Annual report 2015

Accessions considered in the study. Overview of the material considered in this study. For all materials, the GenBank identifier, the accession and species name as used in this study (Species) as well as their species synonyms used in the donor seed banks or in the NCBI GenBank (Material source/Reference) are provided. The genome symbol, and the country of origin, where the material was originally collected are given. The ploidy level measured in the scope of this study and the information if a herbarium voucher could be deposited in the herbarium of IPK Gatersleben (GAT) is given. Genomic formulas of tetraploids and hexploids are given as “female x male parent”. The genomes of Aegilops taxa follow Kilian et al. [74] and Li et al. [84]. Genome denominations for Hordeum follow Blattner [107] and Bernhardt [12] for the remaining taxa. (XLS 84 kb

Genetic analysis of the diallel founder lines.

<p><b>A.</b> Clustering analysis of the 19 <i>Sorghum bicolor</i> inbreds based on unrooted neighbor joining tree. Color coding representing the four identified clusters. <b>B.</b> Model-based ancestry for each founder line with enforcement of the cluster number (K) to 4 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038993#s2" target="_blank">Materials and Methods</a>). Distruct plot is shown with color coding representing the four clusters of the STRUCTURE analysis and the name of each founder line is depicted below.</p

Additional file 2: Table S2. of Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Read numbers mapping to the complete chloroplast sequences and ndhF. Number of reads mapping and mean coverage for the entire chloroplast genome and ndhF after the removal of duplicated reads. Also the proportions of all reads mapping to the chloroplast that mapped to ndhF are given. (XLS 66 kb

Overdominant heterosis (ODH) in the diallel.

<p>ODH distribution of vegetative (height, H; diameter, D; leaf weight, LW; stem weight, SW) and reproductive (dry panicle weight, DPW) traits. Different letters denote significant difference between ODH distributions (Kruskal-Wallis test, <i>P</i><0.0001). Quantile boxes show the range between the 25th and 75th percentiles, including the 50th percentile indicated in between. The bottom and upper outer lines depict the 10th and 90th percentiles, respectively.</p

The <i>Sorghum bicolor</i> lines used for heterosis mapping.

<p><b>A.</b> Origin of the wide collection of lines includes accessions collected worldwide (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038993#pone.0038993.s006" target="_blank">Table S1</a> for details). <b>B.</b> Phylogenetic tree of the wide <i>Sorghum bicolor</i> ssp. bicolor collection. The external nodes and coding of founder lines (FLs) are indicated.</p

The <i>hDPW4.1</i> grain yield heterotic trait locus (HTL).

<p><b>A.</b> Chromosomal location of the Dsenhabm39 SSR marker is indicated by star on the physical map of chromosome 4. Black and white coloring indicate pericentric-heterochromatic and telomeric-euchromatic chromosomal regions, respectively. Gray indicates markers within pericentric-heterochromatic chromosomal regions. <b>B.</b> Cumulative distribution function plot showing the ODH values of the significant hetero-genotypic (154/164) and homo-genotypic (H:H) groups for the same marker in the diallel (year 2011). <b>C.</b> Linkage analysis of the <i>hDPW4.1</i> locus with dry panicle weight (DPW) in the F2 population. Different letters above bars denote significant difference (<i>P</i><0.05; Hsu’s MCB test) between mean values.</p

Hybrid reproductive superiority is induced by release of tradeoff relationship.

<p>Correlations between components of seed number (secondary branching number, SBN; primary branching number, PBN) and seed dry weight (SDW). Analyses of trait values show negative correlations (<b>A, B</b>) while analysis of heterotic values (best parent heterosis; BPH) show either no (<b>C</b>) or positive (<b>D</b>) correlation. <b>E–F.</b> Correlations between vegetative weight (VW) and seed dry weight (SDW). Analysis of trait values (<b>E</b>) shows negative correlation whereas that of heterosis values (<b>F</b>) shows positive correlation.</p

Illustration of the HTL mapping.

<p><b>A.</b> Genotyping of the selected FLs is represented by three loci with different shapes (A, B and C), with each harboring 4 different alleles among the FLs of the diallel. <b>B.</b> Projection of the FLs genotype to the derived hybrids and calculation of the mean heterosis values (ODH) for the r replicates of an hybrid. <b>C.</b> Statistical analysis to identify specific hetero combinations with advantageous ODH values (the purple/green hetero-group in this illustration).</p

Geographical and environmental determinants of the genetic structure of wild barley in southeastern Anatolia

<div><p>Despite the global value of barley, compared to its wild progenitor, genetic variation in this crop has been drastically reduced due to the process of domestication, selection and improvement. In the medium term, this will negatively impact both the vulnerability and yield stability of barley against biotic and abiotic stresses under climate change. Returning to the crop wild relatives (CWR) as sources of new and beneficial alleles is a clear option for enhancing the resilience of diversity and adaptation to climate change. Southeastern Anatolia constitutes an important part of the natural distribution of wild barley in the Fertile Crescent where important crops were initially domesticated. In this study, we investigated genetic diversity in a comprehensive collection of 281 geo-referenced wild barley individuals from 92 collection sites with sample sizes ranging from 1 to 9 individuals per site, collected from southeastern Anatolia and 131 domesticated genotypes from 49 different countries using 40 EST-SSR markers. A total of 375 alleles were detected across entire collection, of which 283 were carried by domesticated genotypes and 316 alleles were present in the wild gene pool. The number of unique alleles in the wild and in the domesticated gene pool was 92 and 59, respectively. The population structure at K = 3 suggested two groups of wild barley namely G1-W consisting wild barley genotypes from the western part and G1-E comprising those mostly from the eastern part of the study area, with a sharp separation from the domesticated gene pool. The geographic and climatic factors jointly showed significant effects on the distribution of wild barley. Using a Latent Factor Mixed Model, we identified four candidate loci potentially involved in adaptation of wild barley to three environmental factors: temperature seasonality, mean temperature of driest quarter, and precipitation of coldest quarter. These loci are probably the targets of genomic regions, with potential roles against abiotic stresses.</p></div

Read numbers mapping to the complete chloroplast sequences and ndhF.

Number of reads mapping and mean coverage for the entire chloroplast genome and ndhF after the removal of duplicated reads. Also the proportions of all reads mapping to the chloroplast that mapped to ndhF are given