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 33: of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Notes S1. Natural population and linkage mapping (Additional file 2: Figure S2 and Additional file 11). Notes S2. Fine mapping of qGL3-3 (Additional file 10). Notes S3. Ho-LAMap – a potential method for validating association peak. Table S2. Summary of the taxa and source of 506 varieties of Oryza sativa L. Table S3. Environments used to evaluate association and linkage populations. Table S4. The heritability of grain traits in MCC1 Panel. Table S9. Summary of causal allele and type of variation about several grain size genes. Table S10. Grain phenotypes of six different parents. Table S11. Quantitative trait loci mapped in the four populations. Table S12. Simulation reveals the cross number need for several known genes (such as TGW6, GS3) about grain size when using Ho-LAMap. Table S13. OsLG3 polymorphisms associated with grain length in the MCC panel. Table S14. Comparison of polymorphisms between three large grain parents and three small grain parents. Table S16. Primers used for fine mapping and sequencing. Table S17. Primers used for DNA constructs and transcript analysis. (DOCX 73 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 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 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 26: Figure S26. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Genetic interactions among OsLG3, GS3, GW8, and TGW6. (a) Varieties were categorized by allelic variations of OsLG3, GS3, and TGW6. (b) Varieties were categorized by allelic variations in the functional SNP of OsLG3, GS3, and GW8. Grain length was measured by Vernier calipers, and the violin map was constructed in R. Multiple comparisons were done by Tukey’ HSD in R. Landraces and raw data were listed in Additional file 32: Table S1. (PDF 143 kb
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