Article Figures & Data
Figures
- Figure 1.
An unrooted phylogenetic tree of CslF genes from barley (HvCslF) and rice (OsCslF). Amino acid sequence identities were used to identify potential orthologs between the gene families of barley and rice. The rice gene numbers are as follows: OsCslF1, Os07g36700; OsCslF2, Os07g36690; OsCslF3, Os07g36750; OsCslF4, Os07g36740; OsCslF6, Os08g06380; OsCslF7, Os10g20260; OsCslF8, Os07g36630; OsCslF9, Os07g36610. The OsCslF5 gene (Os07g36680) is not included because it is a pseudogene and could not be easily aligned with the other CslF genes.
- Figure 2.
Structures of the barley (yellow) and rice (green) CslF genes. The positions of introns are indicated by the triangles and the length of the introns in base pairs is indicated within each triangle. The red bars show the positions of the D,D,D,QVRRW motifs, which are believed to be involved in sugar nucleotide binding and catalytic activity of the enzymes. The lengths of the encoded proteins range from 810 to 947 amino acid residues. The blue bars in the HvCslF3 gene are indicative of the positions of sequences encoding trans-membrane helices, which are located (but not shown here) in similar positions in all the barley and rice genes. The gray bar in the HvCslF6 gene indicates a position encoding a loop of 54 amino acid residues in the HvCslF6 protein that is only 15 to 20 residues in the other barley HvCslF proteins.
- Figure 3.
Genetic maps of barley chromosomes 1H, 2H, 5H, and 7H showing the positions of barley HvCslF genes as mapped in a ‘Clipper’ × ‘Sahara’ population. Additional loci are shown to provide a genetic context for the map positions of the HvCslF genes. Approximate positions of the genes HvGlb1 and HvGlb2 are shown, based on mapping in other populations. Approximate positions of previously reported QTLs for grain (1,3;1,4)-β-d-glucan content are shown (A–G), based on alignment of the ‘Clipper’ × ‘Sahara’ map with genetic maps from other populations. Graphs A and B show statistically significant test statistics (log of the odds) values reported by Han et al. (1995) based on mapping in a ‘Steptoe’ × ‘Morex’ population. The letters C, D, and E show the approximate locations of markers at which Molina-Cano et al. (2007) detected QTLs in a ‘Beka’ × ‘Logan’ population, F shows the approximate location of the peak QTL test statistic value reported by Igartua et al. (2002) based on mapping in a ‘Derkado’ × ‘B83-12/21/5’ population, and G shows the approximate location of a marker at which Kim et al. (2004) detected marker-trait association in a ‘Yonezawa Mochi’ × ‘Neulssalbori’ population.
- Figure 4.
A, Normalized levels of HvCslF6 gene transcripts (arbitrary units) in a range of tissues. These transcripts were detected in all tissues examined and very high levels of HvCslF6 mRNA were detected in some tissues. Error bars on all Q-PCR plots indicate sds for each mRNA. B, Levels of HvCslF gene transcripts in the different tissues. The values for HvCslF6 mRNA have been omitted to more clearly show the relative abundance of other mRNAs from the gene family. C, Levels of the relatively low abundance HvCslF7 mRNA transcripts in the series of tissues. D, Normalized transcript levels of the seven barley HvCslF genes in a range of tissues, expressed as a ratio of maximal levels observed for the specific gene. Values of 1.0 therefore indicate the tissue in which a particular gene is transcribed at its maximal rate.
- Figure 5.
Normalized expression levels for the barley HvCslF genes in developing coleoptiles at various times (days) after the initiation of germination.
- Figure 6.
A, Normalized transcript levels of the barley HvCslF9 genes in developing endosperm at various times postpollination. The two data sets are for the variety ‘Sloop’ (SLP) and ‘Himalaya’ (HIM). B, Levels of the HvCslF6 gene transcripts in developing endosperm at various times postpollination. The two data sets are for the variety ‘Sloop’ (SLP) and ‘Himalaya’ (HIM). C, Levels of HvCslF mRNA for genes that are transcribed at lower levels in the developing endosperm. The two data sets are for the variety ‘Sloop’ (SLP) and ‘Himalaya’ (HIM). D, Levels of HvGlb1 mRNA transcripts in developing endosperm at various times postpollination. The HvGlb1 gene encodes barley (1,3;1,4)-β-d-glucan endohydrolase isoenzyme EI. The two data sets are for the variety ‘Sloop’ (SLP) and ‘Himalaya’ (HIM).
Tables
- Table I.
Sequence similarities between individual barley HvCslF genes and between their products
HvCslF3 851 Amino Acidsa HvCslF4 872 Amino Acids HvCslF6 947 Amino Acids HvCslF7 810 Amino Acids HvCslF8 897 Amino Acids HvCslF9 857 Amino Acids HvCslF10 879 Amino Acids HvCslF3 64 55 54 65 63 69 2,556 bpb 58/72 44/59 42/57 56/73 56/71 63/77 HvCslF4 60 58 66 69 62 2,619 bp 47/61 42/55 57/74 58/72 51/66 HvCslF6 56 58 60 54 2,844 bp 41/53 46/62 44/60 41/56 HvCslF7 53 59 53 2,432 bp 40/55 43/58 38/54 HvCslF8 DNA %c 67 63 2,694 bp Sequence identity/similarity %d 63/75 53/70 HvCslF9 60 2,574 bp 51/67 HvCslF10 2,640 bp ↵a The number of amino acid residues in the coding region of the encoded proteins.
↵b The number of nucleotide base pairs in the corresponding cDNAs.
↵c Values indicate the percentage sequence identity at the nucleotide level in the coding regions of the genes.
↵d Values indicate the percentage sequence identity/similarity between the encoded proteins at the amino acid level.
- Table II.
Gene-specific QPCR primers, with PCR product sizes in base pairs and optimal acquisition temperatures for the genes analyzed
Gene Forward Primer Reverse Primer PCR Size Acquisition Temperature bp °C GAPDH GTGAGGCTGGTGCTGATTACG TGGTGCAGCTAGCATTTGAGAC 198 80 HSP70 CGACCAGGGCAACCGCACCAC ACGGTGTTGATGGGGTTCATG 108 83 α-Tubulin AGTGTCCTGTCCACCCACTC AGCATGAAGTGGATCCTTGG 248 80 Cyclophilin CCTGTCGTGTCGTCGGTCTAAA ACGCAGATCCAGCAGCCTAAAG 122 79 HvCslF3 CTTGTTGCCGGTTGCCTTTACA TCAATTGGCTAAAATGGAAGAAAACTA 90 72 HvCslF4 CCGTCGGGCTCGTGTATGTC TTGCAGTGACTCTGGCTGTACTTG 144 81 HvCslF6 TGGGCATTCACCTTCGTCAT TGTCCGGGCAAACTCATCAA 157 82 HvCslF7 CCCTGCTCTTGCTTGTCGTAG TAGCCAAGCAATTGCATTT 122 76 HvCslF8 GCGTGGATTCTGGTGCTGATCTA CCACCAATGCGATCAAAATAAAC 119 80 HvCslF9 CTGCCACCGCGTCCGTGTA AGGTTTTGCAGCATTACTTGA 101 80 HvCslF10 GGCTATTGTTCAACCTGTGGATTA TGGCCAAGAAAGCAATGGGTAGT 120 77
