1. Volume 8, Issue 10, Pages 1507-1519 (October 2015)
Bulbosum to Go: A Toolbox to Utilize Hordeum vulgare/bulbosum Introgressions for Breeding and Beyond 
Neele Wendler, Martin Mascher, Axel Himmelbach, Paul Johnston, Richard Pickering, Nils Stein 
Molecular Plant 
Volume 8, Issue 10, Pages (October 2015)
DOI: /j.molp
Copyright © 2015 The Author Terms and Conditions

2. Figure 1 Hb-specific SNP Frequency Distribution in a Subset of 7ILs.
Hb-specific SNPs were discovered by genotyping-by-sequencing (GBS). The SNP frequency was visualized as a heat map with resolution of 5 Mbp or 2 cM bins, respectively, along the physical and genetic scale of the seven barley chromosomes (1H–7H). The physical and genetic positions of contigs were taken from the barley reference draft genome information (International Barley Sequencing Consortium, 2012; Mascher et al., 2013a). Relative SNP frequency was visualized in 1/110 (physical map) or 1/150 (genetic map) color steps from white (no detected SNPs) to red (maximum SNP frequency) using heat.colors with the R statistical environment (R Core Team, 2012).
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

3. Figure 2
Overview of the Distribution and Frequency of Detected Hb Segments and Hv/Hb SNPs along the Barley Genome.
The figure includes a set of three concentric circles. The outer circle represents the seven barley chromosomes in a clockwise manner from the short to the long arms, scaled in 5 Mbp bins along the physical barley reference map (International Barley Sequencing Consortium, 2012). Moving inwards, the second circle is a heat map of genotyping-by-sequencing Hv/Hb SNPs frequencies found between Hv cultivar “Emir” and Hb clone “A17/1” at a minimum five-fold sequence read coverage. The frequency is plotted in 5 Mbp bins along the physical barley reference (International Barley Sequencing Consortium, 2012). The color code of these bins is set as: white, 0 SNPs/bin; dark green, 1–20 SNPs/bin; and black, >20 SNPs/bin. The innermost circle is a histogram of the frequency of Hb segments that were detected with genotyping-by-sequencing of the 146 ILs. The frequency is given in 5 Mbp bins along the barley genome and the gridlines of the y-axis are in a scale of 5. The three concentric circles were generated using Circos (Krzywinski et al., 2009). Outside the circles, Hb traits are listed that were uniquely attributed to Hb segments on individual chromosome arms of barley within the panel of 146 characterized ILs. Disease-associated traits are colored in blue, morphological traits are colored in dark green, and other traits are colored in light green. BaMMV, barley mild mosaic virus; BYDV, barley yellow dwarf virus; LR, leaf rust; mil, powdery mildew; (S), susceptible; scald, Rynchosporium commune; SR, stem rust; SSLB, Septoria speckled leaf blotch.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

4. Figure 3 Diversity Analysis of Overlapping Hb Segments.
The diversity of overlapping Hb segments was analyzed across the 14 chromosome arms of barley (1HS–7HL). The identity between orthologous Hb segments in independent ILs was determined based on the genotyping-by-sequencing data (green bar ≥98 identity). Furthermore, the highest potential number of Hb alleles represented by Hb segments on the different chromosomal arms is given (red bar). The latter was calculated based on the Hb donor clones utilized, the Hb clone cytotype, and the breeding scheme of the ILs with Hb segments on individual chromosome arms.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

5. Figure 4
Schematic Visualization of the Setup and Utilization of an Integrated Hv/Hb Sequence Resource.
The integrated Hv/Hb sequence was designed based on exome capture re-sequencing data of five Hb accessions and 13 Hv cultivars.
(A) A FASTA file example for an imaginary integrated Hv/Hb whole-genome shotgun assembly contig of barley cultivar “Morex.” The color code of the nucleotides, given as IUPAC codes (IUPAC-IUB Commission on Biochemical Nomenclature (CBN), 1970), refers to the code of interspecific and intraspecific Hv/Hb SNPs as listed in Table 3. Furthermore, nucleotides with less than five-fold sequence read coverage in any exome capture sample were masked as “N” and potential low-quality SNPs were incorporated as IUPAC codes as well (IUPAC-IUB Commission on Biochemical Nomenclature (CBN), 1970).
(B) A schematic example of the utilization of the integrated Hv/Hb sequence resource. Integrated Hv/Hb sequence and SNP information can be exploited for marker development in ILs if the location of the Hb segment is known based on the barley physical and/or genetic map (International Barley Sequencing Consortium, 2012; Mascher et al., 2013a). Thus, integrated Hv/Hb sequence contigs and associated information on conserved Hv/Hb SNPs, which are located within the Hb segment, can be extracted based on their position within the barley genome.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

6. Figure 5 Alternative Crossing Strategies for Hv/Hb ILs.
Schema of alternative crossing strategies for the production of populations that segregate for introgressed Hb segments.
(A) Usually Hv/Hb IL mapping populations are produced by selfing of an IL plant (here with resistance to powdery mildew [mil]), which is known to be heterozygous for the Hb segment. Progeny of this cross will segregate like an F2 population within the Hb interval and usually exhibit strongly reduced interspecific recombination frequency.
(B) Alternatively, two ILs with overlapping Hb segments might be crossed to produce an F1 hybrid, which is heterozygous for the two combined Hb segments. If the F1 is selfed, the resulting F2 population will segregate between the Hb segments and in theory should exhibit normal intraspecific recombination frequency. Preferably, the introgressed segment from Hb of the respective IL, which is to be mapped (crossing partner1), should be smaller than the Hb segment of the crossing partner (crossing partner2). Hb segments should exhibit a high number of polymorphisms and, if possible, crossing partner2 should be negative for the trait to be mapped.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions