23 research outputs found

    Additional file 5: Figure S5. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Effect of Q structure (indica and japonica) for grain length. (a) Comparison of grain length between big-grain-haplotype and small-grain-haplotype when Q structure exists. (b) Comparison of grain length between big-grain-haplotype and small-grain-haplotype when the phenotype variation from Q structure was removed. Ind, indica; jap, japonica. Data are means ± SEM. Letters indicate a significant difference at P < 0.01 (n = 3) by the Student’s t-test. (PPTX 362 kb

    Additional file 15: Figure S15. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Identification of the causal SNPs of QTL qGL3-2 using Ho-LAMap. We also used Ho-LAMap to clone OsLG3b from qGL3-2, a new gene for grain length, which encodes a MADS-box transcription factor. The top is Manhattan plot for candidate region association mapping for QTL region of qGL3-2; the middle correspond to Ho index plots for QTL region of qGL3-2. The bottom correspond to candidate gene (OsLG3b), the green dashed lines label the region for significant signal. (PDF 82 kb

    Additional file 21: Figure S21. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    The effect of OsLG3 on the expression of genes involved in cell cycle. The expression analysis was conducted using 7-cm long young panicles. OsActin1 was used as the control and the values of expression levels in Nipponbare were set to 1 (n = 3). Data are given as mean ± SEM. Student’s t-test was used to generate the P values; * P < 0.05, ** P < 0.01, respectively. (PDF 135 kb

    Additional file 31: Figure S31. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Identification of the causal SNPs of QTL sd1 using Ho-LAMap. The top is Manhattan plot for candidate region association mapping for QTL region of sd1; the middle corresponds to Ho index plots for QTL region of sd1. The bottom corresponds to candidate gene (sd1), the green dashed lines label the region for significant signal. (PDF 175 kb

    Additional file 12: Figure S12. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Simplified scheme for application of Ho-LAMap to rice. (a) We cross diverse founder varieties (i.e., variety that is significantly different to the reference parent on grain traits) with reference parent (usually has small grain). The founder varieties are deep sequenced by the second-generation sequencing platforms, as in Additional file 30: Figure S30. In several crosses that have detected targeted QTL, the majority of SNPs between the QTL interval will segregate in a 1:1 founder varieties:reference parent ratio. However, the SNP responsible for the change of phenotype is the same in all founder parents, which can detect the targeted QTL. If we define the Ho (observed heterozygosity per locus) index as the ratio between the number of heterozygous crosses corresponding to each SNP locus and the total number of crosses which have detected targeted QTL, we expect this index would equal 1 near the causal SNP and 0.5 for the unlinked loci. (b, d) Candidate region association mapping. The brown horizontal dashed lines indicate the genome-wide significance threshold. The red points indicate significant loci within candidate gene. (c) Ho index plots for the target QTL. Red regression lines were obtained by averaging SNP indices from a sliding window analysis. (PDF 105 kb
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