Extended Legend for the Figure 1

Extended legend for the Figure 1.

Figure 1. Phenotypes of some barley backcross-derived lines from the groups of mutations affecting morphology and developmental processes such as tillering and plant stature (A-E), lateral floret development (F-L), inflorescence branching (M-O), rachis internode length (P-S), awn development (T-Y), color of the floral organs (Z-AH), chlorophyll biosynthesis in leaf blades and culms (AI-AO), development of the ligular region (AP-AV), early maturity (AW and AX) and necrosis (AY-BD). For the full description see Supplementary Data file. Abbreviations: panel (G) ltFLO – lateral floret, cOGL – central outer glumes, cFLO – central floret, ltOGL – lateral outer glumes; panel (AP) LIG – ligule, and AUR – auricles.

Row A – E

Cultivar Bowman (A) can develop 10 or more tillers (depending on the growth conditions). Mutations at the Uniculme-23 (BW200) (B) and Uniculm 3 (BW207) (C) loci cause severe reduction of number of tillers. The opposite effect, increased tillering, is caused by a pale green mutation (BW643) (D), which also causes prostrate growth of the plant. The open crown (BW196) (E) mutation represents one of the extreme plant stature mutations – tillers grow horizontally.

Row F – L

Large proportion of Bowman lines have been developed based on selection of mutations affecting different aspects of the inflorescence development. At each rachis internode cv Bowman (F and G) has 3 spikelets, each consisting of a single floret and two outer glumes. Bowman has sterile lateral florets thus classifying in as a two rowed barley. Mutations at the Intermedium spike-c (BW421) (H), Six-rowed spike 4 (BW606) (I), Intermedium spike-e (BW423) (J) and Intermedium spike-h (BW425) (K) loci typically promote lateral floret development, while one of the mutant alleles of the Six-rowed spike 1, Vrs1.t (BW900) (L) has the opposite effect – severe reduction of the size of lateral florets and outer glumes compared to those of the cv Bowman (F and G). Normally mutations in the Six-rowed spike 1 gene induce development of fertile lateral florets (not shown) resembling those of the Six-rowed spike 4 (BW606) (I) mutation.

Row (M) – (S)

In barley, each tiller develop a single spike (head) as shown for cv Bowman (M). However branching of the spike can be induced by mutations at the Compositum j (BW188) (N) and Compositum k (BW187) (O) loci resulting in a development of additional spike-like branches on each tiller.

By comparison to cv Bowman (Q), the internode length of the inflorescence stem, rachis, can be affected either negatively by a mutation in the Dense spike 9 (BW279) (P) locus, or positively by a mutation in the Accordion rachis 1 (BW009) (R) locus. Panel (S) shows spikes from the same lines as in the panels (P), (Q) and (R), but with removed spikelets.

Row (T) – (Y)

Mutations in many genes have pleiotropic effect on awn length, e.g. Narrow leafed dwarf 2 (BW636) (T) has extra-long awns. In contrary, complete reduction of the awns is caused by the Awnless 1 (BW490) (U) mutation. But Curly 2 (BW220) (V) mutation induces formation of curly awns. Awns can be transformed to either a leaf-like structure as in Leafy lemma 1 (BW474) (W) mutant, or to the floret-like structures, called hoods as in Calcaroides-a (BW103) (X) and Calcaroides-d (BW106) (Y) mutant lines.

Row (Z) – (AH)

Different coloring of bracts, caryopses, and rachises can be caused either by pigment accumulation or depletion as in lines carrying Shrunken endosperm 2 (BW835) (Z), Purple lemma and pericarp 2 (BW648) (AA), Black lemma and pericarp 1 (BW062) (AB, AC), Intense blue aleurone 1 (BW418) (AD), Albino lemma 1 (BW011) (AE) and Orange lemma 1 (BW666) (AF and AH) mutations. Panels (AG) and (AH) show exposed Bowman and Orange lemma 1 (BW666) rachises with removed central florets.

Row (AI) – (AO)

Extensive variation in differential accumulation of the chlorophyll in the leaf blades and stems can be caused by the mutations in the Chlorina seedling ac (BW349) (AI), Chlorina seedling 9 (BW365) (AJ), Chlorina seedling aa (BW336) (AK), Yellow streak 3 (BW926) (AL), Yellow streak 2 (BW925) (AM) and White streak n (BW907) (AN and AO) loci.

Row (AP) – (AX)

Extreme variation in the development of the auricles and ligules compared to cv Bowman (AP) can be induced by mutations in the Leafless 1 (BW476) (AQ), Uniculme 21 (BW202) (AR), Eligulum 12 (BW292) (AS), Eligulum-b (BW297) (AT), Erectoides-ii (BW312) (AU) and Leafless 2 (BW477) (AV) loci.

Panels (AW) and (AX) show flag leaves of the cv Bowman and one of the lines carrying early maturity mutation, respectively. The phenotyping of the earliness mutants is based on the observation of the appearance of the awn from the flag leaf, early flowering lines (ax) have awns emerging sooner than those in cv Bowman (AW).

