for the selected core collection individuals. (PDF 1.72 MB

Sweet cherry SNP RosBREED markers located in different LGs within the sweet cherry high density linkage maps in comparison with the peach genome v1.0.

<p>Sweet cherry SNP RosBREED markers located in different LGs within the sweet cherry high density linkage maps in comparison with the peach genome v1.0.</p

Minor allele frequency (MAF) distribution of heterozygous SNP for each four mapping parent cultivars.

<p>Percentages of heterozygous SNPs for each of the four mapping parent cultivars (‘Black Tartarian’, ‘Kordia’, ‘Regina’ and ‘Lapins’) that fell within six previously determined minor allele frequency (MAF) classes based on an analysis of 1825 polymorphic SNPs genotyped using 269 sweet cherry accessions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054743#pone.0054743-Peace1" target="_blank">[23]</a>. The percentages of the 1825 SNPs that were monomorphic or failed for each parent are also indicated.</p

genotyping data

Genotyping data for the five mapping population

Haplotype analysis using SNPs markers spanning the self-incompatibility S locus in each population.

<p>(a) ‘Black Tartarian’ × ‘Kordia’ (BT×K) and (b) ‘Regina’ × ‘Lapins’ (R×L).</p

Sweet cherry highly dense linkage maps of two intraspecific progenies and their parental lines.

<p>Sweet cherry linkage maps constructed from two intraspecific progenies ‘Black Tartarian’ × ‘Kordia’ (BT×K) and ‘Regina’ × ‘Lapins’ (R×L) were created using 723 and 687 molecular markers, respectively. (a) BT×K linkage map and their parental maps (BT and K linkage maps). (b) R×L linkage map and their parental maps (R and L linkage maps). Anchored markers are indicated by connecting lines and are represented in green. Markers in black are unique to each map. Distance between markers is represented in cM. Skewed markers mapped are represented by asterisks to indicate distortion level (* for p<0.1; ** p<0.05; ***p<0.01; **** p<0.005; ***** p<0.001; ****** p<0.0005; ******* p<0.0001). See larger Figure-2-SI-Figure in the supporting information.</p