Row (AY) – (BD)

A distinctive group of disease lesion mimic mutations characterized by a localized, spontaneous leaf necrosis is represented by the mutations in the Necrotic leaf spot 6 (BW633) (AY and AZ), Dusky 2 (BW252) (BA), Necrotic leaf spot 1 (BW627) (BB), Premature ripe 2 (adult-plant necrosis) (BW647) (BC) and Necrotic leaf spot 3 (BW630) (BD) loci.

File ‘Supplemental_Table1.xls’ contains Supplemental Table 1 ‘Summary of the Bowman backcross-derived line population’. It has the following column headings:

Line ID – SCRI indentificators of the Bowman lines. Please use these identificators if requesting seeds or mapping information from the SCRI.

backcross – number of backcrosses. =<BC7 indicates that seven or more backcrosses have been made.

mutant group – gene name without specifying the actual gene or allele (see the note below about naming barley genes).

locus or allele name - see the note below about naming barley genes and distinguishing alleles from genes.

locus or allele abbreviation - see the note below about naming barley genes and distinguishing alleles from genes.

BGS – Barley Genetic Stock identificator. Latest BGS descriptions can be found here http://wheat.pw.usda.gov/ggpages/bgn/38/BarleyGeneticStocksBGN38.htm.

GSHO – a seed stock identificator used by USDA National Small Grains Collection in Aberdeen, ID, USA.

mutant type – more general than ‘mutant group’ category.

historical mapping (chromosome) – barley chromosome, indicating in some cases arm S – short, L – long where the mutation was mapped previously. For more details see http://wheat.pw.usda.gov/ggpages/bgn/.

donor – barley cultivar where the mutation was found in the first case.

mutagen and author – mutagen and author.

Table value designations:

NA – not available

The ? marker generally indicates where a name has not been assigned or the stock selected did appear to have the mutant phenotype.

The + indicated more than one mutant is likely present in that stock. Several such stocks were derived from crosses to R.I Wolfe's master or multiple marker stocks.

File ‘Supplemental_Table2.xls’ contains Supplemental Table2. ‘Bowman backcross-derived line mapping data’. It has the following column headings:

Line ID – SCRI indentificators of the Bowman lines. Please use these identificators if requesting seeds or mapping information from the SCRI.

manifest SNP – name of the SNP as in the manifest file that was received as part of the genotyping data set.

POPA SNP - name of the SNP according to Close et al 2009 (column ‘Cons123L_POPA’ in the Additional file 3: Supplemental_TableS1.xls).

chromosome – SNP mapping chromosome according to Close et al 2009 (column ‘Cons123L_chrom’ in the Additional file 3: Supplemental_TableS1.xls)

position (cM) - SNP mapping position (cM) according to Close et al 2009 (column ‘Cons123L_cM’ in the Additional file 3: Supplemental_TableS1.xls)

File ‘Supplemental_Table3.xls’ contains Supplemental Table3. ‘Supplemental Table 3. Rice-barley synteny regions.’. It has the following column headings:

synteny blocks – identificator of the regions in the barley genetic map used for building a synteny model.

rice chromosome – rice chromosome according to TIGR Rice Pseudomolecule build v5.

rice start (bp) – start position of the synteny block in rice. Position in the rice genome according to TIGR Pseudomolecule build v5. bp – base pairs

rice end (bp) - end position of the synteny block in rice. Position in the rice genome according to TIGR Pseudomolecule build v5. bp – base pairs

rice distance (bp) – difference between values from the columns rice end (bp) and rice start (bp).

number of rice genes – number of rice genes within the interval defined by the rice distance (bp). Note that genes representing highly repeated sequences have been excluded from the gene list.

barley chromosome – barley chromosome based on the integrated barley gene map (SNPs and TDMs) (Druka, unpublished).

barley start (cM) - start position of the synteny block in barley based on the integrated barley gene map (SNPs and TDMs) (Druka, unpublished). cM – centimorgans.

barley end (cM) - end position of the synteny block in barley based on the integrated barley gene map (SNPs and TDMs) (Druka, unpublished). cM – centimorgans.

barley distance (cM) - difference between values from the columns barley end (bp) and barley start (bp).

model – the best model selected based on the regression analysis of the barley and rice gene orders.

R2 – the highest R-squared value selected from assessing the exponential, linear, logarithmic, polynomial and power regression types.

Mb (barley)/cM – predicted physical/genetic distance ratio in barley taking into account about 10 times bigger barley genome. Mb – megabase pairs, cM – centimorgans.

Supplemental Figure 1. Reduction of the gene-containing interval by using

groups of complementary overlapping introgressions (COIs) for two genes from

the mutant groups Laxatum (A) and Semidwarf (B). Bars show introgression

regions for separate lines, with x-axis and numbers within the bars showing the

map units according to Close et al 2009.